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Mikaël Capelle
2016-02-18 14:53:30 +01:00
commit 8e93ca7a95
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26
.emacs.d/elpa/ess-20160208.453/etc/BACKBUG5.BAT Normal file
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@echo off
rem ESS[BUGS]: 02/18/2004
rem runs BUGS taking commands from command file
if not "%2"=="" goto 20
if not "%1"=="" goto 10
echo usage: backbug5 [default_output_name] command_file
goto 40
:10
if exist bugs.bog attrib -r bugs.bog
bugs05.exe bugs.buf bugs.bog bugs.out bugs.ind bugs1.out bugs1.ind %1
copy /y bugs.log bugs.bog
attrib +r bugs.bog
goto 40
:20
set one=1
if exist %1.bog attrib -r %1.bog
bugs05.exe %1.buf %1.bog %1.out %1.ind %1%one%.out %1%one%.ind %2
copy /y %1.log %1.bog
attrib +r %1.bog
goto 40
:40

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.emacs.d/elpa/ess-20160208.453/etc/BACKBUGS.BAT Executable file
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@echo off
rem ESS[BUGS]: 02/13/2003
rem runs BUGS taking commands from command file
if not "%3"=="" goto 30
if not "%2"=="" goto 20
if not "%1"=="" goto 10
echo usage: backbugs [[number_of_bins] default_output_name] command_file
goto 40
:10
bugs0603.exe 32 bugs %1
if exist bugs.bog attrib -r bugs.bog
copy /y bugs.log bugs.bog
attrib +r bugs.bog
goto 40
:20
bugs0603.exe 32 %1 %2
if exist %1.bog attrib -r %1.bog
copy /y %1.log %1.bog
attrib +r %1.bog
goto 40
:30
bugs0603.exe %1 %2 %3
if exist %2.bog attrib -r %2.bog
copy /y %2.log %2.bog
attrib +r %2.bog
:40

122
.emacs.d/elpa/ess-20160208.453/etc/C-cC-c-probl.R Normal file
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foobar <- function(...) {}
rm(list=ls())
##--------> consequence of the above experiments:
## the 2nd form is numerically "uniformly better" than the first
##--------> 2011-05-27: Change Frank's psiInv() to
## psiInv = function(t,theta)
## -log1p(exp(-theta)*expm1((1-t)*theta)/expm1(-theta))
##--- In the following block, in the first line, C-c C-c did *NOT* behave
th <- 48 # now do ls() and see what happened ... the horror !!!
d <- 3
cpF <- list("Frank", list(th, 1:d))
cop <- acF <- cpF$copula
### Here, the bug (12.09-2, e.g.) has been that
### the function beginning is not found reliably:
### C-M-q -> should go to end; then C-M-a should go back to beginning (here)
mplot4 <- function(x, vList, xvar, cvar, rvar, log = "",
verbose=FALSE, show.layout=verbose)
{
dn <- dimnames(x)
## the variable displayed in one plot (with different colors):
v <- setdiff(names(dn), c(xvar, cvar, rvar))
stopifnot(length(v) == 1, 1 <= (nv <- length(dn[[v]])), nv <= length(pcol),
length(pspc) == 2, length(spc) == 2, length(axlabspc) == 2,
length(labspc) == 2, length(auxcol) == 4)
v.col <- colorRampPalette(pcol, space="Lab")(nv) # colors for v
## permute to know the component indices:
x <- aperm(x, perm=c(rvar, cvar, v, xvar))
if(is.null(xlab)) # default: the expression from varlist
xlab <- vList[[xvar]]$expr
z <- as.numeric(vList[[xvar]]$value) # pick out different x values
zrange <- range(z) # for forcing the same x axis limits per row
## set up the grid layout
nx <- length(dn[[cvar]]) # number of plot columns
nx. <- nx+1+(nx-1)+1 # +1: for y axis label; +(nx-1): for gaps; +1: for row labels
ny <- length(dn[[rvar]]) # number of plot rows
ny. <- ny+1+(ny-1)+1 # +1: for column labels; +(ny-1): for gaps; +1: for x axis label
## plot settings, restored on exit
opar <- par(no.readonly=TRUE); on.exit(par(opar))
plot.new() # start (empty) new page with 'graphics'
gl <- grid.layout(nx., ny.,
## units in npc as for pdf(); no square plotting region otherwise:
default.units="npc",
widths=c(axlabspc[1], rep(c(pspc[1], spc[1]), nx-1), pspc[1], labspc[1]),
heights=c(labspc[2], rep(c(pspc[2], spc[2]), ny-1), pspc[2], axlabspc[2]))
if(show.layout) grid.show.layout(gl, vp=viewport(width=1.25, height=1.25))
pushViewport(viewport(layout=gl)) # use this layout in a viewport
## --- plot data ---
for(i in 1:nx) { # rows
i. <- 2*i # column index in layout (for jumping over gaps)
if(verbose) cat(sprintf("plot row %d (%d): [columns:] ", i, i.))
yrange <- range(x[i,,,]) # for forcing the same y axis limits per row
for(j in 1:ny) { # columns
j. <- 2*j # row index in layout (for jumping over gaps)
if(verbose) cat(sprintf("%d (%d) ", j, j.))
pushViewport(viewport(layout.pos.row=i., layout.pos.col=j.))
## plot
grid.rect(gp=gpar(col=NA, fill=auxcol[3])) # background
## start a 'graphics' plot
par(plt = gridPLT())
## Hmm, this is not really useful for debugging:
## rp <- tryCatch(par(plt=gridPLT()), error = function(e)e)
## if(inherits(rp, "error")) {
## cat("\n *** ERROR in mplot() :\n", rp$message,"\n"); return(gl)
## }
par(new=TRUE) # always do this before each new 'graphics' plot
## set up coordinate axes:
plot(zrange, yrange, log=log, type="n", ann=FALSE, axes=FALSE)
## background grid:
grid(col=auxcol[4], lty="solid", lwd=grid.lwd, equilogs=FALSE)
## plot corresponding points/lines
for(k in 1:nv) points(z, x[i,j,k,], type="b", col=v.col[k])
## axes
c1 <- auxcol[1]
if(i == nx) # x axes
axis(1, lwd=ax.lwd, col=NA, col.ticks=c1, col.axis=c1)
if(j == 1) { # y axes
if(packageVersion("sfsmisc") >= "1.0-21")
## allow for adjusting colors of small ticks
eaxis(2, lwd=ax.lwd, col=NA, col.ticks=c1, col.axis=c1,
small.args=list(col=NA, col.ticks=c1, col.axis=c1))
else
eaxis(2, lwd=ax.lwd, col=NA, col.ticks=c1, col.axis=c1)
}
upViewport()
## column labels
if(i == 1) {
pushViewport(viewport(layout.pos.row=1, layout.pos.col=j.))
grid.rect(gp=gpar(col=NA, fill=auxcol[2]))
grid.text(parse(text=dn[[cvar]][j]), x=0.5, y=0.5, gp=gpar(cex=tx.cex))
upViewport()
}
## row labels
if(j == 2) {
pushViewport(viewport(layout.pos.row=i., layout.pos.col=nx.))
grid.rect(gp=gpar(col=NA, fill=auxcol[2]))
grid.text(parse(text=dn[[rvar]][i]), x=0.5, y=0.5, gp=gpar(cex=tx.cex), rot=-90)
upViewport()
}
}## for(j ..)
if(verbose) cat("\n")
}## for(i ..)
## legend
pushViewport(viewport(layout.pos.row=ny., layout.pos.col=2:(ny.-1)))
ll <- 0.01 # line length
## [... ... made example smaller ... ESS-bug still shows ....]
upViewport()
invisible(gl)
}

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.emacs.d/elpa/ess-20160208.453/etc/ESSR/BUILDESSR Executable file
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#!/usr/bin/Rscript
## -*- mode: R -*-
## code to build ESSR environemnt.
## Assume that current directory is etc/ESSR
## run "./BUILDESSR destdir" to create ESSR_<version>.rda in destdir
## where <version> is picked form ./VERSION file
args <- commandArgs(TRUE)
dir <- if(length(args)) args[[1]] else "."
ver <- scan("./VERSION", what = "character", quiet = TRUE)
rda_file <- sprintf("%s/ESSR_%s.rda", dir, ver)
## exactly as in ess--R-load-ESSR in ess-r-d.el
source('./R/.load.R', local=TRUE)
ESSR <- load.ESSR('./R/')
save(ESSR, file = rda_file)

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.emacs.d/elpa/ess-20160208.453/etc/ESSR/LOADREMOTE Normal file
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## -*- mode: R -*-
## loading code which is first sent to R on remote sessions
local({
curver <- '%s'
## MM: ok for Windows?
## VS: Should be fine (who is using win remote anyways?)
.c.dir <- '~/.config/ESSR'
verfile <- file.path(.c.dir, 'VERSION')
envfile <- file.path(.c.dir, 'ESSR.rda')
ver <- if(file.exists(verfile)) scan(verfile, what = "string") else "0.0"
tryCatch({
if(ver < curver) {
url <- paste('http://vitalie.spinu.info/ESSR/ESSR_', curver, '.rda', sep = '')
if(!file.exists(.c.dir))
dir.create(.c.dir, recursive = TRUE)
utils::download.file(url, envfile)
cat(curver, file = verfile)
}
load(envfile)
attach(ESSR)
print(TRUE)
} , error = function(e) print(FALSE))
})

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.emacs.d/elpa/ess-20160208.453/etc/ESSR/R/.basic.R Normal file
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#### Essential functionality needed by ESS
## Should work on *all* vesions of R.
## Do not use _ in names, nor :: , nor 1L etc, as they
## cannot be parsed in old R versions
## loading ESSR.rda might fail, so re-assign here:
.ess.Rversion <-
if( exists("getRversion", mode="function") ){
getRversion()
} else {
paste(R.version$major, R.version$minor, sep=".")
}
.ess.R.has.utils <- (.ess.Rversion >= "1.9.0")
.ess.utils.name <- paste("package",
if(.ess.Rversion >= "1.9.0") "utils" else "base",
sep = ":")
## Instead of modern utils::help use one that works in R 1.0.0:
.ess.findFUN <- get("find", .ess.utils.name)
.ess.sourceFUN <- get("source", pos="package:base")
.ess.helpFUN <- get("help", envir=.GlobalEnv)# so it also works with d..tools
### HELP
.ess.help <- function(..., help.type = getOption('help_type'))
{
if (.ess.Rversion > '2.10')# abbreviating 'help_type' on purpose:
.ess.helpFUN(..., help = help.type)
else # not using identical(), and working also for NULL:
.ess.helpFUN(..., htmlhelp = (length(help.type) && help.type=='html'))
}
.ess.getHelpAliases <- function(){
readrds <-
if(.ess.Rversion >= '2.13.0') readRDS
else .readRDS
rds.files <- paste(searchpaths(), "/help/aliases.rds", sep = "")
unlist(lapply(rds.files,
function(f){
if( file.exists(f) )
try(names(readrds(f)))
}),
use.names = FALSE)
}
### SOURCING
.ess.eval <- function(string, echo = TRUE, print.eval = TRUE,
max.deparse.length = 300,
file = tempfile("ESS"),
local = if (.ess.Rversion > '2.13') parent.frame() else FALSE)
{
## create FILE, put string into it. Then source.
## arguments are like in source and .ess.source
cat(string, file = file)
on.exit(file.remove(file))
.ess.source(file, echo = echo, print.eval = print.eval,
max.deparse.length = max.deparse.length, local = local)
}
.ess.source <- function(file, echo = TRUE, print.eval = TRUE,
max.deparse.length = 300,
local = if (.ess.Rversion > '2.13') parent.frame() else FALSE)
{
ss <- # drop 'keep.source' for older versions
if(.ess.Rversion >= "2.8") .ess.sourceFUN
else function(..., keep.source) .ess.sourceFUN(...)
invisible(ss(file, echo = echo, local = local, print.eval = print.eval,
max.deparse.length = max.deparse.length,
keep.source = TRUE)$value) ## return value for org-babel
}
if(.ess.Rversion < "1.8")
## (works for "1.7.2"): bquote() was new in 1.8.0
bquote <- function(expr, where=parent.frame()){
unquote <- function(e)
if (is.pairlist(e)) as.pairlist(lapply(e, unquote))
else if (length(e) <= 1) e
else if (e[[1]] == as.name(".")) eval(e[[2]], where)
else as.call(lapply(e, unquote))
unquote(substitute(expr))
}

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.emacs.d/elpa/ess-20160208.453/etc/ESSR/R/.load.R Normal file
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## Do not use _ in names, nor :: as they cannot be parsed in old R versions
## load .base.R and all other files into ESSR environment; then attach ESSR
load.ESSR <- function(dir){
.source <-
if(any("keep.source" == names(formals(sys.source))))
sys.source
else
function(..., keep.source) sys.source(...)
Rver <-
if(exists("getRversion", mode="function")) getRversion()
else paste(R.version$major, R.version$minor, sep=".")
oldR <- Rver <= "1.3.0"
ESSR <-
if(oldR) ## really old library() revert order a bit
attach(NULL, name = "ESSR")
else if(length(nn <- names(formals(new.env))) && any(nn == "parent"))
new.env(parent =
if(Rver >= "1.9.0") getNamespace("utils")
else .BaseNamespaceEnv)
else
new.env()
assign(".ess.Rversion", Rver, envir = ESSR)
ESSRver <- scan(paste(dirname(dir), "/VERSION", sep = ""),
what = "character", quiet = TRUE)
assign(".ess.ESSRversion", ESSRver, envir = ESSR)
## .basic.R:
try(.source(paste(dir,'/.basic.R', sep = ""), envir = ESSR, keep.source = FALSE))
## all others try(*) as it will fail in old R
if(!oldR) # no sense if(oldR)
for( f in dir(dir, pattern='\\.R$', full.names=TRUE) )
try(.source(f, envir = ESSR, keep.source = FALSE))
if(Rver >= "2.4.0")
attach(ESSR)
else if(!oldR) { ## borrow from older library()
e <- attach(NULL, name = "ESSR")
.Internal(lib.fixup(ESSR, e))
} else { ## if(oldR), use as in that old library():
.Internal(lib.fixup(ESSR, .GlobalEnv))
}
## BUILDESSR needs this:
invisible(ESSR)
}

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.emacs.d/elpa/ess-20160208.453/etc/ESSR/R/completion.R Normal file
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## Do *NOT* use 1L -- it gives parse errors in historical versions of R
.ess_funargs <- function(funname) {
if(.ess.Rversion > '2.14.1') {
comp <- compiler::enableJIT(0)
op <- options(error=NULL)
on.exit({ options(op); compiler::enableJIT(comp) })
}
## don't remove; really need eval(parse( here!!
fun <- tryCatch(eval(parse(text=funname)),
error=function(e) NULL) ## also works for special objects containing @:$ etc
if(is.function(fun)) {
special <- grepl('[:$@[]', funname)
args <- if(!special){
fundef <- paste(funname, '.default',sep='')
do.call('argsAnywhere', list(fundef))
}
if(is.null(args))
args <- args(fun)
if(is.null(args))
args <- do.call('argsAnywhere', list(funname))
fmls <- formals(args)
fmls_names <- names(fmls)
fmls <- gsub('\"', '\\\"',
gsub("\\", "\\\\", as.character(fmls),fixed = TRUE),
fixed=TRUE)
args_alist <-
sprintf("'(%s)",
paste("(\"", fmls_names, "\" . \"", fmls, "\")",
sep = '', collapse = ' '))
allargs <-
if(special) fmls_names
else tryCatch(gsub('=', '', utils:::functionArgs(funname, ''), fixed = TRUE),
error=function(e) NULL)
allargs <- sprintf("'(\"%s\")",
paste(allargs, collapse = '\" "'))
envname <- environmentName(environment(fun))
if(envname == "R_GlobalEnv") envname <- ""
cat(sprintf('(list \"%s\" %s %s)\n',
envname, args_alist, allargs))
}
}
.ess_get_completions <- function(string, end){
if(.ess.Rversion > '2.14.1'){
comp <- compiler::enableJIT(0)
op <- options(error=NULL)
on.exit({ options(op); compiler::enableJIT(comp) })
}
utils:::.assignLinebuffer(string)
utils:::.assignEnd(end)
utils:::.guessTokenFromLine()
utils:::.completeToken()
c(get('token', envir=utils:::.CompletionEnv),
utils:::.retrieveCompletions())
}
.ess_arg_help <- function(arg, func){
op <- options(error=NULL)
on.exit(options(op))
fguess <-
if(is.null(func)) get('fguess', envir=utils:::.CompletionEnv)
else func
findArgHelp <- function(fun, arg){
file <- help(fun, try.all.packages=FALSE)[[1]]
hlp <- utils:::.getHelpFile(file)
id <- grep('arguments', tools:::RdTags(hlp), fixed=TRUE)
if(length(id)){
arg_section <- hlp[[id[[1]]]]
items <- grep('item', tools:::RdTags(arg_section), fixed=TRUE)
## cat('items:', items, fill=TRUE)
if(length(items)){
arg_section <- arg_section[items]
args <- unlist(lapply(arg_section,
function(el) paste(unlist(el[[1]][[1]], TRUE, FALSE), collapse='')))
fits <- grep(arg, args, fixed=TRUE)
## cat('args', args, 'fits', fill=TRUE)
if(length(fits))
paste(unlist(arg_section[[fits[1]]][[2]], TRUE, FALSE), collapse='')
}
}
}
funcs <- c(fguess, tryCatch(methods(fguess),
warning=function(w) {NULL},
error=function(e) {NULL}))
if(length(funcs) > 1 && length(pos <- grep('default', funcs))){
funcs <- c(funcs[[pos[[1]]]], funcs[-pos[[1]]])
}
i <- 1; found <- FALSE
out <- 'No help found'
while(i <= length(funcs) && is.null(out <-
tryCatch(findArgHelp(funcs[[i]], arg),
warning=function(w) {NULL},
error=function(e) {NULL})
))
i <- i + 1
cat('\n\n', as.character(out), '\n')
};

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.emacs.d/elpa/ess-20160208.453/etc/ESSR/R/debug.R Normal file
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### BREAKPOINTS
.ESSBP. <- new.env()
### DEBUG/UNDEBUG
.ess_find_funcs <- function(env)
{
objs <- ls(envir = env, all.names = TRUE)
objs[sapply(objs, exists, envir = env,
mode = 'function', inherits = FALSE)]
}
.ess_all_functions <- function(packages = c(), env = NULL)
{
if(is.null(env))
env <- parent.frame()
empty <- emptyenv()
coll <- list()
for(p in packages){
## package might not be attached
try({objNS <- .ess_find_funcs(asNamespace(p))
objPKG <- .ess_find_funcs(as.environment(paste0('package:', p)))
coll[[length(coll) + 1]] <-
paste0(p, ':::`', setdiff(objNS, objPKG), '`')
}, silent = TRUE)
}
while(!identical(empty, env)){
coll[[length(coll) + 1]] <- .ess_find_funcs(env)
env <- parent.env(env)
}
grep('^\\.ess', unlist(coll, use.names = FALSE),
invert = TRUE, value = TRUE)
}
.ess_dbg_getTracedAndDebugged <- function(packages = c())
{
tr_state <- tracingState(FALSE)
on.exit(tracingState(tr_state))
generics <- methods::getGenerics()
all_traced <- c()
for(i in seq_along(generics)){
genf <- methods::getGeneric(generics[[i]],
package=generics@package[[i]])
if(!is.null(genf)){ ## might happen !! v.2.13
menv <- methods::getMethodsForDispatch(genf)
traced <- unlist(eapply(menv, is, 'traceable', all.names=TRUE))
if(length(traced) && any(traced))
all_traced <- c(paste(generics[[i]],':',
names(traced)[traced],sep=''), all_traced)
tfn <- getFunction(generics[[i]], mustFind=FALSE, where = .GlobalEnv)
if(!is.null(tfn ) && is(tfn, 'traceable')) # if the default is traced, it does not appear in the menv :()
all_traced <- c(generics[[i]], all_traced)
}
}
debugged_pkg <- unlist(lapply(packages, function(pkgname){
ns <- asNamespace(pkgname)
funcs <- .ess_find_funcs(ns)
dbged <- funcs[unlist(lapply(funcs,
function(f){
isdebugged(get(f, envir = ns, inherits = FALSE))
}))]
if(length(dbged))
paste0(pkgname, ':::`', dbged, '`')
}))
env <- parent.frame()
## traced function don't appear here. Not realy needed and would affect performance.
all <- .ess_all_functions(packages = packages, env = env)
which_deb <- lapply(all, function(nm){
## if isdebugged is called with string it doess find
tryCatch(isdebugged(get(nm, envir = env)),
error = function(e) FALSE)
## try(eval(substitute(isdebugged(nm), list(nm = as.name(nm)))), silent = T)
})
debugged <- all[which(unlist(which_deb, recursive=FALSE, use.names=FALSE))]
unique(c(debugged_pkg, debugged, all_traced))
}
.ess_dbg_UntraceOrUndebug <- function(name, env = parent.frame())
{
tr_state <- tracingState(FALSE)
on.exit(tracingState(tr_state))
if( grepl('::', name) ){
## foo:::bar name
eval(parse(text = sprintf('undebug(%s)', name)))
}else{
## name is a name of a function to be undebugged or has a form
## name:Class1#Class2#Class3 for traced methods
name <- strsplit(name, ':', fixed = TRUE)[[1]]
if( length(name)>1 ){
## a method
fun <- name[[1]]
sig <- strsplit(paste(name[-1], collapse=''), '#', fixed=TRUE)[[1]]
untrace(fun, signature = sig)
}else{
## function
if( is(getFunction(name, where = parent.frame()), 'traceable') )
untrace(name)
else if(grepl(":", name))
undebug(name)
else
undebug(get(name, envir = env))
}}
}
.ess_dbg_UndebugALL <- function(funcs)
{
tr_state <- tracingState(FALSE)
on.exit(tracingState(tr_state))
env <- parent.frame()
invisible(lapply(funcs, function( nm ) {
## ugly tryCatch, but there might be several names pointing to the
## same function, like foo:::bar and bar. An alternative would be
## to call .ess_dbg_getTracedAndDebugged each time but that might
## be ery slow
try(.ess_dbg_UntraceOrUndebug(nm, env = env), TRUE)
}))
}
### WATCH
.ess_watch_expressions <- list()
.ess_watch_eval <- function()
{
env <- as.environment("ESSR")
exps <- get('.ess_watch_expressions', envir = env)
if(length(exps) == 0) {
## using old style so this can be parsed by R 1.9.1 (e.g):
cat('\n# Watch list is empty!\n',
'# a append new expression',
'# i insert new expression',
'# k kill',
'# e edit the expression',
'# r rename',
'# n/p navigate',
'# u/d,U move the expression up/down',
'# q kill the buffer',
sep="\n")
} else {
.parent_frame <- parent.frame()
.essWEnames <- allNames(exps)
len0p <- !nzchar(.essWEnames)
.essWEnames[len0p] <- seq_along(len0p)[len0p]
for(i in seq_along(exps)) {
cat('\n@---- ', .essWEnames[[i]], ' ',
rep.int('-', max(0, 35 - nchar(.essWEnames[[i]]))), '-@\n', sep = '')
cat(paste('@---:', deparse(exps[[i]][[1]])), ' \n', sep = '')
tryCatch(print(eval(exps[[i]],
envir = .parent_frame)),
error = function(e) cat('Error:', e$message, '\n' ),
warning = function(w) cat('warning: ', w$message, '\n' ))
}
}
}
.ess_watch_assign_expressions <- function(elist){
assign(".ess_watch_expressions", elist, envir = as.environment("ESSR"))
}
.ess_log_eval <- function(log_name)
{
env <- as.environment("ESSR")
if(!exists(log_name, envir = env, inherits = FALSE))
assign(log_name, list(), envir = env)
log <- get(log_name, envir = env, inherits = FALSE)
.essWEnames <- allNames(.ess_watch_expressions)
cur_log <- list()
.parent_frame <- parent.frame()
for(i in seq_along(.ess_watch_expressions)) {
capture.output( {
cur_log[[i]] <-
tryCatch(eval(.ess_watch_expressions[[i]]),
envir = .parent_frame,
error = function(e) paste('Error:', e$message, '\n'),
warning = function(w) paste('warning: ', w$message, '\n'))
if(is.null(cur_log[i][[1]]))
cur_log[i] <- list(NULL)
})
}
names(cur_log) <- .essWEnames
assign(log_name, c(log, list(cur_log)), envir = env)
invisible(NULL)
}
.ess_package_attached <- function(pack_name){
as.logical(match(paste0("package:", pack_name), search()))
}

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## COMMENT ON S3 METHODS: New S3 methods are not automatically registered. You can
## register them manually after you have inserted method_name.my_class into your
## package environment using ess-developer, like follows:
##
## registerS3method("method_name", "my_class", my_package:::method_name.my_class)
##
## If an S3 methods already exists in a package, ESS-developer will do the right
## thing.
## evaluate the STRING by saving into a file and calling .essDev_source
.essDev.eval <- function(string, package, file = tempfile("ESSDev")){
cat(string, file = file)
on.exit(file.remove(file))
.essDev_source(file,, package = package)
}
## sourcing SOURCE file into an environment. After having a look at each new
## object in the environment, decide what to do with it. Handles plain objects,
## functions, existing S3 methods, S4 classes and methods. .
.essDev_source <- function(source, expr, package = "")
{
## require('methods')
oldopts <- options(warn = 1)
on.exit(options(oldopts))
MPattern <- methods:::.TableMetaPattern()
CPattern <- methods:::.ClassMetaPattern()
allPlainObjects <- function() allObjects[!(grepl(MPattern, allObjects) |
grepl(CPattern, allObjects))]
allMethodTables <- function() allObjects[grepl(MPattern, allObjects)]
allClassDefs <- function() allObjects[grepl(CPattern, allObjects)]
pname <- paste("package:", package, sep = "")
envpkg <- tryCatch(as.environment(pname), error = function(cond) NULL)
if(is.null(envpkg)){
library(package, character.only = TRUE)
envpkg <- tryCatch(as.environment(pname), error = function(cond) NULL)
}
if (is.null(envpkg))
stop(gettextf("Can't find an environment corresponding to package name '%s'",
package), domain = NA)
envns <- tryCatch(asNamespace(package), error = function(cond) NULL)
if (is.null(envns))
stop(gettextf("Can't find a namespace environment corresponding to package name '%s\"",
package), domain = NA)
## evaluate the SOURCE into new ENV
env <- .essDev_evalSource(source, substitute(expr), package)
envPackage <- getPackageName(env, FALSE)
if (nzchar(envPackage) && envPackage != package)
warning(gettextf("Supplied package, %s, differs from package inferred from source, %s",
sQuote(package), sQuote(envPackage)), domain = NA)
allObjects <- objects(envir = env, all.names = TRUE)
allObjects <- allObjects[!(allObjects %in% c(".cacheOnAssign", ".packageName"))]
## PLAIN OBJECTS and FUNCTIONS:
funcNs <- funcPkg <- newFunc <- newNs <- newObjects <- newPkg <- objectsNs <- objectsPkg <- character()
for (this in allPlainObjects()) {
thisEnv <- get(this, envir = env)
thisNs <- NULL
## NS
if (exists(this, envir = envns, inherits = FALSE)){
thisNs <- get(this, envir = envns)
if(is.function(thisNs) || is.function(thisEnv)){
if(is.function(thisNs) && is.function(thisEnv)){
if(.essDev_differs(thisEnv, thisNs)){
environment(thisEnv) <- environment(thisNs)
.essDev_assign(this, thisEnv, envns)
funcNs <- c(funcNs, this)
if(exists(".__S3MethodsTable__.", envir = envns, inherits = FALSE)){
S3_table <- get(".__S3MethodsTable__.", envir = envns)
if(exists(this, envir = S3_table, inherits = FALSE))
.essDev_assign(this, thisEnv, S3_table)
}
}
}else{
newNs <- c(newNs, this)
}
}else{
if(!identical(thisEnv, thisNs)){
.essDev_assign(this, thisEnv, envns)
objectsNs <- c(objectsNs, this)}
}
}else{
newNs <- c(newNs, this)
}
## PKG
if (exists(this, envir = envpkg, inherits = FALSE)){
thisPkg <- get(this, envir = envpkg)
if(is.function(thisPkg) || is.function(thisEnv)){
if(is.function(thisPkg) && is.function(thisEnv)){
if(.essDev_differs(thisPkg, thisEnv)){
environment(thisEnv) <- environment(thisPkg)
.essDev_assign(this, thisEnv, envpkg)
funcPkg <- c(funcPkg, this)}
}else{
newPkg <- c(newPkg, this)}
}else{
if(!identical(thisPkg, thisEnv)){
.essDev_assign(this, thisEnv, envpkg)
objectsPkg <- c(objectsPkg, this)}}
}else{
newPkg <- c(newPkg, this)}
}
## deal with new plain objects and functions
for(this in intersect(newPkg, newNs)){
thisEnv <- get(this, envir = env, inherits = FALSE)
if(exists(this, envir = .GlobalEnv, inherits = FALSE)){
thisGl <- get(this, envir = .GlobalEnv)
if(.essDev_differs(thisEnv, thisGl)){
if(is.function(thisEnv)){
environment(thisEnv) <- envns
newFunc <- c(newFunc, this)
}else{
newObjects <- c(newObjects, this)
}
.essDev_assign(this, thisEnv, .GlobalEnv)
}
}else{
if(is.function(thisEnv)){
environment(thisEnv) <- envns
newFunc <- c(newFunc, this)
}else{
newObjects <- c(newObjects, this)
}
.essDev_assign(this, thisEnv, .GlobalEnv)
}
}
if(length(funcNs))
objectsNs <- c(objectsNs, sprintf("FUN[%s]", paste(funcNs, collapse = ", ")))
if(length(funcPkg))
objectsPkg <- c(objectsPkg, sprintf("FUN[%s]", paste(funcPkg, collapse = ", ")))
if(length(newFunc))
newObjects <- c(newObjects, sprintf("FUN[%s]", paste(newFunc, collapse = ", ")))
## CLASSES
classesPkg <- classesNs <- newClasses <- character()
for(this in allClassDefs()){
newPkg <- newNs <- FALSE
thisEnv <- get(this, envir = env)
if(exists(this, envir = envpkg, inherits = FALSE)){
if(!.essDev_identicalClass(thisEnv, get(this, envir = envpkg))){
.essDev_assign(this, thisEnv, envir = envpkg)
classesPkg <- c(classesPkg, this)
}
}else{
newPkg <- TRUE
}
if(exists(this, envir = envns, inherits = FALSE)){
if(!.essDev_identicalClass(thisEnv, get(this, envir = envns))){
.essDev_assign(this, thisEnv, envir = envns)
classesNs <- c(classesNs, this)
}
}else{
newNs <- TRUE
}
if(newNs && newPkg){
if(exists(this, envir = .GlobalEnv, inherits = FALSE)){
if(!.essDev_identicalClass(thisEnv, get(this, envir = .GlobalEnv))){
.essDev_assign(this, thisEnv, envir = .GlobalEnv)
newClasses <- c(newClasses, this)
}
}else{
.essDev_assign(this, thisEnv, envir = .GlobalEnv)
newClasses <- c(newClasses, this)
}
}
}
if(length(classesPkg))
objectsPkg <- gettextf("CLS[%s]", sub(methods:::.ClassMetaPattern(), "", paste(classesPkg, collapse = ", ")))
if(length(classesNs))
objectsNs <- gettextf("CLS[%s]", sub(methods:::.ClassMetaPattern(), "", paste(classesNs, collapse = ", ")))
if(length(newClasses))
newObjects <- gettextf("CLS[%s]", sub(methods:::.ClassMetaPattern(), "", paste(newClasses, collapse = ", ")))
## METHODS:
## Method internals: For efficiency reasons setMethod() caches
## method definition into a global table which you can get with
## 'getMethodsForDispatch' function, and when a method is dispatched that
## table is used. When ess-developer is used to source method definitions the
## two copies of the functions are identical up to the environment. The
## environment of the cached object has namespace:foo as it's parent but the
## environment of the object in local table is precisely namspace:foo. This
## does not cause any difference in evaluation.
methodNames <- allMethodTables()
methods <- sub(methods:::.TableMetaPrefix(), "", methodNames)
methods <- sub(":.*", "", methods)
methodsNs <- newMethods <- character()
for (i in seq_along(methods)){
table <- methodNames[[i]]
tableEnv <- get(table, envir = env)
if(exists(table, envir = envns, inherits = FALSE)){
inserted <- .essDev_insertMethods(tableEnv, get(table, envir = envns), envns)
if(length(inserted))
methodsNs <- c(methodsNs, gettextf("%s{%s}", methods[[i]], paste(inserted, collapse = ", ")))
}else if(exists(table, envir = .GlobalEnv, inherits = FALSE)){
inserted <- .essDev_insertMethods(tableEnv, get(table, envir = .GlobalEnv), envns)
if(length(inserted))
newMethods <- c(newMethods, gettextf("%s{%s}", methods[[i]], paste(inserted, collapse = ", ")))
}else{
.essDev_assign(table, tableEnv, envir = .GlobalEnv)
newMethods <- c(newMethods, gettextf("%s{%s}", methods[[i]], paste(objects(envir = tableEnv, all.names = T), collapse = ", ")))
}
}
if(length(methodsNs))
objectsNs <- c(objectsNs, gettextf("METH[%s]", paste(methodsNs, collapse = ", ")))
if(length(newMethods))
newObjects <- c(newObjects, gettextf("METH[%s]", paste(newMethods, collapse = ", ")))
if(length(objectsPkg))
cat(sprintf("%s PKG: %s ", package, paste(objectsPkg, collapse = ", ")))
if(length(objectsNs))
cat(sprintf("NS: %s ", paste(objectsNs, collapse = ", ")))
if(length(newObjects))
cat(sprintf("GlobalEnv: %s\n", paste(newObjects, collapse = ", ")))
if(length(c(objectsNs, objectsPkg, newObjects)) == 0)
cat(sprintf("*** Nothing explicitly assigned ***\n"))
invisible(env)
}
.essDev_insertMethods <- function(tableEnv, tablePkg, envns)
{
inserted <- character()
for(m in ls(envir = tableEnv, all.names = T)){
if(exists(m, envir = tablePkg, inherits = FALSE)){
thisEnv <- get(m, envir = tableEnv)
thisPkg <- get(m, envir = tablePkg)
if(is(thisEnv, "MethodDefinition") && is(thisPkg, "MethodDefinition") &&
.essDev_differs(thisEnv@.Data, thisPkg@.Data)){
environment(thisEnv@.Data) <- envns
## environment of cached method in getMethodsForDispatch table is still env
## not a problem as such, but might confuse users
.essDev_assign(m, thisEnv, tablePkg)
inserted <- c(inserted, m)
}}}
inserted
}
.essDev_evalSource <- function (source, expr, package = "")
{
envns <- tryCatch(asNamespace(package), error = function(cond) NULL)
if(is.null(envns))
stop(gettextf("Package \"%s\" is not attached and no namespace found for it",
package), domain = NA)
env <- new.env(parent = envns)
env[[".packageName"]] <- package
methods:::setCacheOnAssign(env, TRUE)
if (missing(source))
eval(expr, envir = env)
else if (is(source, "character"))
for (text in source) sys.source(text, envir = env, keep.source = TRUE)
else stop(gettextf("Invalid source argument: got an object of class \"%s\"",
class(source)[[1]]), domain = NA)
env
}
.essDev_assign <- function (x, value, envir)
{
if (exists(x, envir = envir, inherits = FALSE) && bindingIsLocked(x, envir)) {
unlockBinding(x, envir)
assign(x, value, envir = envir, inherits = FALSE)
op <- options(warn = -1)
on.exit(options(op))
lockBinding(x, envir)
} else {
assign(x, value, envir = envir, inherits = FALSE)
}
invisible(NULL)
}
.essDev_identicalClass <- function(cls1, cls2, printInfo = FALSE){
slots1 <- slotNames(class(cls1))
slots2 <- slotNames(class(cls2))
if(identical(slots1, slots2)){
vK <- grep("versionKey", slots1)
if(length(vK))
slots1 <- slots2 <- slots1[-vK]
out <- sapply(slots1, function(nm) identical(slot(cls1, nm), slot(cls2, nm)))
if(printInfo) print(out)
all(out)
}
}
.essDev_differs <- function(f1, f2) {
if (is.function(f1) && is.function(f2)){
!(identical(body(f1), body(f2)) && identical(args(f1), args(f2)))
}else
!identical(f1, f2)
}

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.ess_weave <- function(command, file, encoding = NULL){
cmd_symb <- substitute(command)
if(grepl('knit|purl', deparse(cmd_symb))) require(knitr)
od <- getwd()
on.exit(setwd(od))
setwd(dirname(file))
frame <- parent.frame()
if(is.null(encoding))
eval(bquote(.(cmd_symb)(.(file))), envir = frame)
else
eval(bquote(.(cmd_symb)(.(file), encoding = .(encoding))), envir = frame)
}
.ess_knit <- function(file, output = NULL){
library(knitr)
frame <- parent.frame()
od <- getwd()
on.exit(setwd(od))
setwd(dirname(file))
## this bquote is really needed for data.table := operator to work correctly
eval(bquote(knit(.(file), output = .(output))), envir = frame)
}
.ess_sweave <- function(file, output = NULL){
od <- getwd()
frame <- parent.frame()
on.exit(setwd(od))
setwd(dirname(file))
eval(bquote(Sweave(.(file), output = .(output))), envir = frame)
}
## Users might find it useful. So don't prefix with .ess.
htsummary <- function (x, hlength = 4, tlength = 4, digits = 3)
{
## fixme: simplify and generalize
snames <- c("mean", "sd", "min", "max", "nlev", "NAs")
d <- " "
num_sumr <- function(x){
c(f(mean(x, na.rm = TRUE)),
f(sd(x, na.rm = TRUE)),
f(min(x, na.rm = TRUE)),
f(max(x, na.rm = TRUE)),
d,
f(sum(is.na(x), na.rm = TRUE)))
}
f <- function(x) format(x, digits = digits)
if (is.data.frame(x) | is.matrix(x)) {
if (nrow(x) <= tlength + hlength){
print(x)
} else {
if (is.matrix(x))
x <- data.frame(unclass(x))
## conversion needed, to avoid problems with derived classes suchs as data.table
h <- as.data.frame(head(x, hlength))
t <- as.data.frame(tail(x, tlength))
for (i in 1:ncol(x)) {
h[[i]] <- f(h[[i]])
t[[i]] <- f(t[[i]])
}
## summaries
sumr <- sapply(x, function(c){
if(is.logical(c))
## treat logical as numeric; it's harmless
c <- as.integer(c)
if(is.numeric(c))
num_sumr(c)
else if(is.factor(c)) c(d, d, d, d, nlevels(c), sum(is.na(c)))
else rep.int(d, length(snames))
})
sumr <- as.data.frame(sumr)
row.names(sumr) <- snames
dots <- rep("...", ncol(x))
empty <- rep.int(" ", ncol(x))
lines <- rep.int(" ", ncol(x))
df <- rbind(h, ...= dots, t, `_____` = lines, sumr, ` ` = empty)
print(df)
}
} else {
cat("head(", hlength, "):\n", sep = "")
print(head(x, hlength))
if(length(x) > tlength + hlength){
cat("\ntail(", tlength, "):\n", sep = "")
print(tail(x, tlength))
}
cat("_____\n")
if(is.numeric(x) || is.logical(x))
print(structure(num_sumr(x), names = snames), quote = FALSE)
else if(is.factor(x)){
cat("NAs: ", sum(is.na(x), na.rm = TRUE), "\n")
cat("levels: \n")
print(levels(x))
}
}
invisible(NULL)
}
.ess_vignettes <- function(){
vs <- unclass(browseVignettes())
vs <- vs[sapply(vs, length) > 0]
mat2elist <- function(mat){
if(!is.null(dim(mat))){
apply(mat, 1, function(r)
sprintf("(list \"%s\")",
paste0(gsub("\"","\\\\\"",
as.vector(r[c("Title", "Dir", "PDF", "File", "R")])),
collapse = "\" \"")))
}
}
cat("(list \n",
paste0(mapply(function(el, name) sprintf("(list \"%s\" %s)",
name,
paste0(mat2elist(el), collapse = "\n")),
vs, names(vs)), collapse = "\n"), ")\n")
}

1
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1.1.8

56
.emacs.d/elpa/ess-20160208.453/etc/Extract.factor.Rd Normal file
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%% ESS BUG: Indentation ([Tab]) does not work if point is after \arguments{..}
%% ------- almost surely because of the (non-escaped) "[".
%% and this, all below is original from the R sources (R-devel, 2014-03-05)
% File src/library/base/man/Extract.factor.Rd
% Part of the R package, http://www.R-project.org
% Copyright 1995-2010 R Core Team
% Distributed under GPL 2 or later
\name{Extract.factor}
\title{Extract or Replace Parts of a Factor}
\alias{[.factor}
\alias{[<-.factor}
\alias{[[.factor}
\alias{[[<-.factor}
\description{
Extract or replace subsets of factors.
}
\usage{
\method{[}{factor}(x, \dots, drop = FALSE)
\method{[[}{factor}(x, \dots)
\method{[}{factor}(x, \dots) <- value
\method{[[}{factor}(x, \dots) <- value
}
\arguments{
\item{x}{a factor}
\item{\dots}{a specification of indices -- see \code{\link{Extract}}.}
\item{drop}{logical. If true, unused levels are dropped.}
\item{value}{character: a set of levels. Factor values are coerced to
character.}
}
\value{
A factor with the same set of levels as \code{x} unless \code{drop = TRUE}.
}
\details{
When unused levels are dropped the ordering of the remaining levels is
preserved.
If \code{value} is not in \code{levels(x)}, a missing value is
assigned with a warning.
Any \code{\link{contrasts}} assigned to the factor are preserved
unless \code{drop = TRUE}.
The \code{[[} method supports argument \code{exact}.
}
\seealso{
\code{\link{factor}}, \code{\link{Extract}}.
}
\examples{
## following example(factor)
(ff <- factor(substring("statistics", 1:10, 1:10), levels = letters))
ff[, drop = TRUE]
factor(letters[7:10])[2:3, drop = TRUE]
}
\keyword{category}

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### Makefile - for scripts and icons (./etc) of ESS distribution.
###
## Before making changes here, please take a look at Makeconf
include ../Makeconf
# In ../Makefile we already construct the ESSR-VERSION file :
# ESSR_VERSION = $(shell cat ESSR-VERSION)
#ETCFILES = $(wildcard BACKBUG[S5].BAT backbug[s5] *.S sas-keys.*)
#ETCFILES = ESSR.R ess-developer.R SVN-REVISION *.S sas-keys.* ess-sas-sh-command
ETCFILES_1 = *.S sas-keys.* ess-sas-sh-command *.jl
isRELEASE=$(shell test -f .IS.RELEASE && echo 'yes')
ifeq ($(isRELEASE),yes)
ETCFILES = .IS.RELEASE git-ref $(ETCFILES_1)
else
ETCFILES = $(ETCFILES_1)
endif
#ICONS = $(wildcard icons/*.xpm)
ICONS = icons/*.xpm
ESSR_UTIL_FILES = ESSR/LOADREMOTE ESSR/VERSION
ESSR_CODE_FILES = ESSR/R/*.R ESSR/R/.*.R
# ESSR_tarball = ESSR_$(ESSR_VERSION).tar.gz
all: #ESSR-VERSION $(ESSR_tarball) library/ESSR
show-etc:
@echo $(ETCFILES)
ls -l $(ETCFILES)
## happens "above" as it is need also in ../lisp/ :
# ESSR-VERSION: $(ESSR_FILES)
# (cd .. ; make etc/ESSR-VERSION)
# $(ESSR_tarball): $(ESSR_FILES)
# R CMD build ESSR
# library/ESSR: $(ESSR_tarball)
# R CMD INSTALL -l library ESSR
# rel: $(ESSR_tarball)
# [ x$$USER = xmaechler ] || (echo 'must be maechler'; exit 1 )
# $(INSTALL) $(ESSR_tarball) $(UPLOAD_DIR)/pkgs/src/contrib
install :
$(INSTALLDIR) $(ETCDIR)/icons
$(INSTALLDIR) $(ETCDIR)/ESSR/R
$(INSTALL) $(ETCFILES) $(ETCDIR)
$(INSTALL) $(ICONS) $(ETCDIR)/icons
$(INSTALL) $(ESSR_UTIL_FILES) $(ETCDIR)/ESSR
$(INSTALL) $(ESSR_CODE_FILES) $(ETCDIR)/ESSR/R
chmod +x $(ETCDIR)/ess-sas-sh-command
uninstall :
-cd $(ETCDIR) && $(UNINSTALL) $(ETCFILES)
-cd $(ETCDIR) && $(UNINSTALL) $(ICONS)
-cd $(ETCDIR) && $(UNINSTALL) $(ESSR_UTIL_FILES)
-cd $(ETCDIR) && $(UNINSTALL) $(ESSR_CODE_FILES)
## 'clean' shall remove *exactly* those things that are *not* in version control
clean:
rm -rf SVN-REVISION
## 'distclean' removes also things in VC (svn, when they are remade by "make"):
# distclean: clean
# rm -rf ESSR_*.tar.gz

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#### File showing off things that go wrong or *went* wrong in the past #### -- with R-mode (mostly coded in ../lisp/ess-mode.el )
### NOTE: this file is indented with RRR style !!!!!
### but do not change indentations anymore of anything in here:
### expressions are written as we *want* them, not as ESS currently puts them
options(keep.source = FALSE) # so we see R's deparse() + print() indentation
### --- 1 --------- extraneous comment chars : This seems fixed
## From: Robert Gentleman <rgentlem@fhcrc.org>
## To: Martin Maechler <maechler@stat.math.ethz.ch>
## Subject: ESS buglet
## Date: Sun, 01 Jul 2007 21:41:24 -0700
## Hi Martin,
## It seems that the following buglet exists (at least in what ever
## version I am using)
##a silly comment
##and a second one
foo <- function(x=a, abc = list("def", a=1,3,3), more.args, and, bla,
blu, bl,
another, plus, yet.another, and_mbasd,
lots = NULL,
more = NULL,
args = NULL) {
x
}
##- when the line before a function def is a comment, and adding args,
##- then new lines, when generated have a comment char at the beginning of
##- the line. It is slightly annoying as I have to remove the comment char.
##-
##- If I add a blank line after the comment line, then the problem does not
##- occur.
## and another ''anonymous'' function:
function(x=a, abc = list("def", a=c(1,3,3)), more.args, and, bla, blu,
blo, Abc,
def,
another, and_another, and_this) {
...; ...
}
## This is a "TRUE" example (from Matrix/tests/ ):
NA.or.True <- function(x) is.na(x) | x
abc <- function(x, y, ...) this.is.just.a.one.liner(x,y, z=TRUE, ...)
## A more-liner function with no "{...}" -- this one even works (but not all!)
mindiff <- function(df) df[which.min(df$diff),
which.max(df$daff)]
## Two functions in one line - can I "send" just one of them? {no, not "simply"}
f1 <- function(x) be.friendly(x, force=TRUE); f2 <- function(x,y) x*sin(pi*x)
### --- 2 ----------------------------------------------------------------
### --- Suggestion (Jenny Brian): --> Create a (defun ess-eval-multiline .)
## Here is useful valid R "test code":
## From 'example(plot.default)' :
Speed <- cars$speed
Distance <- cars$dist
plot(Speed, Distance, panel.first = grid(8,8),
pch = 0, cex = 1.2, col = "blue")
pp <- plot(Speed, Distance, panel.first = grid(8,8),
pch = 0, cex = 1.2, col = "blue")
plot(Speed, Distance,
panel.first = lines(lowess(Speed, Distance), lty = "dashed"),
pch = 0, cex = 1.2, col = "blue")
## Note: We now at least C-c C-c {ess-eval-function-or-paragraph-and-step}
### --- 3 ----------------------------------------------------------------
###--- This one (from the Matrix package) is for testing ess-roxy...,
## i.e., C-c C-o
## not exported but used more than once for "dimnames<-" method :
## -- or do only once for all "Matrix" classes ??
dimnamesGets <- function (x, value) {
d <- dim(x)
if (!is.list(value) || length(value) != 2 ||
!(is.null(v1 <- value[[1]]) || length(v1) == d[1]) ||
!(is.null(v2 <- value[[2]]) || length(v2) == d[2]))
stop(gettextf("invalid dimnames given for '%s' object", class(x)))
x@Dimnames <- list(if(!is.null(v1)) as.character(v1),
if(!is.null(v2)) as.character(v2))
x
}
### --- 4 ----------------------------------------------------------------
### continued statements
a <- function(ch) {
if(ch == Inf) {
E.cond <- numeric(nb)
}
else {
indic <- ifelse(jinf+1 <= 1 & jsup >= 1,1,0)
E.cond <- ch*(-pbinom(jinf,ni,prb) + 1-pbinom(js.n,ni,prb)) +
ifelse(ni == 1, prb*indic,
mu*(pbinom(js.n-1,pmax(ni-1,1),prb) -
pbinom(jinf-1,pmax(ni-1,1),prb))) / sV -
### ^-- now here (better)
mu/sV*(pbinom(js.n,ni,prb) - pbinom(jinf,ni,prb))
### ^-- now here (ok; more indentation would also be ok)
indic2 <- ifelse(jinf+1 <= 1 & jsup >= 1 & ni == 2,1,0)
}
}
### --- 5 ----------------------------------------------------------------
### The beginning of function is not found correctly, and hence
### all "ess-*-function" (C-M-a, C-M-e, ...) fail:
setMeneric <-
## It is clearly allowed to have comments here.
## S version 4, and John Chambers in particular like it.
##
## BUG: M-C-e or M-C-a fails from ``here'' --
## --- effectively because of ess-beginning-of-function fails
## and that really relies on finding ess-function-pattern;
## i.e., ess-R-function-pattern in ~/emacs/ess/lisp/ess-cust.el
##
function(name, def = NULL, group = list(), valueClass = character(),
where = topenv(parent.frame()), genericFunction = NULL)
{
## comments in here are at least kept via "source" attribute
if(exists(name, "package:base") &&
typeof(get(name, "package:base")) != "closure") {
FALSE
}
"ABC"
}
### --- 6 ----------------------------------------------------------------
## In one-liners without "{ ... }" body, the end-of-function is also
## not correctly found:
## Use C-M-e to see: In these two, the "end-of-function" is after
## 'class' :
## ---- these all work now (ESS version 5.3.8) :
## no it doesn't VS[10-03-2012|ESS 12.03]:
onelinerFails <- function(x, ...) class(x)
onelinerFailsToo <-
function(x, ...)
class(x)
onelinerWorks <- function(x, ...) { class(x) }
onelinerWorksToo <-
function(x, ...) {
class(x)
}
### --- 7 ----------------------------------------------------------------
## idem:
## this has one line more before 'function' than "typically:"
setMethod("[", signature(x = "dgTMatrix", i = "numeric", j = "missing",
drop = "logical"),
function (x, i, j, ..., drop) { ## select rows
storage.mode(i) <- "integer"
xi <- x@i + 1:1 # 1-indexing
## ...................
if (drop && any(nd == 1)) drop(as(x,"matrix")) else x
})
### --- 8 ----------------------------------------------------------------
## idem:
## all bellow are ok VS[10-03-2012|ESS 12.03]:
"dimnames<-.data.frame" <- function(x, value) {
d <- dim(x)
if(!is.list(value) || length(value) != 2
|| d[[1]] != length(value[[1]])
|| d[[2]] != length(value[[2]]))
stop("invalid 'dimnames' given for data frame")
row.names(x) <- as.character(value[[1]]) # checks validity
names(x) <- as.character(value[[2]])
x
}
'[.foo' <- function(x, i, value)
{
###
y <- x
y[i] <- value
y
}
'[[.bar' <- function(x, i, value)
{
## bla bla bla
y <- as.foo(x) ; y[[i]] <- value
y
}
"[<-.foobar" <- function(x,i,j,value) {
## just something
x
}
"names<-.foobar" <- function(x, value) {
## just something else
x
}
`[<-.data.frame` <- function(x, i, j, value)
{
nA <- nargs() # value is never missing, so 3 or 4.
###..........
class(x) <- cl
x
}
"[[<-.data.frame"<- function(x, i, j, value)
{
cl <- oldClass(x)
## delete class: Version 3 idiom
## to avoid any special methods for [[<-
class(x) <- NULL
###...........
class(x) <- cl
x
}
"$<-.data.frame" <- function(x, i, value)
{
cl <- oldClass(x)
## delete class: Version 3 idiom
## to avoid any special methods for [[<-
###...........
class(x) <- cl
return(x)
}
## swanky functions:
`swank:quit-inspector` <- function(slimeConnection, sldbState) {
resetInspector(slimeConnection)
FALSE
}
'swank:quit-inspector' <- function(slimeConnection, sldbState) {
resetInspector(slimeConnection)
FALSE
}
### --- 9 ----------------------------------------------------------------
## VS[03-2012|12.03]:FIXED:
## From: "Sebastian P. Luque" <spluque@gmail.com>
## To: ess-bugs@stat.math.ethz.ch
## Subject: [ESS-bugs] ess-mode 5.12; `ess-indent-line' error
## Date: Tue, 17 Aug 2010 13:08:25 -0500
## With the following input, and point on the line with "Table 8.3":
## it was the parenthetical expression at the beg of line
if (require(lme4)) {
## Model in p. 213
(fm1 <- lmer(logFEV1 ~ age + log(height) + age0 + log(height0) + (age | id),
data=fev1, subset=logFEV1 > -0.5))
## Table 8.3
VarCorr(fm1)$id * 100
## Model in p. 216
(fm2 <- update(fm1, . ~ . - (age | id) + (log(height) | id)))
}
### -----
## hitting TAB (`ess-indent-command'), which calls `ess-indent-line' I get
## the following trace:
## ....: (scan-error "Containing expression ends prematurely" 20 20)
## scan-sexps(177 -2)
## forward-sexp(-2)
## ...
## ess-continued-statement-p()
## ......
## Interestingly, if the lines 2-4 are absent, then the problem is gone.
## The problem is also there in ESS 5.11.
## I'll try to find out what is going on in `ess-continued-statement-p' but
## given that I'm not very familiar with the stuff in ess-mode.el, I'm
## submitting the report in case somebody can detect the issue sooner.
## another example: hitting Tab at }else line
.essDev_differs <- function(f1, f2){
if (is.function(f1) && is.function(f2)){
!(identical(body(f1), body(f2)) && identical(args(f1), args(f2)))
}else
!identical(f1, f2)
}
### --- 10 ---------------------------------------------------------------
## indent at 0 after }else:
## VS:[03-2012|12.03]:FIXED:
if (is.function(f1) && is.function(f2)){
!(identical(body(f1), body(f2)) && identical(args(f1), args(f2)))
}else
!identical(f1, f2)
### --- 11 ---------------------------------------------------------------
## --------------- C-c C-c was finding the wrong "beginning of function"
## [:FIXED:, 2011-05-28]
foobar <- function(...) {}
rm(list=ls())
##--------> consequence of the above experiments:
## the 2nd form is numerically "uniformly better" than the first
##--------> 2011-05-27: Change Frank's psiInv() to
## psiInv = function(t,theta)
## -log1p(exp(-theta)*expm1((1-t)*theta)/expm1(-theta))
### --- 12 ---------------------------------------------------------------
##--- In the following block, in the first line, C-c C-c does *NOT* behave
## VS[10-03-2012|ESS 12.03]: works fine for me:
th <- 48 # now do ls() and see what happened ... the horror !!!
d <- 3
cpF <- list("Frank", list(th, 1:d))
cop <- acF <- cpF$copula
### --- 13 ---------------------------------------------------------------
## VS[05-05-2012|ESS 12.04]: looks like :FIXED:
## From: Aleksandar Blagotic <aca.blagotic@gmail.com>
## To: <ess-help@stat.math.ethz.ch>
## Subject: [ESS] R-mode: forward-sexp: Scan error: "Unbalanced parentheses"
## Date: Tue, 6 Dec 2011 01:24:11 +0100
#
## Let's presuppose that I have a function like this:
#
fn <- function(x, ...){
re <- "^#{1,6} [[:print:]]+$"
grepl(re, x, ...)
}
## As soon as I put my cursor at the end of the line with regexp, and
## press RET, I get this error:
## forward-sexp: Scan error: "Unbalanced parentheses"
##
##-------
## Rodney S: I can reproduce it ...
## Martin M: I can NOT reproduce it, neither with 'emacs -Q';
## tried both ESS 5.14 and ESS from svn
## VS[03-2012|12.03]: Cannot reproduce it either, solved?
### --- 14 ---------------------------------------------------------------
## check the behavior of ess-arg-function-offset-new-line
a <- some.function(
arg1,
arg2)
## ^--- RRR has ess-arg-function-offset-new-line (4) ==> should indent here
a <- some.function(arg1,
arg2)
## ^--- here
### --- 15 --------------------------------------------------------------
## VS[05-05-2012|ESS 12.04]:FIXED:
## indentation of the 3rd line is wrong
for(s in seq(10, 50, len = 5))
for(a in seq(.5, 1, len = 5))
pt_dif_plot(s, a)
## ^-- here
### --- 16 ----
## VS[05-05-2012|ESS 12.04]:FIXED:
## MM[2014-04-28]: added '}' before else (=> "{" after if(.))
## so parse(<file>) works at all!
## Gives error unbalanced para at else lines and indentation is wrong
## error: Point is not in a function according to 'ess-function-pattern'.
getOrCreateForm <- function(bindName, whereEnv)
if(exists(bindName, envir = get(".forms", envir = whereEnv))) {
get(bindName, envir = whereEnv)
### ^-- here
} else
new("protoForm")
### ^-- here
parentContainer <-
if(is.null(.getPrototype(.Object@host))) { emptyenv()
} else sdf
### ^-- here
parentContainer <-
if(is.null(.getPrototype(.Object@host))) emptyenv()
else sdf
### ^-- here
### --- 17 ---
## Indentation ----- "expression" is special
expremmion <- c(1, 3,
9876)# was always ok
## Had wrong indentation here:
expression <- c(2343,
23874, 239487)
## or here:
foo <- function(x) {
expression <- c(2343,
23874, 239487)
10 + expression
}
## Where as here, we *do* want the indentation to
## *NOT* go all the way to the right:
{
my.long.Expression <- expression(
x[a[j]] == exp(theta[1] + theta[2]^2),
x[b[i]] == sin(theta[3] ~~ theta[4])
)
ausdruck <- expression
my.long.Expr...... <- ausdruck(
x[a[j]] == exp(theta[1] + theta[2]^2),
)
}
## VS[18-08-2012]: redundant feature. This is a feature for long subexpressions
## imidiately folowing new line. Documented in ess-arg-function-offset-new-line
### --- 18 ---
## M-C-a (beginning of function)
## ----- anywhere inside the following function, M-C-a must go to beginning
Ops.x.x <- function(e1, e2)
{
d <- dimCheck(e1,e2)
if((dens1 <- extends(c1 <- class(e1), "denseMatrix")))
gen1 <- extends(c1, "generalMatrix")
if((dens2 <- extends(c2 <- class(e2), "denseMatrix")))
gen2 <- extends(c2, "generalMatrix")
if(dens1 && dens2) { ## both inherit from ddense*
geM <- TRUE
if(!gen1) {
if(!gen2) { ## consider preserving "triangular" / "symmetric"
geM <- FALSE
le <- prod(d)
isPacked <- function(x) length(x@x) < le
}
}
## now, in all cases @x should be matching & correct {only "uplo" part is used}
r <- callGeneric(e1@x, e2@x)
if(geM)
new(paste0(.M.kind(r), "geMatrix"), x = r, Dim = d, Dimnames = dimnames(e1))
else
new(paste0(.M.kind(r), Mclass), x = r, Dim = d, .....)
}
else {
r <- ....
## criterion "2 * nnz(.) < ." as in sparseDefault() in Matrix() [./Matrix.R] :
if(2 * nnzero(r, na.counted = TRUE) < prod(d))
as(r, "sparseMatrix") else r
}
}
### --- 19 ---
## indentation with regexp (bug in ess-backward-to-noncomment)
parse_roc <- function(lines, match = "^\\s*+\' ?") {
lines <- lines[str_detect(lines, match)]
if (length(lines) == 0) return(NULL)
### ^-- here (2014-11: fixed)
}
### --- 20 ---
## continuation indentation must be consistent in/out {}:
{
a <- ggplot(data = overtime.by.month,
aes(x="", y=Percent, fill = Overtime)) +
geom_bar(width = 1) +
xlab('') +
ylab(sub.txt) +
labs(title = title.txt) +
facet_wrap(~Year.Month)
}
a <- ggplot(data = overtime.by.month,
aes(x="", y=Percent, fill = Overtime)) +
geom_bar(width = 1) +
xlab('') +
ylab(sub.txt) +
labs(title = title.txt) +
facet_wrap(~Year.Month)
### ^-- face_wrap must be here
### --- 20b ---
## From https://github.com/emacs-ess/ESS/issues/120
mean(rnorm(100, mean = runif(1, 1, 10)), na.rm =TRUE) +
2
## ^--- 2 is here
mean(rnorm(100, mean = runif(1, 1, 10)),
na.rm =TRUE) +
2
## ^--- 2 is here
mean(rnorm(100,
mean = runif(1, 1, 10)), na.rm=TRUE) +
2
## ^--- 2 is here
### --- 21 ---
## From: Marius Hofert <marius.hofert@math.ethz.ch>
## Date: Fri, 15 Mar 2013 21:00:45 +0100
## Hi,
## The following bug happens in ESS 12.09-2 [rev. 5395 (2013-01-10)]. Put the
## cursor in the line before the function head and hit C-c C-c.
foo <- function(x)
x # bar
x <- 1:10
## I'll see
## > + > [1] 1 2 3 4 5 6 7 8 9 10
## ESS 15.03: Error in eval(expr, .... : object 'x' not found
foo <- function(x) x*x
bar <- function(y) y
## via C-c C-c leads to "Error: object 'bar' not found". -- fixed
### --- 22 ----
## now correct indentation (inspite of # {was same reason as 19})
if (!grepl("#", x))
return(res)
### --- 23 ----
### three ways to indent closing parent depending on context:
foo <-
function_call(
a,
b,
c
)
### ^-- ) is here now
foo <- function_call(
a,
b,
c
)
### ")" is at column 0
foo <- function_call(a,
b,
c
)
### ^-- ) is here
### --- 24 ---
### shift comma in function calls
foo <- function_call(a
, b
, c
### ^-- c is here
)
### ^-- ) is here
### --- 25 ---
## if/else in function calls and nested
function_call(abc =
if (test)
do_something
else
do_something_else)
function_call(
abc =
if (test)
do_something
else
do_something_else)
function_call(abc = if (test)
do_something
else
do_something_else)
## real example is smooth.spline() source code [still (2015-04-08) wrong / bug!]
ss <- function (x, all.knots, nknots, ...)
{
if (all.knots) {
if (!missing(nknots) && !is.null(nknots))
warning("'all.knots' is TRUE; 'nknots' specification is disregarded")
nknots <- nx
} else if (is.null(nknots)) # <- for back compatibility
nknots <- .nknots.smspl(nx)
else {
### ^ want 'else' there
if (is.function(nknots))
nknots <- nknots(nx)
else if (!is.numeric(nknots))
stop("'nknots' must be numeric (in {1,..,n})")
if (nknots < 1)
stop("'nknots' must be at least 1")
else if (nknots > nx)
stop("cannot use more inner knots than unique 'x' values")
}
### ^-- want '}' there
}
## "if" conditional is an exception of the continuation rules:
## Here, we do not want subsequently further indentation of the c1 || c2 || c3
## part:
t2 <- function(x) {
if(long.expression.of.some.size(x, pi) ||
another.longish.expression(sin(x)*exp(x)) ||
a.third.condition.under.which.A.is.chosen)
### ^-- here
A
else
B
}
r <-
(some.function (x, 2342) +
another.f (x^3) + sdfsdf - sdfsdf +
and(x) + the(x) - last(x)*part(3))
### --- 26 ----
## This is formally correct R, though help(parse) mentions the line-length limit of
## 4095 __when reading from the console__
## ESS gives syntax errors ("Error: unexpected ','" ...) when evaluating this
## because line length >= 4096 :
##
x <- c(1, 3.075819, 1.515999, 2.156169, 1.480742, 1.765485, 1.460206, 1.603707, 1.427429, 1.504712, 1.334528, 1.48297, 1.355308, 1.383867, 1.319241, 1.36065, 1.307467, 1.365596, 1.255259, 1.352741, 1.239381, 3.15342, 1.799889, 2.258497, 1.688312, 1.906779, 1.548203, 1.724785, 1.500873, 1.573442, 1.417137, 1.540805, 1.395945, 1.472596, 1.394247, 1.377487, 1.337394, 1.369354, 1.333378, 1.3181, 1.313813, 1.315528, 2.12777, 2.718898, 1.993509, 2.220433, 1.820585, 1.97782, 1.672455, 1.770151, 1.587478, 1.685352, 1.539295, 1.584536, 1.499487, 1.50702, 1.41952, 1.449058, 1.393042, 1.432999, 1.369964, 1.400997, 1.333824, 2.950549, 2.145387, 2.382224, 1.927077, 2.032489, 1.8371, 1.877833, 1.710891, 1.756053, 1.620778, 1.657761, 1.558978, 1.56257, 1.508633, 1.534406, 1.46709, 1.468734, 1.432529, 1.455283, 1.386975, 1.417532, 2.229573, 2.494447, 2.016117, 2.190061, 1.877996, 1.978964, 1.767284, 1.836948, 1.677372, 1.743316, 1.616383, 1.655964, 1.55484, 1.594831, 1.502185, 1.543723, 1.467005, 1.491123, 1.44402, 1.446915, 1.401578, 2.580264, 2.109121, 2.240741, 1.944719, 2.043397, 1.821808, 1.89725, 1.748788, 1.786988, 1.659333, 1.697012, 1.610622, 1.616503, 1.538529, 1.562024, 1.499964, 1.529344, 1.474519, 1.483264, 1.441552, 1.434448, 2.165233, 2.320281, 2.007836, 2.086471, 1.884052, 1.950563, 1.76926, 1.843328, 1.708941, 1.741039, 1.627206, 1.644755, 1.580563, 1.593402, 1.527312, 1.568418, 1.501462, 1.502542, 1.464583, 1.467921, 1.431141, 2.340443, 2.048262, 2.161097, 1.926082, 1.995422, 1.81446, 1.853165, 1.738533, 1.784456, 1.679444, 1.696463, 1.612931, 1.629483, 1.548186, 1.580026, 1.52198, 1.531111, 1.482914, 1.484824, 1.442726, 1.447838, 2.093386, 2.185793, 1.948989, 2.02804, 1.867137, 1.907732, 1.771923, 1.800413, 1.691612, 1.720603, 1.642705, 1.649769, 1.589028, 1.598955, 1.539759, 1.55096, 1.503965, 1.50703, 1.471349, 1.469791, 1.436959, 2.218315, 1.997369, 2.041128, 1.887059, 1.928524, 1.79626, 1.827538, 1.716748, 1.735696, 1.658329, 1.664211, 1.599286, 1.611511, 1.553925, 1.562637, 1.516805, 1.529894, 1.476064, 1.482474, 1.453253, 1.458467, 2.0247, 2.07899, 1.921976, 1.949376, 1.824629, 1.851671, 1.744713, 1.765647, 1.683525, 1.685592, 1.625113, 1.624961, 1.571921, 1.581223, 1.535257, 1.537464, 1.497165, 1.504879, 1.468682, 1.469319, 1.448344, 2.092315, 1.941412, 1.969843, 1.844093, 1.866133, 1.766145, 1.783829, 1.703613, 1.709714, 1.646078, 1.654264, 1.594523, 1.598488, 1.545105, 1.555356, 1.514627, 1.521353, 1.483958, 1.487677, 1.449191, 1.459721, 1.958987, 1.985144, 1.87739, 1.879643, 1.786823, 1.799642, 1.720015, 1.724688, 1.663539, 1.662997, 1.609267, 1.615124, 1.56746, 1.562026, 1.520586, 1.52503, 1.493008, 1.502496, 1.471983, 1.468546, 1.435064, 1.994706, 1.880348, 1.894254, 1.805827, 1.815965, 1.744296, 1.743389, 1.665481, 1.681644, 1.624466, 1.626109, 1.584028, 1.5818, 1.54376, 1.547237, 1.504878, 1.515087, 1.479032, 1.47936, 1.450758, 1.45073, 1.892685, 1.91087, 1.825301, 1.827176, 1.745363, 1.746115, 1.693373, 1.701692, 1.648247, 1.637112, 1.594648, 1.592013, 1.554849, 1.55013, 1.522186, 1.520901, 1.492606, 1.493072, 1.460868, 1.46733, 1.440956, 1.92771, 1.835696, 1.841979, 1.775991, 1.766092, 1.703807, 1.708791, 1.654985, 1.655917, 1.602388, 1.611867, 1.570765, 1.573368, 1.53419, 1.529033, 1.506767, 1.503596, 1.481126, 1.471806, 1.444917, 1.451682, 1.850262, 1.855034, 1.778997, 1.789995, 1.718871, 1.717326, 1.667357, 1.666291, 1.619743, 1.631475, 1.582624, 1.58766, 1.546302, 1.545063, 1.512222, 1.517888, 1.489127, 1.487271, 1.466722, 1.463618, 1.444137, 1.8709, 1.794033, 1.80121, 1.736376, 1.740201, 1.673776, 1.682541, 1.638153, 1.642294, 1.604417, 1.597721, 1.559534, 1.559108, 1.533942, 1.529348, 1.499517, 1.501586, 1.473147, 1.473031, 1.457615, 1.452348, 1.805753, 1.812952, 1.746549, 1.747222, 1.696924, 1.694957, 1.652157, 1.650568, 1.607807, 1.613666, 1.577295, 1.570712, 1.543704, 1.538272, 1.515369, 1.517113, 1.487451, 1.491593, 1.464514, 1.464658, 1.439359, 1.823222, 1.758781, 1.767358, 1.70872, 1.712926, 1.666956, 1.667838, 1.62077, 1.621445, 1.592891, 1.58549, 1.55603, 1.559042, 1.521501, 1.523342, 2, 3, 4)
### --- 27 ----
## Indentation after open brace
.a.lst <-
list(ex1 = function(p) {
cMah <- qchisq(0.975, p)
function(d) as.numeric(d < cMah)
### ^--- now here (less indented than prev.)
},
ex2 = function(p) {
cM <- qchisq(0.95, p)
function(d) as.numeric(d < cM)
### ^--- here
})
### ^--- '}' here
.a.lst <- list(ex1 = function(p) {
cMah <- qchisq(0.975, p)
function(d) as.numeric(d < cMah)
}, ## <- now at column 0 {also the next line}
ex2 = function(p) {
cM <- qchisq(0.95, p)
function(d) as.numeric(d < cM)
})
.a.lst <- list(list(aa = {
bbb
### ^--- here
},
aaa = function(p) {
qchisq(0.95, p)
### ^--- here
},
aaaa = {
cccc
### ^--- here
}))
list(function(p){
abc
### ^-- here
})
### at column 0
(ab) {
sfdsf
### ^-- here
}
### --- 27b --- [new, 2015-04-09]
print.MethodsFunction <- function(x, byclass = attr(x, "byclass"), ...)
{
info <- attr(x, "info")
values <- if (byclass) {
unique(info$generic)
} else {
visible <- ifelse(info$visible, "", "*")
paste0(rownames(info), visible)
### ^-- both lines above should start here
}
### ^-- "}" here
## 2nd version:
val <-
if (byclass) {
unique(info$generic)
} else {
visible <- ifelse(info$visible, "", "*")
paste0(rownames(info), visible)
### ^-- both lines above should start here
}
### ^-- "}" here
invisible(x)
}
### --- 28 --- [2015-02-17; still unfixed, 2015-11-21]
## Indentation of end-line comments (to column 40 = 'indent-column')
## {this is part of "real" code in Rmpfr/R/hjk.R}:
hjk <- function(x,n) { # <--- C-M-q "on {" -- does *no longer* indent the "# .."
##-- Setting steps and stepsize -----
nsteps <- floor(log2(1/tol)) # number of steps
steps <- 2^c(-(0:(nsteps-1))) # decreasing step size
dir <- diag(1, n, n) # orthogonal directions
x <- par # start point
fx <- f(x) # smallest value so far
fcount <- 1 # counts number of function calls
if (info) cat(sprintf("step nofc %-12s | %20s\n",
"fmin", "xpar"))
##-- Start the main loop ------------
ns <- 0
while (ns < nsteps && fcount < maxfeval && abs(fx) < target) {
ns <- ns + 1
hjs <- .hjsearch(x, f, steps[ns], dir, fcount, maxfeval, target)
}
hjs
}
### --- 29 ---
foreach(a = 1:3) %do% {
a^2
### ^--- here
}
foreach(a = 1:3) %:%
foreach(b = 10:13) %dopar% {
### ^--- here
a + b
### ^---- here
}
### ^--- here
read.csv('file.csv') %>%
mutate(X = X+2, Y = Y/2) %>%
### ^--- here
filter(X < 5)
### ^-- here (*was* indented earlier)
### --- 30 ---
## a) ok:
{
r <- array(if (d[3L] == 3L)
rgb(t(x[,,1L]), t(x[,,2L]), t(x[,,3L]), maxColorValue = max)
else if (d[3L] == 4L)
rgb(t(x[,,1L]), t(x[,,2L]), t(x[,,3L]), t(x[,,4L]), maxColorValue = max)
else stop("foo"),
dim = d[1:2])
}
## b) ok :
{
obj <- obj && (condition1 || class2 %in% .BasicClasses ||
condition3)
}
## c) ok:
{
if (any(abs(d) < .001*abs(dd) |
(is.na(d) & x == y)))
TRUE
}
### --- 31 --------
## C-s "recog"; M-C-a -- should go to beginning of function, does not
glmmTMB <- function (formula, data = NULL)
{
## glFormula <- function(formula, data=NULL, family = gaussian,
## subset, weights, na.action, offset,
## contrasts = NULL, mustart, etastart,
## control = glmerControl(), ...) {
## FIXME: check for offsets in ziformula/dispformula, throw an error
call <- mf <- mc <- match.call()
if (is.null(family$family)) {
print(family)
stop("'family' not recognized")
}
}
### --- 32 --- 2015-11-07 --- indentation again! --------
{
yl <- if(strictlim) {
ylim
}
else {
range(y, ylim)
}
## room below for weights
dy <- 4*dy
}
## -- 32 b)
{
yl <- if(strictlim) {
ylim
}
else
range(y, ylim)
## continue
}
## -- 32 c)
{
U <- if(is.matrix(x))
apply(x, 2, foo) / (nrow(x) + 1)
else
foo(x) / (length(x) + 1)
}
## 'else' now aligns with 'if' (and their code too)
### --- 33 -- Treat `<<-` as `<-`
{
f(X <-
callme(arg))
f(X <<-
callme(arg))
}
## the 2nd callme() now indents like the first
### Local Variables:
### page-delimiter: "^### --- [1-9]"
### End:

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;;;; Things that go wrong or *went* wrong in the past
;;;; (from list side) see R-ESS-bugs.R for the R's side.
;;;; 1 ess-get-words-from-vector stumbles over \"
(ess-get-words-from-vector "c('aaa','bbb\"ccc', 'dddd')\n")
;;-> (" " "ccc" "dddd"): SOLVED
;;;; 2 ess-get-words-from-vector disregards max.print
;; options(max.print=1000) (warning added to the docs)
(length (ess-get-words-from-vector "as.character(1:10000)\n"))
;;-> 1001 with "max.print" at the end; added a comment in the function doc
;;;; 3 Inferior-ess-primary-prompt does not capture "+ + > "
;; this hangs emacs; SOLVED
(ess-command "tf<-function(N){
N}\n")
;;;; 4 ess-command detects the prompt prematurely
;; this outputs str(iris) in the inferior buffer; SOLVED
(ess-command "
lm_test <- function (formula, data, subset, weights, na.action, method = 'qr',
model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE,
contrasts = NULL, offset, ...)
{
cl <- match.call()
mf <- match.call(expand.dots = FALSE)
m <- match(c('formula', 'data', 'subset', 'weights', 'na.action',
'offset'), names(mf), 0L)
mf <- mf[c(1L, m)]
mf$drop.unused.levels <- TRUE
mf[[1L]] <- as.name('model.frame')
mf <- eval(mf, parent.frame())
if (method == 'model.frame')
return(mf)
else if (method != 'qr')
warning(gettextf('method is not supported. Using',
method), domain = NA)
mt <- attr(mf, 'terms')
y <- model.response(mf, 'numeric')
w <- as.vector(model.weights(mf))
if (!is.null(w) && !is.numeric(w))
stop('weights must be a numeric vector')
offset <- as.vector(model.offset(mf))
if (!is.null(offset)) {
if (length(offset) != NROW(y))
stop(gettextf('number of offsets is %d, should equal %d (number of observations)',
length(offset), NROW(y)), domain = NA)
}
if (is.empty.model(mt)) {
x <- NULL
z <- list(coefficients = if (is.matrix(y)) matrix(, 0,
3) else numeric(0L), residuals = y, fitted.values = 0 *
y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w !=
0) else if (is.matrix(y)) nrow(y) else length(y))
if (!is.null(offset)) {
z$fitted.values <- offset
z$residuals <- y - offset
}
}
else {
x <- model.matrix(mt, mf, contrasts)
z <- if (is.null(w))
lm.fit(x, y, offset = offset, singular.ok = singular.ok,
...)
else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok,
...)
}
class(z) <- c(if (is.matrix(y)) 'mlm', 'lm')
z$na.action <- attr(mf, 'na.action')
z$offset <- offset
z$contrasts <- attr(x, 'contrasts')
z$xlevels <- .getXlevels(mt, mf)
z$call <- cl
z$terms <- mt
if (model)
z$model <- mf
if (ret.x)
z$x <- x
if (ret.y)
z$y <- y
if (!qr)
z$qr <- NULL
z
}
str(iris)
")
;;;; 5 double prompt > > used to stall emacs; SOLVED
(ess-command "\n\n\n")

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24
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### Go inside the "preamble" section and type C-e C-e C-r (ess-roxy-preview-Rd)
### to get an R error message about 'col(m)' --> there's a buglet somewhere
##' Computes different parameter estimates for foo bars and variations
##'
##' @title Estimation procedures for Foo Bar
##' @param x data matrix
##' @param op object to be estimated
##' @param method estimation method; can be
##' "mle" MLE
##' "smle" SMLE
##' "dmle" MLE based on the diagonal
##' "mde.normal" minimum distance estimation based on the chisq distribution and CvM distance
##' "mde.log" minimum distance estimation based on the Erlang distribution and CvM distance
##' "tau.tau.mean" averaged pairwise Kendall's tau estimator
##' "tau.theta.mean" average of Kendall's tau estimators
##' "beta" multivariate Blomqvist's beta estimator
##' @return estimated value/vector according to the chosen method
##' @author Foo Bar
estimateFoo <- function(x, op, method=c("mle", "smle", "dmle", "mde.normal", "mde.log",
"tau.tau.mean", "tau.theta.mean", "beta"))
{
....
}

18
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mypager <- function(files, header, title, delete.file) {
tfile <- tempfile(paste(basename(files[1]),"__", sep=""))
Tf <- file(tfile, open="w+")
stopifnot(file.append(tfile, files))
system(paste("emacsclient -n", tfile))
}
file.show(file.path(R.home("doc"), "COPYRIGHTS"),
pager = mypager)
options(pager = mypager)
## test :
file.show(file.path(R.home("doc"), "COPYRIGHTS"))
## or
RShowDoc('NEWS')
## using a suboptimal file name

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## 1
Error: chunk 7 (label = OP4)
Error in disp.Rnw:656:31: unexpected symbol
655: par(mgp = c(2.5, 1, 1), mar = c(0, 0, 0, 0),
656: plt= c(0.08, 0.9, 0.25, 0.p9
))
## 2
Browse[2]> Error in x %*% y (from models.R#46) :
Cholmod error 'X and/or Y have wrong dimensions' at file ../MatrixOps/cholmod_sdmult.c, line 90
## 3
Error in source("~/works/protoClasses/R/funcs.R") (from hierarchy.R#6) :
~/works/protoClasses/R/funcs.R:1797:5: unexpected '[['
1796: b[[2]] <- quote(browser())
1797: [[
^
## 4
source("basicModel.R")
Error in source("basicModel.R") : basicModel.R:95:1: unexpected symbol
94:
95: ixQ
^
## 5.a
> + Error in source(file = "/home/vitoshka/works/pbm/R/S4.R") (from #1) :
/home/vitoshka/works/pbm/R/S4.R:36:62: unexpected ')'
35: }, list(vname = as.name(".pix_v")),
36: pname = as.name(".pix_p"))))
^
## 5.b
> + Error in source(file = "/home/vitoshka/works/pbm/R/S4.R") (from #1) :
c:/home/vitoshka/works/pbm/R/S4.R:36:62: unexpected ')'
35: }, list(vname = as.name(".pix_v")),
36: pname = as.name(".pix_p"))))
^
>
## 6 first line is not a pattern!
+ . + Error in base::source(file = file, echo = echo, local = local, print.eval = print.eval, (from #95) :
/tmp/model_mixture.R@4:5:13: unexpected symbol
4: Mq$DATA$ixs$clust <- data$ixQ
5: Mq
## 7 don't highlight dates
id lat lon obs_date
Min. : 1.00 Min. :21.57 Min. :-179.88 01/02/1997 04:16:53: 1
1st Qu.: 99.25 1st Qu.:24.36 1st Qu.:-147.38 01/02/1997 05:56:25: 1
Median :197.50 Median :25.64 Median :-119.64 01/04/1997 17:41:54: 1
Mean :197.50 Mean :27.21 Mean : -21.52 01/05/1997 17:20:07: 1
3rd Qu.:295.75 3rd Qu.:27.41 3rd Qu.: 153.66 01/06/1997 04:31:13: 1
Max. :394.00 Max. :39.84 Max. : 179.93 01/06/1997 06:12:56: 1
(Other) :388

31
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<<coxph>>=
## reported by Terry Therneau
coxph <- function(formula, data, weights, subset, na.action,
init, control, ties= c("efron", "breslow", "exact"),
singular.ok =TRUE, robust=FALSE,
model=FALSE, x=FALSE, y=TRUE, tt, method=ties, ...) {
ties <- match.arg(ties)
Call <- match.call()
... (20 lines omitted)
timetrans <- attr(Terms, "specials")$tt
if (length(timetrans)) {
<<coxph-transform>>
}
## next lines should not be ofsetted
<<coxph-setup>>
<<coxph-penal>>
<<coxph-compute>>
<<coxph-finish>>
}
@

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/********************/
/* comment box*/
/********************/
ods listing;
/* From: Star Ying <starying@outlook.com> */
/* Subject: [ESS] Another indentation error */
/* To: "ess-help@r-project.org" <ess-help@r-project.org> */
/* Date: Tue, 26 Mar 2013 14:33:22 -0400 (5 minutes, 16 seconds ago) */
/* X-Boundary: ________________________________________________________________________________________________________________________________________________________________________________________________________ */
/* So I have another indentation error with ess and emacs that I have run into. For the example below: */
data example;
merge
lib.data lib.data2
%if val=ue %then %do;
lib.data3
%end;
;
by var;
/* The last line produces an error if I hit tab or if I try to indent that */
/* region. Emacs produces the error */
/* "invalid search bound (wrong side of point)". The code itself is valid and runs */
/* in sas proper. Is this just me or is this a reproducible error? */

200
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* COMPLETION
** DONE make eldoc automatically pick available sub-process :13_09:
:LOGBOOK:
- State "DONE" from "DONE" [2013-06-26 Wed 16:51]
:END:
** TODO make eldoc (actually ess--fun.start) work from withing strings
* TRACEBUG
** DONE put back ess-debug-goto-input-event-marker
:LOGBOOK:
- State "DONE" from "TODO" [2013-06-21 Fri 01:18]
:END:
[2013-06-18 Tue] [[gnus:nnfolder%2Barchive:sent-2013-June#87sj0fulny.fsf@gmail.com][Email to Marius Hofert: Re: {ESS} A suggestion for deb]]
** TODO make ess-selection-mode-map or just use ess-debug-mode-map
When recover mode is on, it would be very convenient to exit it with M-Q.
[2013-06-12 Wed]
** DONE tracebug detects only english error messages.
:LOGBOOK:
- State "DONE" from "TODO" [2013-06-21 Fri 01:18]
:END:
Try to solve with gettext R's functionality. Partially solved (for most
important cases) by relaxing regular expressions.
** DONE C-c C-c with ess-inject-source=t deletes files faster than R can process
- State "DONE" from "TODO" [2013-06-26 Wed 16:46]
** DONE tramp references not found
:LOGBOOK:
- State "DONE" from "TODO" [2013-08-12 ma 23:40]
:END:
[2013-07-08 ma] [[file:~/works/pbm/R/hierarchy.R::..st_is_old..%20<-][file:~/works/pbm/R/hierarchy.R::..st_is_old.. <-]]
** DONE watch window behaves unexpectedly
:LOGBOOK:
- State "DONE" from "TODO" [2014-03-31 Mon 20:13]
:END:
[2013-06-27 Thu]
* DEVELOPER
** DONE [#A] Eval in developer is broken
:LOGBOOK:
- State "DONE" from "TODO" [2013-06-26 Wed 16:51]
:END:
** TODO "initialize" method is not injected
** DONE don't ask on C-t l for package if already in a package and dev is active
:LOGBOOK:
- State "DONE" from "TODO" [2013-08-12 ma 23:42]
:END:
It interrupts the workflow unnecessarily and feels differently from C-c C-l
[2013-07-10 wo]
* SAS
** DONE remote M-x ess-sas-interactive via shell with ssh
:LOGBOOK:
- State "DONE" from "TODO" [2013-08-12 ma 23:38]
:END:
sets ess-process-name-list to (("shell")) This prevents iESS[SAS] evaluation
since a value of (("SAS")) would be necessary for that.
* INDENTATION
** TODO closing ) match the function keyword
foo(a,
b
)
instead of current:
foo(a,
b
)
And
foo(
a,
b
)
instead of
foo(
a,
b
)
* EVALUATION
** TODO implement block-based evaluation
>>>>> Peter Meilstrup on Fri, 10 Jan 2014 23:25:01 -0800 wrote:
>>
>>> Over both eval-function (which doesn't usually do what I want when I
>>> have inner functions) and eval-paragraph (which doesn't when I put a
>>> line break in a function definition), I would prefer a command that
>>> did "evaluate all lines that include the top-level bracket enclosing
>>> point." That would be easy to implement using parse-partial-sexp and
>>> cover the case discussed here.
>> I would be happy to implement this. Then we would be able to inject the
>> source code reliably.
>>
>> A bit of an issue is the paragraph evaluation. A common pattern in R
>> interactive code is to have a bunch of one-liners to be evaluated at
>> once. Top-level-form evaluation will break this pattern unless we expand
>> the evaluated region to the whole paragraph containing the form.
>>
>> Sometimes I need to evaluate an inner form as well. A natural thing
>> would be to put it on C-u, but C-u is historically taken for a not very
>> useful visual evaluation toggling.
>>
>> Any ideas/proposals are welcome.
>>
>> Vitalie
>>
* MISC
** TODO [#A] populate ess-autoload.el and call it from ess-site.el :13_09:
This will ensure that very quick start both for (require "ess-start") and
MELPA users.
** TODO [#B] build ert based unit test suit :13_09:
** TODO split ess-mode into specialized derived modes
** DONE set PAGER="cat" environment variable for tramp process if unset?
:LOGBOOK:
- State "DONE" from "TODO" [2014-03-31 Mon 20:13]
:END:
** TODO cleanup ESS namespace
[2013-06-27 Thu]
** DONE remove reference to ssh.el from manual + add tramp workflow
:LOGBOOK:
- State "DONE" from "TODO" [2013-10-16 Wed 19:17]
:END:
[2013-07-10 wo] [[gnus:nnimap%2BSpinuVit:INBOX#51DD58EF.1010702@yahoo.de][Email from Jannis: Re: {ESS} ess-eldoc via ssh re]]
** TODO check Rodney's report on bastard symlinks
[2013-07-11 do]
** DONE check if ess-remote works
:LOGBOOK:
- State "DONE" from "TODO" [2013-10-16 Wed 19:17]
:END:
[2013-08-12 ma]
** CANCELLED Help focus does not honor focus-follows-mouse/mouse-autoselect-window :CANCELLED:
:LOGBOOK:
- State "CANCELLED" from "TODO" [2013-10-16 Wed 19:16] \\
was not a bug: said users may want to consider setting ess-help-pop-to-buffer to nil
:END:
If you have focus-follows-mouse and mouse-autoselect-window set to t,
then ask for help in an *R* buffer, i.e.
> ?setwd
The help buffer steals focus permanently instead of surrendering it
to mouse movement; you need to physically click in the *R*
buffer to restore the focus following the mouse. C-c C-d C-d
behaves similarly. Ideally, we should respect the user's settings
of focus-follows-mouse/mouse-autoselect-window in this common
help/*R* buffer arrangement.
** TODO Make an option to remember eval-and-go code in comint history
** DONE DESCRIPTION file is killed if set to R-mode
:LOGBOOK:
- State "DONE" from "TODO" [2013-10-16 Wed 18:15]
:END:
** TODO eldoc should ignore some functions
Some functions have no useful argument information to report and they
should simply be ignored. Ideally, this feature would be customizable
so that each user could add their unfavorite functions. To start, I
would put suggest: (), c(), list(), sqrt(), t()
** TODO ess-doc-map, ess-extra-map, and ess-dev-map are present "everywhere"
notably in ess-help, inferior-ess, and ess-mode. It would be *really*
user friendly if we have a "submenu" for each of these maps, and them
in both ESS and iESS (or all 4: ESS, iESS, ESS-help, ESS-transcript, ..).
** DONE ess-execute-screen-options wrong in terminal
:LOGBOOK:
- State "DONE" [2014-03-31 Mon 20:11]
:END:
[2013-12-19 Thu] [[gnus:nnimap%2BSpinuVit:ESS#CAD%3D7RJZ4EHETKF4LPJpzuw0uO9AuzOtWDYVnV1cZAVQxAotVxg@mail.gmail.com][Email from Ali Tofigh: {ESS} ess-execute-screen-optio]]
** TODO Implement "Extract Function" functionality
Proposed by Andreas Leha:
,----
| RStudio can analyze a selection of code from within the source editor
| and automatically convert it into a re-usable function. Any "free"
| variables within the selection (objects that are referenced but not
| created within the selection) are converted into function arguments
`----
** DONE > a + b + c is not cleaned correctly with C-u C-u C-y
:LOGBOOK:
- State "DONE" from "TODO" [2014-03-31 Mon 20:05]
:END:
While you are in this part of the code, can you add C-u C-u C-y to the ESS
menu item, although maybe it belongs on the Edit menu. Not clear to me
which would be better.
Thanks
Rich
[2014-02-20 Thu] [[gnus:nnimap%2BSpinuVit:ESS/ESS-core#CAGx1TMCSfK3XK6YghxomP03R_tFD2AiC4X%3D0NDcvoje%3D%2B9vMWw@mail.gmail.com][Email from Richard M. Heiberger: bug in ess-transcript-clean-re]]
* RStudio (excerpts from Hadley's R-packages book)
** TODO Build & reload
Available in RStudio via Cmd + Shift + B. This in- stalls the package,
restarts R, and then reloads the package with library() (doing this by hand
is painful).
** TODO Jump to github file view. If lines are selected jump to those lines.
This is probably there in projectile.

27
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#!/bin/sh
# ESS[BUGS]: 02/18/2004
# runs BUGS taking commands from command file
#
case `config.guess` in
alpha*-dec-*) BUGS=bugs05.decalpha;;
hppa*-hp-hpux*) BUGS=bugs05.hp;;
i?86-pc-cygwin) BUGS=bugs05.exe;;
i?86-*-freebsd*) BUGS=bugs05.freebsd;;
powerpc*-*-*) BUGS=bugs05.rs6000;;
sparc-sun-solaris*) BUGS=bugs05.sparc;;
mips-sgi-irix*) BUGS=bugs05.sgi;;
mips-dec-*) BUGS=bugs05.decmips;;
esac
case $# in
1) test -f bugs.bog && rm -f bugs.bog || true
$BUGS bugs.buf bugs.bog bugs.out bugs.ind bugs1.out bugs1.ind $1
chmod -w bugs.bog
;;
2) test -f $1.bog && rm -f $1.bog || true
$BUGS $1.buf $1.bog $1.out $1.ind ${1}1.out ${1}1.ind $2
chmod -w $1.bog
;;
*) echo "usage: $0 [default_output_name] command_file";;
esac

20
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#!/bin/sh
# ESS[BUGS]: 02/17/2004
# runs BUGS taking commands from command file
#
case $# in
1) bugs05.sparc 32 bugs $1
cp -fp bugs.log bugs.bog
chmod -w bugs.bog
;;
2) bugs05.sparc 32 $1 $2
cp -fp $1.log $1.bog
chmod -w $1.bog
;;
3) bugs05.sparc $1 $2 $3
cp -fp $2.log $2.bog
chmod -w $2.bog
;;
*) echo "usage: $0 [[number_of_bins] default_output_name] command_file";;
esac

27
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#!/bin/sh
# ESS[BUGS]: 02/18/2004
# runs BUGS taking commands from command file
#
case `config.guess` in
i?86-pc-cygwin) BUGS=bugs0603.exe;;
i?86-*-linux*) BUGS=bugs0600.linux;;
sparc-sun-solaris*) BUGS=bugs603.sparc;;
mips-sgi-irix*) BUGS=bugs06.sgi;;
esac
case $# in
1) $BUGS 32 bugs $1 2>> bugs.log
cp -fp bugs.log bugs.bog
chmod -w bugs.bog
;;
2) $BUGS 32 $1 $2 2>> $1.log
cp -fp $1.log $1.bog
chmod -w $1.bog
;;
3) $BUGS $1 $2 $3 2>> $2.log
cp -fp $2.log $2.bog
chmod -w $2.bog
;;
*) echo "usage: $0 [[number_of_bins] default_output_name] command_file";;
esac

20
.emacs.d/elpa/ess-20160208.453/etc/backbugs.sparc Normal file
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#!/bin/sh
# ESS[BUGS]: 02/17/2004
# runs BUGS taking commands from command file
#
case $# in
1) bugs603.sparc 32 bugs $1
cp -fp bugs.log bugs.bog
chmod -w bugs.bog
;;
2) bugs603.sparc 32 $1 $2
cp -fp $1.log $1.bog
chmod -w $1.bog
;;
3) bugs603.sparc $1 $2 $3
cp -fp $2.log $2.bog
chmod -w $2.bog
;;
*) echo "usage: $0 [[number_of_bins] default_output_name] command_file";;
esac

67
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\name{checkTriple}
\title{Check Consistency of Conditional Independence for a Triple of Nodes}
\usage{
"An Rd file exposing an ESS bug in (ess-next-code-line) :
Jump to '\examples{' and the first code line (= all '##...') and
use C-c C-n to send it to R. It works, *but* point does not advance to
the next line; but rather jumps backward to the 50'percent' line.
Adding a percent 'o/o' sign here ``fixes'' this bug (so I don't do it) "
checkTriple(version.unf = c(NA, NA),
maj.rule = FALSE, verbose = FALSE)
}
\arguments{
\item{version.unf}{
(integer) vector of length two: .............}
\item{maj.rule}{logical indicating that the following majority rule
is applied: if \code{b} is in less than
50\% of the checked sepsets, we say that \code{b} is in \bold{no} sepset. If
\code{b} is in more than 50\% of the checked sepsets, we say that
\code{b} is in \bold{all} sepsets. If \code{b} is in exactly 50\% of the
checked sepsets, the triple is considered \sQuote{ambiguous}.}
\item{verbose}{Logical asking for detailed output of intermediate steps.}
}
\description{
For each subset .........
}
\references{
D. Colombo and M.H. Maathuis (2013).
Order-independent constraint-based causal structure learning,
(arXiv:1211.3295v2).
}
\examples{
##################################################
## Using Gaussian Data
##################################################
## Load predefined data
data(gmG)
n <- nrow(gmG8$x)
p <- ncol(gmG8$x)
## define independence test (partial correlations), and test level
indepTest <- gaussCItest
alpha <- 0.01
## define sufficient statistics
suffStat <- list(C = cor(gmG8$x), n = n)
## estimate CPDAG
pc.fit <- pc(suffStat, indepTest, p=p, alpha=alpha, verbose = TRUE)
if (require(Rgraphviz)) {
## show estimated CPDAG
par(mfrow=c(1,2))
plot(pc.fit, main = "Estimated CPDAG")
plot(gmG8$g, main = "True DAG")
}
checkTriple(a = 6, b = 1, c = 8,
nbrsA = c(1,5,7),
nbrsC = c(1,5),
sepsetA = pc.fit@sepset[[a]][[c]],
sepsetC = pc.fit@sepset[[c]][[a]],
suffStat=suffStat, indepTest=indepTest, alpha=alpha,
version.unf = c(2,2),
verbose = TRUE)
}
\keyword{manip}

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\title{chol2inv}
\name{chol2inv-methods}
\description{
Invert a symmetric, positive definite square matrix from its Choleski
decomposition. Equivalently, compute \eqn{(X'X)^{-1}}{(X'X)^(-1)}
from the (\eqn{R} part) of the QR decomposition of \eqn{X}.
}
\seealso{
\code{\link[base]{chol2inv}} (from the \pkg{base} package),
\code{\link{solve}}.
}
%%-- In Rd preview (after C-c C-p), "se" ([s]kip to [e]xamples):
%%-- "l" works at the 1st line, but does not go further from the 2nd
\examples{
(M <- cbind(1, 1:3, c(1,3,7)))
(cM <- chol(M)) # a "Cholesky" object...
chol2inv(cM) \%*\% M # the identity
stopifnot(all(chol2inv(cM) \%*\% M - Diagonal(nrow(M))) < 1e-10)
}
\keyword{algebra}

30
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## inspired by:
## https://github.com/rstudio/rstudio/pull/191
## nested calls should work
df[a][, |]
## matrix, list, environments
l <- list(aaaa = 1111, bbbb = 2222)
l[a|] ## -> "aaaa" (quoted!)
## data table
dt <- data.table(aaaa = 1111, bbbb = 22222)
dt[, a|] # -> aaaa (unquoted!)
## attributes
x <- ""
attr(x, "foo") <- function(alpha, beta) {}
attr(x, "foo")(al| # -> "alpha"
## chains
mtcars %>% dplyr::select(mp| #-> mpg (unquoted))
## models
lm(mpg ~ cy| , data = mtcars) #-> cyl
## "by" keyword in data.table, inner_join, etc
inner_join(foo, bar, by = c(| # provides completions for variables in foo when
# on the left side of an =, and bar when on the
# right side of an =.

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114
.emacs.d/elpa/ess-20160208.453/etc/ess-julia.jl Normal file
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module ESS
function all_help_topics()
Base.Help.init_help()
## show all categories
for (func, _ ) in Base.Help.MODULE_DICT
if !isempty(Base.Help.MODULE_DICT[func])
println()
show(func);
end
end
end
function help(topic::AbstractString)
VERSION >= v"0.4-" ?
eval(current_module(), parse("@doc $topic")) :
Base.Help.help(topic)
end
## modified version of function show(io::IO, m::Method)
function fun_args(m::Method)
tv, decls, file, line = Base.arg_decl_parts(m)
io = STDOUT::IO
if !isempty(tv)
Base.show_delim_array(io, tv, '{', ',', '}', false)
end
li = m.func.code
e = Base.uncompressed_ast(li)
argnames = e.args[1]
print(io, "(")
print_joined(io, [escape_string(isempty(d[2]) ? d[1] : d[1]*"::"*d[2]) for d in decls], ",", ",")
print(io, ")")
end
VERSION >= v"0.4-" && (Base.function_module(f::Function)=f.env.module)
## modified versionof show(io::IO, mt::MethodTable)
function fun_args(f::Function)
mt = f.env
mod = Base.function_module(f)
if mod == Main
mod = "nil"
end
print("(list \"$mod\" nil '(")
d = mt.defs
while d != nothing && d != ()
print("\"")
## method
fun_args(d)
print("\" ")
d = d.next
end
print("))")
end
function fun_args(s::ASCIIString)
try
m = eval(current_module(), parse(s))
if typeof(m) != ASCIIString
fun_args(m)
end
catch
print("(list nil nil nil)")
end
end
function fun_args(t::DataType)
print("(list nil nil '(")
for d = fieldnames(t)
print("\"$d\" ")
end
print("))")
end
### OBJECT COMPLETION
function components(m::Module)
for v in sort(names(m))
s = string(v)
if isdefined(m,v)
println(rpad(s, 30), summary(eval(m,v)))
end
end
end
function components(t::DataType)
for v in sort(fieldnames(t))
println(rpad(string(v), 30), "field")
end
end
function components(v)
t = typeof(v)
if isa(t, DataType)
return components(t)
end
end
### MISC
function main_modules()
mainmod = current_module()
for nm in names(mainmod)
if isdefined(mainmod, nm)
mod = eval(mainmod, nm)
if isa(mod, Module)
print("\"$nm\" ")
end
end
end
end
end

221
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##' \code{loadings(object)} and then design your own plotting method.
##' @title Side by side scores and loadings plot
##' @usage slplot(object, pcs=c(1,2), scoresLoadings=c(TRUE, TRUE),
##' sl="def", ll="def", hotelling=0.95, rug=TRUE, sub=NULL,...)
##' @param object
##' @param pcs
##' @param tjo
##' @return None, used for side effect.
##' @export
##' @author Henning Redestig
setMethod("slplot", "pcaRes",
function(object, pcs=c(1,2), tjo) {
#(ess-roxy-get-function-args)
opar <- par(no.readonly=TRUE)
cl <- match.call()
})
##' .. content for \description{} (no empty lines) ..
##'
##' .. content for \details{} ..
##' @title
##' @param a
##' @param b
##' @param d
##' @param asd
##' @return
##' @author Henning Redestig
trickyInArgsComments <- function(a,#comment
b,#hejhopp trams
d,asd) {
print("hello")
}
##' .. content for \description{} (no empty lines) ..
##'
##' .. content for \details{} ..
##' @title
##' @param a
##' @param b
##' @param cc
##' @return
##' @author Henning Redestig
withdef <- function(a, b=c("asd","ffd", "asd", "ffd",
"asd",
"ffd","asd",
"ffd"), cc) {
print("hello")
}
setClass(Class="inference", representation=representation(model="character"
, sample.size="numeric"
, robust.se="logical"
, two.sided="logical"
, ci.level="numeric"), contains=c("matrix"))
##' .. content for \description{} (no empty lines)
##'
##' .. content for \details{} ..
##' @title asd
##' @param a
##' @param asdsd
##' @param sd
##' @param ...
##' @return s
##' @author Henning Redestig
tempFixNasFunction <- function(a,asdsd, sd, ...) {
asds
}
setGeneric("updateMu", function(respM, gamma, ...)
standardGeneric("updateMu"))
## (make-local-variable 'adaptive-fill-regexp)
## (setq adaptive-fill-regexp (concat ess-roxy-str adaptive-fill-regexp))
## (make-local-variable 'adaptive-fill-first-line-regexp)
## (setq adaptive-fill-first-line-regexp (concat ess-roxy-str adaptive-fill-first-line-regexp))
## (make-local-variable 'paragraph-start)
## (setq paragraph-start (concat "\\(" ess-roxy-str "\\)*" paragraph-start))
## (make-local-variable 'paragraph-separate)
## (setq paragraph-separate (concat "\\(" ess-roxy-str "\\)*" paragraph-separate))
## (auto-fill-mode)
asd
##' aqdasd lksa odnsl dlsakdn lsakdn sladn asijdi j 1. asdsd alksnd
##' lasdn ldnad
##'
##'
##' alkdnal dl lakd lasdnladna ld aldan lda dlakd nladn a amd lakdn
##' ajdn asjdns
##'
##' lajnsd jasdn aksjdnaksjnd asjdnaksdnajsdnajsd aksdn askdjn
##' akjdn aksdnkasjdnka
##'
##' 1. aldn adlnsald ladn saldnlaksd naskl
##' 2. ad asdjnksadn adjn skajan kda dksadkas dkjan dkasndkadn
##' ajsd nkj dakjd sd
##' @title hej
##' @param fitta asdadsd
##' 1.
##' 2. asd
##' @param diagonals pung asa as a sad s dsa da das d asd asd add
##' @param tjo asd
##' @param asdasd
##' @return me
##' @author Henning Redestig
tempFixNas <- function(fitta, diagonals, tjo, asdasd) {
for(i in index) {
data <- otherdata[i]
}
}
##' Simply replace completely ajksbdkjsa djskbdkajbd
##'
##' ksdb skdb skasdaj ahd (ess-roxy-beg-of-field) (newline-and-indent)
##' aksndlsakndlksdn jkahd ksn dkjands
##' @title Temporary fix for missing values
##' @param diagonals The diagonal to be replaced, i.e. the first,
##' second and so on when looking at the fat version of the matrix
##' @param tjo asdsdsdw
##' @return The original matrix with completely missing rows/cols
##' filled with zeroes. oasndsnd aksdnkasdnskans dkas ndkjasndksdn
##' skandkand ksjandknsd
##' @export
##' @examples
##' tempFixNas(iris)
##' pi <- 1
##' plot(x)
##' @author Henning Redestig
tempFixNas <- function(diagonals, tjo) {
(ess-roxy-delete-args)
wilcox.test
(ess-roxy-goto-end-of-entry)
badRows <- apply(mat, 1, function(x) all(is.na(x)))
badCols <- apply(mat, 2, function(x) all(is.na(x)))
mat[ badRows,] <- 0 (ess-roxy-get-args-list-from-def)
mat[,badCols ] <- 0 (ess-roxy-get-args-list-from-entry)
mat
}
##' <description>
##'
##' <details>
##' @title asdsd
##' @param asd asd
##' @param test1 asd
##' @param asdsd
##' @param tjo asdasd
##' @return aa
##' @author Henning Redestig
tempFixNas <- function(asd,test1,asdsd,tjo=c("asd", "asdasd")) {
## (ess-roxy-goto-end-of-entry)
## (setq fun (ess-roxy-get-args-list-from-def))
## (setq ent (ess-roxy-get-args-list-from-entry))
## (ess-roxy-merge-args fun ent)
## (ess-roxy-mrg-args fun ent)
## (ess-roxy-get-args-list-from-entry)
## (ess-roxy-get-function-args)
## (ess-roxy-goto-end-of-entry)
## (setq here (ess-roxy-delete-args))
## (ess-roxy-insert-args (ess-roxy-get-args-list-from-def) here)
badRows <- apply(mat, 1, function(x) all(is.na(x)))
badCols <- apply(mat, 2, function(x) all(is.na(x)))
mat[ badRows,] <- 0
mat[,badCols ] <- 0
mat
}
##' <description>
##'
##' <details>
##' @title my title
##' @param test1
##' @param tjo
##' @param pung
##' @param str
##' @return value
##' @author Henning Redestig
tempFixNasBad <- function(test1,tjo=c("asd", "asdasd"), pung, str) {
asdsd# (car (cdr (ess-end-of-function nil t)))
}
##' Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse
##' Non-Linear PCA and the conventional SVD PCA. A cluster based
##' method for missing value estimation is included for comparison.
##' BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete
##' data as well as for accurate missing value estimation. A set of
##' methods for printing and plotting the results is also provided.
##' All PCA methods make use of the same data structure (pcaRes) to
##' provide a unique interface to the PCA results. Developed at the
##' Max-Planck Institute for Molecular Plant Physiology, Golm,
##' Germany, RIKEN Plant Science Center Yokohama, Japan, and CAS-MPG
##' Partner Institute for Computational Biology (PICB) Shanghai,
##' P.R. China
##'
##' @name pcaMethods
##' @aliases pcaMethods
##' @docType package
##' @title pcaMethods
##' @useDynLib pcaMethods
##' @author Wolfram Stacklies, Henning Redestig
NULL
#' Title
#'
#' @param par Lorem ipsum dolor sit amet, consectetur adipiscing
#' elit. Vivamus ligula purus, ultricies quis odio non, vulputate
#' finibus risus. Donec eleifend quis dolor ut rhoncus.
#' @param par2 Lorem ipsum dolor sit amet, consectetur adipiscing
#' elit. Vivamus ligula purus, ultricies quis odio non.
#' @examples
#' # This long comment line can be paragraph-filled without squashing
#' # the following lines of code into the comment
#' fun(arg)
#' print(object)

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.emacs.d/elpa/ess-20160208.453/etc/ess-rutils-help-start.R Normal file
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## Hacked help.start() to use with ess-rutils.el
.rutils.help.start <- function (update=FALSE, remote=NULL) {
home <- if (is.null(remote)) {
if (tools:::httpdPort == 0L)
tools::startDynamicHelp()
if (tools:::httpdPort > 0L) {
if (update)
make.packages.html()
paste("http://127.0.0.1:", tools:::httpdPort, sep="")
}
else stop(".rutils.help.start() requires the HTTP server to be running",
call.=FALSE)
} else remote
paste(home, "/doc/html/index.html", sep="")
}

56
.emacs.d/elpa/ess-20160208.453/etc/ess-s4.S Normal file
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#### This is a dump of the S library used by S-mode with Version 4 of S.
#### (from John Chambers ??)
#### S-mode session functions.
#### assign(..., where=0) makes them last only for the current session.
### Martin Maechler: see also ./ess-sp3.S
### which uses assign(.., wh=0) which seems better
".SmodeDump" <- function(x, name)
{
## dump function for S-mode
assign(".SmodeTmp", options(error = dump.calls), where = 0, i = T)
on.exit( {
options(.SmodeTmp)
remove(".SmodeTmp", where = 0)
} )
dump(x, file = name)
}
".SmodeLoad" <- function(x)
{
## skeleton of a dump.calls interface, enough to keep s-mode
## informed that an error took place.
pseudo <- function()
cat(get.message(), "Dumped\n", sep = "", file = "|stderr")
## source function for S-mode
assign(".SmodeTmp", options(error = pseudo), where = 0, i = T)
on.exit( {
options(.SmodeTmp)
remove(".SmodeTmp", where = 0)
} )
invisible(source(x))
}
".SmodeObs" <- function(where, pattern)
{
if(pattern == "") objects(where) else objects(where, pattern)
}
".SmodePaths" <- function()
{
## the paths for the directories in the search list
temp <- search()
value <- character(length(temp))
for(i in seq(along.with = temp)) {
obj <- database.object(i)
if(is.character(obj) && length(obj) == 1)
value[[i]] <- obj
}
value
}
"smode.lvsave" <-
c(".Last.value",
".SmodeDump", ".SmodeLoad", ".SmodeObs", ".SmodePaths",
"smode.lvsave")

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#!/bin/sh
### (C) 1997, Richard M. Heiberger.
### This file is part of ESS.
## This file is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 2, or (at your option)
## any later version.
## This file is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
## A copy of the GNU General Public License is available at
## http://www.r-project.org/Licenses/
# For executing SAS, and running it in the proper manner for ESS
# (feeding output back into appropriate ESS buffers).
#echo $0 $@
#sas </dev/tty 1>$1 2>$2 $3
set -x
stdout=$1
stderr=$2
shift 2
set +x
echo sas \</dev/tty 1\>$stdout 2\>$stderr $@
sas </dev/tty 1>$stdout 2>$stderr $@
## From the SAS online tech support:
##
## Redirecting the SAS Log and Output under UNIX.
##
## There are several ways of redirecting the SAS Log and Output under
## UNIX.
##
## To redirect the SAS Log, follow one of these steps:
##
## 1.
## In the source code, place the following line:
##
## proc printto log=stdout;
##
## to make a duplicate copy of the log in a file in addition
## to redirecting it to stdout, use this command to invoke
## SAS:
##
## sas -altlog doit.log doit.sas
##
## 2.Execute SAS in the background and use the UNIX 'tail' command
## to copy lines to stdout as they are added to the log. Use the
## command:
##
## sas doit.sas &; tail -f doit.log
##
## To redirect the SAS Log and Output under the Korn shell, use the
## following command:
##
## sas -stdio < doit.sas > doit.lst 2> doit.log
##
## To redirect the SAS Log and Output under the C-Shell, use the
## following command:
##
## (sas -stdio < doit.sas > doit.lst) >& doit.log
## From WWW.SAS.COM:
## How can I make SAS in batch mode behave like interactive SAS,
## continue running my SAS job, and not enter syntax check mode when
## it encounters an error?
##
## You can specify the NOSYNTAXCHECK option when you invoke your SAS
## program.

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#### S-mode session functions.
#### assign(..., where=0) makes them last only for the current session.
#### Well, turns out we have two slightly different versions of the S code.
#### This is the one that I think gets used with S-Plus; I'll send along
#### the other version as well, but morally they should be equivalent, there
#### are just a couple of changes I seem to have made for S4. /John
### Martin Maechler: see also ./ess-s4.S
### which does *not* use assign (why?)
assign(".SmodeObs",
function(where, pattern) {
if(pattern == "") objects(where)
else objects(where, pattern)
}, where=0)
assign(".SmodeLoad",
function(x)
## source function for S-mode
{
assign(".SmodeTmp", options(error=dump.calls), where=0, i=T)
on.exit({options(.SmodeTmp); remove(".SmodeTmp",where=0)})
source(x)
},
where = 0)
assign(".SmodeDump",
function(x, name)
## dump function for S-mode
{
assign(".SmodeTmp", options(error=dump.calls), where=0, i=T)
on.exit({options(.SmodeTmp); remove(".SmodeTmp",where=0)})
dump(x, file=name)
},
where = 0)
assign(".SmodePaths",
function()
## the paths for the directories in the search list
{
temp <- search()
value <- character(length(temp))
for(i in seq(along.with = temp)) {
obj <- database.object(i)
if(is.character(obj) && length(obj) == 1)
value[[i]] <- obj
}
value
},
where = 0)

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.emacs.d/elpa/ess-20160208.453/etc/function-outline.S Normal file
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f <- function()
{
## Purpose:
## ----------------------------------------------------------------------
## Arguments:
## ----------------------------------------------------------------------
## Author: $A$, Date: $D$
}

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#!/bin/sh
if [ $# -eq 0 -o "$1" = "-h" -o "$1" = "-help" -o "$1" = "--help" ]
then
echo "usage: gpl-check [-h|-help|--help|-2|-3|-u|-n] file1 [file2 ...]"
echo " -h|-help|--help print this help"
echo " -2 print file names found with GPLv2+"
echo " -3 print file names found with GPLv3+"
echo " -u print file names found with a GPL of unknown version"
echo " -n print file names with no GPL found"
echo " file1 [file2 ...] list of files to check"
else
GPLV2=0
GPLV3=0
GPLVUNK=0
NOGPL=0
for i
do
case $i in
-2) GPLV2=1;;
-3) GPLV3=1;;
-23) GPLV2=1;GPLV3=1;;
-u) GPLVUNK=1;;
-n) NOGPL=1;;
-nu|-un) GPLVUNK=1;NOGPL=1;;
*) if [ $GPLV2 -eq 0 -a $GPLV3 -eq 0 -a $GPLVUNK -eq 0 -a $NOGPL -eq 0 ]
then
GPLV2=1
GPLV3=1
GPLVUNK=1
NOGPL=1
fi
if grep -l 'either version 2, or' $i > /dev/null
then
if [ $GPLV2 -eq 1 ]
then echo "$i GPLv2+"
fi
elif grep -l 'either version 3' $i > /dev/null
then
if [ $GPLV3 -eq 1 ]
then echo "$i GPLv3+"
fi
elif grep -l 'GNU General Public License' $i > /dev/null
then
if [ $GPLVUNK -eq 1 ]
then echo "$i GPLv unknown"
fi
else
if [ $NOGPL -eq 1 ]
then echo "$i no GPL"
fi
fi;;
esac
done
fi

31
.emacs.d/elpa/ess-20160208.453/etc/icons/README Normal file
View File

@@ -0,0 +1,31 @@
Creating pixmaps:
* spluslogo.xpm was dontated by David Smith at Insightful.
* Other icons were created by SJE, using mostly `kiconedit' and
hand-editing.
* Transparency
Need to add backgrounToolBarColor for XEmacs to show okay.
e.g. /usr/share/xemacs-21.4.12/etc/toolbar/folder-cap-up.xpm
has header:
"X c Gray75 s backgroundToolBarColor",
whereas I have set "c None" to indicate the background pixel; this line
seems to work for both toolbars:
". c None s backgroundToolBarColor",
* splus_letters_small.xpm
2010-05-18 & -21: SJE made this new Splus icon from the
splus_letters_large.xpm (then image001.png from Louis Bajuk-Yorgan
@tibco.com) file that Rich provided. I had to move the
cross over to the left by one pixel, to then allow the image to be
cropped to 48x48 (cropping performed in gimp). kiconedit was then
used to rescale the icon to 24x24. Finally, background transparency
added manually to the file, as noted above.
2010-05-21: updated file based on new image from TIBCO. Original
51x38 cropped to 50x38 in xv, then shrunk to 25x19 in kiconedit.
Transparency added, and removed a lot of the extra white pixels into
background colours manually in kiconedit.

30
.emacs.d/elpa/ess-20160208.453/etc/icons/rbuffer.xpm Normal file
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@@ -0,0 +1,30 @@
/* XPM */
static char *rbuffer[]={
"24 24 3 1",
". c None s backgroundToolBarColor",
"a c #000000",
"# c #1532ed",
"........................",
"...............#........",
"...............##.......",
".....#############......",
".....##############.....",
".....#############......",
"...............##.......",
"...............#........",
"........................",
"........................",
"........................",
"...aaaaaaaaaaaaaaaaaa...",
"........................",
"........................",
"...aaaaaaaaaaaaaaaaaa...",
"........................",
"........................",
"...aaaaaaaaaaaaaaaaaa...",
"........................",
"........................",
"...aaaaaaaaaaaaaaaaaa...",
"........................",
"........................",
"...aaaaaaaaaaaaaaaaaa..."};

45
.emacs.d/elpa/ess-20160208.453/etc/icons/rfunction.xpm Normal file
View File

@@ -0,0 +1,45 @@
/* XPM */
static char *rfunction[]={
"24 24 18 1",
"B c #000000",
"k c #181818",
"Q c #1f1f1f",
"z c #232323",
"L c #313131",
"Z c #3c3c3c",
"O c #404040",
"a c #5e5e5e",
"W c #676767",
"U c #757575",
"N c #848484",
"P c #969696",
"0 c #a0a0a0",
". c None s backgroundToolBarColor",
"G c #b9b9b9",
"I c #c6c6c6",
"T c #d5d5d5",
"# c #1532ed",
"........................",
"...............#........",
"...............##.......",
".....#############......",
".....##############.....",
".....#############......",
"...............##.......",
"...............#........",
"........................",
"........................",
"........................",
"..............az..zU....",
"....ILBBz...GkP....aO...",
"....zU......BG......LP..",
"....BG.....UO.......0z..",
"..BBBBBBP..zP.......GB..",
"....BG.....BG........BI.",
"....BG.....BG........BI.",
"....BG.....LP.......GB..",
"....BG.....NO.......PL..",
"....BG......Q0......z0..",
"....BG......TQU0..0ZW...",
"..............NL..Z0....",
"........................"};

30
.emacs.d/elpa/ess-20160208.453/etc/icons/rline.xpm Normal file
View File

@@ -0,0 +1,30 @@
/* XPM */
static char *rline[]={
"24 24 3 1",
". c None s backgroundToolBarColor",
"a c #000000",
"# c #1532ed",
"........................",
"...............#........",
"...............##.......",
".....#############......",
".....##############.....",
".....#############......",
"...............##.......",
"...............#........",
"........................",
"........................",
"........................",
"........................",
"........................",
"........................",
"........................",
"........................",
"........................",
"...aaaaaaaaaaaaaaaaaa...",
"........................",
"........................",
"........................",
"........................",
"........................",
"........................"};

30
.emacs.d/elpa/ess-20160208.453/etc/icons/rregion.xpm Normal file
View File

@@ -0,0 +1,30 @@
/* XPM */
static char *rregion[]={
"24 24 3 1",
". c None s backgroundToolBarColor",
"a c #000000",
"# c #1532ed",
"........................",
"...............#........",
"...............##.......",
".....#############......",
".....##############.....",
".....#############......",
"...............##.......",
"...............#........",
"........................",
"........................",
"........................",
"........................",
"........................",
"........................",
"...aaaaaaaaaaaaaaaaaa...",
"........................",
"........................",
"...aaaaaaaaaaaaaaaaaa...",
"........................",
"........................",
"...aaaaaaaaaaaaaaaaaa...",
"........................",
"........................",
"........................"};

173
.emacs.d/elpa/ess-20160208.453/etc/icons/splus_letter_small.xpm Normal file
View File

@@ -0,0 +1,173 @@
/* XPM */
static char *dummy[]={
"25 19 151 2",
"Qt c None s backgroundToolBarColor",
"#M c #044b83",
"#R c #044c86",
"#t c #044c87",
"ae c #044d87",
"an c #044e7f",
".o c #044e81",
"#l c #044e8d",
"ak c #044f84",
".B c #044f88",
"#m c #044f8e",
"am c #045188",
".j c #04518b",
".O c #045191",
"#6 c #04528f",
"#O c #045388",
".k c #04538c",
"#U c #04538e",
"#Y c #045392",
".l c #045489",
"## c #04548c",
"#i c #045490",
"#v c #045492",
"#. c #04558e",
"#C c #045593",
"#k c #04568d",
"#B c #045695",
"#G c #045698",
".Y c #045795",
".R c #045890",
"#j c #04598f",
".4 c #045995",
"aj c #054e7b",
"al c #054e89",
"#h c #054e8d",
"#S c #055188",
"#V c #05518d",
".m c #055282",
".K c #055284",
".5 c #055583",
".t c #055791",
"#u c #055894",
".n c #064e86",
"#s c #074d76",
".p c #074e83",
"a. c #074f89",
"#a c #074f8a",
"af c #075389",
"#9 c #07548e",
".A c #075592",
".F c #075594",
"#1 c #075a99",
".c c #094d79",
".9 c #094f89",
".J c #095681",
"#A c #0b568d",
".s c #0c4f85",
"#5 c #0c5188",
"#w c #0d5486",
".b c #0e4e7d",
".N c #105287",
".X c #105685",
"#H c #115789",
"#Z c #13508a",
"#2 c #135287",
"#F c #195c8a",
".i c #1a5c8b",
"#8 c #1b5684",
"ai c #1b5a81",
"ad c #1c5d87",
"#P c #1d5c8c",
"#r c #1d5f8a",
"#N c #1f5b7d",
"ao c #1f5c85",
"#0 c #205a86",
"#n c #206292",
".u c #216794",
".d c #245b81",
".G c #256390",
".3 c #265f85",
"a# c #266287",
"#x c #296286",
"#b c #2a5f96",
"#g c #2b6395",
".a c #2c658f",
".Q c #307195",
".E c #326897",
".S c #356f98",
".Z c #35789b",
"ag c #396c94",
"#I c #3a6a78",
"#z c #3f7497",
".1 c #3f7c9e",
"#J c #427585",
"aa c #42768f",
"#X c #447ca1",
".C c #457b9a",
".z c #457ba8",
"ac c #48778f",
".q c #4e86b0",
"#7 c #4f86b5",
".6 c #50829b",
"#q c #538db5",
"#D c #538eb3",
".e c #547f91",
"ab c #5487a1",
"#T c #58859c",
"ah c #5983a7",
"#c c #5a7d99",
".2 c #5b809c",
".P c #5d94bb",
"#K c #6c91a0",
"#4 c #6c99ba",
"#L c #6c9cb7",
"#o c #7097a7",
"ap c #739eb3",
".v c #73a7c0",
".0 c #7cacc3",
"#y c #7faac6",
".# c #82a0a8",
"#Q c #84aec8",
".I c #86a8bd",
".L c #89b3cd",
"#d c #8aa7b6",
"as c #8db2cc",
".y c #8db9cd",
".h c #8eb5c9",
".8 c #8eb9d3",
"#W c #8fb2c9",
"at c #91b7c8",
"#3 c #94b4cb",
"ar c #95b7cb",
".T c #979798",
".U c #99999a",
"#f c #99b9cd",
".g c #9b9b9b",
".V c #9c9c9c",
".r c #9cc2d4",
".w c #a7c8d0",
".x c #a9c8d1",
"#p c #a9cbda",
".f c #abc5cd",
"#E c #abcad6",
"aq c #b1d0e0",
"au c #b3d2e2",
".7 c #b8cfd6",
"#e c #baced7",
".W c #d4e0e4",
".H c #d7e7ed",
".M c #dae6ef",
".D c #eef8f8",
"QtQtQtQt.#.a.b.c.d.e.fQtQtQtQtQtQtQtQt.g.gQtQtQtQt",
"QtQt.h.i.j.k.l.m.n.o.p.qQtQtQtQtQtQtQt.g.gQtQtQtQt",
"Qt.r.s.t.u.v.w.x.y.z.A.B.CQtQtQtQtQtQt.g.gQtQtQtQt",
".D.E.F.G.HQtQtQtQtQt.I.J.K.LQtQtQtQtQt.g.gQtQtQtQt",
".M.N.O.PQtQtQtQtQtQtQt.Q.R.SQt.g.T.U.g.g.g.V.V.g.g",
".W.X.Y.ZQtQtQtQtQtQtQt.0.1.2Qt.g.g.g.g.g.g.g.g.g.g",
"Qt.3.4.5.6.7QtQtQtQtQtQtQtQtQtQtQtQtQt.g.gQtQtQtQt",
"Qt.8.9#.###a#b#c#d#eQtQtQtQtQtQtQtQtQt.g.gQtQtQtQt",
"QtQt#f#g#h#i#j#k#l#m#n#oQtQtQtQtQtQtQt.g.gQtQtQtQt",
"QtQtQtQt#p#q#r#s#t#u#v#w#xQtQtQtQtQtQt.g.gQtQtQtQt",
"QtQtQtQtQtQtQtQt#y#z#A#B#C#DQtQtQtQtQtQtQtQtQtQtQt",
"QtQtQtQtQtQtQtQtQtQt#E#F#G#HQtQtQtQtQtQtQtQtQtQtQt",
"#I#J#KQtQtQtQtQtQtQtQt#L.B#MQtQtQtQtQtQtQtQtQtQtQt",
"#N#O#PQtQtQtQtQtQtQtQt#Q#R#SQtQtQtQtQtQtQtQtQtQtQt",
"#T#U#V#WQtQtQtQtQtQtQt#X#Y#ZQtQtQtQtQtQtQtQtQtQtQt",
"Qt#0#1#2#3QtQtQtQtQt#4#5#6#7QtQtQtQtQtQtQtQtQtQtQt",
"QtQt#8#9a.a#aaabacadaeafagQtQtQtQtQtQtQtQtQtQtQtQt",
"QtQtQtahaiajakalamanaoapQtQtQtQtQtQtQtQtQtQtQtQtQt",
"QtQtQtQtQtaqarasatauQtQtQtQtQtQtQtQtQtQtQtQtQtQtQt"};

BIN
.emacs.d/elpa/ess-20160208.453/etc/icons/splus_letters_large.png Normal file
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Width:  |  Height:  |  Size: 4.2 KiB

281
.emacs.d/elpa/ess-20160208.453/etc/icons/splus_letters_large.xpm Normal file
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@@ -0,0 +1,281 @@
/* XPM */
static char *splus_letters_large[] = {
/* width height num_colors chars_per_pixel */
" 51 38 236 2",
/* colors */
".. c #043e74",
".# c #74a29c",
".a c #547a74",
".b c #bcb2b9",
".c c #0c6a9c",
".d c #045282",
".e c #bcdae8",
".f c #94c2cc",
".g c #245678",
".h c #e4e2e3",
".i c #94a2a4",
".j c #04528f",
".k c #5c8aa4",
".l c #346688",
".m c #848a8c",
".n c #04427c",
".o c #e4f4fc",
".p c #94b4b4",
".q c #cceef4",
".r c #045e99",
".s c #4c7a88",
".t c #a4d6f0",
".u c #6c8e94",
".v c #f4f2e4",
".w c #7cb2d4",
".x c #b4b2b4",
".y c #145274",
".z c #044c74",
".A c #acc2d4",
".B c #dcdddc",
".C c #34729c",
".D c #c4c6c4",
".E c #144e84",
".F c #94b4cc",
".G c #fcfaeb",
".H c #245a88",
".I c #5496b9",
".J c #044a80",
".K c #c4e6f1",
".L c #9cc6ec",
".M c #347aac",
".N c #6c96a8",
".O c #145a80",
".P c #6ca2c8",
".Q c #045a91",
".R c #d4fafc",
".S c #145e8c",
".T c #144264",
".U c #446e89",
".V c #949594",
".W c #5c7e84",
".X c #548ec4",
".Y c #e4fdfc",
".Z c #044a8c",
".0 c #e4eef2",
".1 c #a4a3a4",
".2 c #346aa0",
".3 c #dceef4",
".4 c #bcd2d4",
".5 c #f4faf9",
".6 c #74aacc",
".7 c #044669",
".8 c #246696",
".9 c #045a84",
"#. c #ccdedc",
"## c #9ccad8",
"#a c #a4b6b7",
"#b c #144a6e",
"#c c #94bacc",
"#d c #346288",
"#e c #6c9bbc",
"#f c #bcbebc",
"#g c #c4e2ec",
"#h c #0c548c",
"#i c #7c9e9c",
"#j c #f4f2f4",
"#k c #14527c",
"#l c #0c4c7f",
"#m c #0c5379",
"#n c #c4dae4",
"#o c #245e7c",
"#p c #6492a4",
"#q c #346e94",
"#r c #ecf4f2",
"#s c #44829c",
"#t c #b4cad0",
"#u c #145a8e",
"#v c #447490",
"#w c #246294",
"#x c #448abc",
"#y c #fcfefb",
"#z c #2c6f9a",
"#A c #a4bacc",
"#B c #bcbaba",
"#C c #94a6c0",
"#D c #04569c",
"#E c #648aa0",
"#F c #d4f6fc",
"#G c #8cb2c4",
"#H c #acbabc",
"#I c #d4e8f0",
"#J c #84aabc",
"#K c #1c5b82",
"#L c #7ca2c1",
"#M c #5486a4",
"#N c #ecebe9",
"#O c #0c5fa4",
"#P c #9cbdce",
"#Q c #accee4",
"#R c #0c4270",
"#S c #6c6e6c",
"#T c #a4c4cc",
"#U c #0c467c",
"#V c #9cb6b4",
"#W c #d4eef8",
"#X c #447c98",
"#Y c #b4d4e8",
"#Z c #6c92a4",
"#0 c #0c4b6f",
"#1 c #cccccc",
"#2 c #2c5e8c",
"#3 c #649cc0",
"#4 c #cce7f1",
"#5 c #a4cee8",
"#6 c #4482ac",
"#7 c #d4d6d4",
"#8 c #648abc",
"#9 c #9c9b9c",
"a. c #acadac",
"a# c #547a98",
"aa c #34627c",
"ab c #1c669c",
"ac c #84badc",
"ad c #bcced4",
"ae c #6c8ea4",
"af c #bcd4e8",
"ag c #dcf6fc",
"ah c #8cbad4",
"ai c #7c9bb1",
"aj c #9cc6dc",
"ak c #3c6a84",
"al c #7496a7",
"am c #1c5e94",
"an c #5c90b8",
"ao c #b4dee4",
"ap c #4c728c",
"aq c #4c86ac",
"ar c #dce6e9",
"as c #8caebc",
"at c #94aec0",
"au c #7ca2a8",
"av c #5c96c4",
"aw c #0c5a90",
"ax c #2c668c",
"ay c #2c5e70",
"az c #5c86a4",
"aA c #ece6dc",
"aB c #8c8d8f",
"aC c #748c8c",
"aD c #fcf6ec",
"aE c #84b6cc",
"aF c #1c5470",
"aG c #3c7aa4",
"aH c #74a6c4",
"aI c #7cacc8",
"aJ c #a4cbd7",
"aK c #1c4e6c",
"aL c #749bc1",
"aM c #c4c2c4",
"aN c #fcf6f5",
"aO c #1c5682",
"aP c #b4cbe1",
"aQ c #747274",
"aR c #4c7a9c",
"aS c #04468c",
"aT c #94b2c4",
"aU c #0462a4",
"aV c #84a6b4",
"aW c #9ccaf4",
"aX c #6c9ab4",
"aY c #dcfbfc",
"aZ c #14629c",
"a0 c #14466c",
"a1 c #ecfdfc",
"a2 c #dcf2fc",
"a3 c #0c5384",
"a4 c #c4dcf4",
"a5 c #ecf5fc",
"a6 c #44749c",
"a7 c #2c6ea4",
"a8 c #648eac",
"a9 c #8cb6d4",
"b. c #7ca6cc",
"b# c #eceef4",
"ba c #a4c6dc",
"bb c #9cb2c4",
"bc c #b4daf4",
"bd c #9ca29c",
"be c #c4d2dc",
"bf c #3c6e90",
"bg c #b4babb",
"bh c #4c82a4",
"bi c #045a9c",
"bj c #044674",
"bk c #0c5a84",
"bl c #4c829c",
"bm c #5486b4",
"bn c #044272",
"bo c #bcb6b8",
"bp c #045684",
"bq c #bcdee7",
"br c #245a7c",
"bs c #e4e6e4",
"bt c #045691",
"bu c #5c8ea9",
"bv c #04467e",
"bw c #ccf2f9",
"bx c #04629c",
"by c #f4f6ec",
"bz c #b4b6b5",
"bA c #fcfeec",
"bB c #245e88",
"bC c #044e81",
"bD c #9ccae4",
"bE c #347ea4",
"bF c #5c828c",
"bG c #044e8d",
"bH c #346e9c",
"bI c #dcf2ec",
"bJ c #0c6298",
"bK c #f4fefc",
"bL c #74aec4",
"bM c #a4babc",
"bN c #94bed4",
"bO c #f4f6f4",
"bP c #145680",
/* pixels */
".mbgbobo.bbo#Bbg#aaVa8.l#ba0.7a0br.U.N.p#abg#Bbobobo#B#Bbo.b.bbz#B#Bbg#Bbz#B.V#SaQ#SaB.x#B#B#B#Bbg#B#B",
".x.5#yaN#y#yar#a.Way#l#h#hbtaw.d#l#K.gay.uada5#ybO#j#y#yaN#yaN#y#y#y#y#y#y#y#1.V#9.V#BbO#y#y#y#y#y#y#y",
"#B#y#ybKagbDaq#u.JbGbtbtbt.QbpbC#h.d.JbC.JbP.X.ta1bK#y#y#y#y#y#y#y#y#y#y#y#y.D#9#9#9#BbO#y#y#y#y#y#y#y",
"bo.G#y.oas.lbj.Jbt.Qbt.J.J.9bk.JbvbG.d.dbtbvbvbf#Ta1#y#y#yaN#y#y#y#y#y#y#y#y.D.V#9.V#BbO#y#y#y#y#y#y#y",
"#B#y.Yah.8bv.QbJ.j#m#K#X#palal.Na8#qaO#l#Dbt.j.J#zaja1#yaN#y#y#y#y#y#y#y#y#y.D#9#9#9#faN#y#y#y#y#y#y#y",
"bg#ybqa6...jbi.J.S#3.tbw.Y.Ya1aY.Rbw.Lbm#ubGbtbC.7ap#n#y#y#yaN#y#y#y#y#y#y#y.D#9.V#9#B#y#y#y#y#y#y#y#y",
"bza1b..J.ZbibC.g.F.0#y#y.G#y#y#ybK#y#yb##CaF.d.c.da3.Pa2#yaN.G#y#y#y#y#y#y#y.D#9#9.V#BbO#y#y#y#y#y#y#y",
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"#Ha4aObG#DbG#ubabK#y.G#y#y#y#y.5#yaNaNaN#y#W#s.JbxbtbC.6a1#yaAa.#9.1#9.1.1#9#9#9#9#9bd#9.1.1.1#9#9.1.B",
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37
.emacs.d/elpa/ess-20160208.453/etc/icons/spluslogo.xpm Normal file
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@@ -0,0 +1,37 @@
/* XPM */
static char *spluslogo[]={
"24 24 10 1",
"a c None s backgroundToolBarColor",
"g c #000000",
"h c #838383",
"# c #ce3000",
"f c #ce3062",
"e c #ce6262",
". c #ce629b",
"b c #cecece",
"d c #ffcece",
"c c #ffceff",
".##aaaa###aa#aab#a#ba.##",
"#a#caaa#db#a#aab#a#bd#a#",
"##caaaa#b#.a#aad#a#ba##c",
"a.#a##a##.ca#aab#a#daa.#",
"ea#aaaa#daaa#aab#a#bbea#",
"##.aaaa#daaa###a.f#ac##.",
"aaaaaaaaaaaaaaaaaaaaaaaa",
"aaaaaaaaaaaaaaaaaaaaaaaa",
"aaaaaggga###ahhhaaaaaaaa",
"aaaaaggga###ahhhaaaaaaaa",
"aaaaaggga###ahhhaaaaaaaa",
"aaaaaaaaaaaaaaaaaaaaaaaa",
"aaaaa###ahhhaaaahhhaaaaa",
"aaaaa###ahhhaaaahhhaaaaa",
"aaaaa###ahhhaaaahhhaaaaa",
"aaaaaaaaaaaaaaaaaaaaaaaa",
"aaaaahhhaaaahhha###aaaaa",
"aaaaahhhaaaahhha###aaaaa",
"aaaaahhhaaaahhha###aaaaa",
"aaaaaaaaaaaaaaaaaaaaaaaa",
"aaaaaaaahhha###agggaaaaa",
"aaaaaaaahhha###agggaaaaa",
"aaaaaaaahhha###agggaaaaa",
"aaaaaaaaaaaaaaaaaaaaaaaa"};

44
.emacs.d/elpa/ess-20160208.453/etc/icons/spluslogo.xpm.safe Normal file
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@@ -0,0 +1,44 @@
/* XPM */
static char *spluslogo[] = {
/* width height num_colors chars_per_pixel */
" 24 24 13 1",
/* colors */
". c #000000",
"# c #303062",
"a c #494949",
"b c #626262",
"c c #838383",
"d c #ce3000",
"e c #ce3062",
"f c #ce6262",
"g c #ce629b",
"h c #cecece",
"i c #ffcece",
"j c #ffceff",
"k c None",
/* pixels */
"gddkkkkdddiidkkhdkdhkgdd",
"dkdjkkkdihdidkkhdkdhidkd",
"ddjkkkkdhdgidkkidkdhkddj",
"kgdkddkddgjidkkhdkdikkgd",
"fkdiiikdikkidkkhdkdhhfkd",
"ddgkkkkdikkidddkgedkjddg",
"kkkkkkkkkkkkkkkkkkkkkkkk",
"kkkkkkkkkkkkkkkkkkkkkkkk",
"kkkkk...kdddkccckkkkkkkk",
"kkkkk...kdddkccckkkkkkkk",
"kkkkk...kdddkccckkkkkkkk",
"kkkkkkkkkkkkkkkkkkkkkkkk",
"kkkkkdddkccckkkkccckkkkk",
"kkkkkdddkccckkkkccckkkkk",
"kkkkkdddkccckkkkccckkkkk",
"kkkkkkkkkkkkkkkkkkkkkkkk",
"kkkkkccckkkkccckdddkkkkk",
"kkkkkccckkkkccckdddkkkkk",
"kkkkkccckkkkccckdddkkkkk",
"kkkkkkkkkkkkkkkkkkkkkkkk",
"kkkkkkkkccckdddk...kkkkk",
"kkkkkkkkccckdddk...kkkkk",
"kkkkkkkkccckdddk...kkkkk",
"kkkkkkkkkkkkkkkkkkkkkkkk"
};

161
.emacs.d/elpa/ess-20160208.453/etc/icons/startr.xpm Normal file
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@@ -0,0 +1,161 @@
/* XPM */
static char *rlogo3[] = {
/* width height num_colors chars_per_pixel */
" 24 24 130 2",
/* colors */
".. c None s backgroundToolBarColor",
".# c #747684",
".a c #acaeac",
".b c #8492bc",
".c c #94a2c4",
".d c #c4cacc",
".e c #84868c",
".f c #3c424c",
".g c #949aac",
".h c #bcbec4",
".i c #545e74",
".j c #d4dae4",
".k c #94a2d4",
".l c #8492c4",
".m c #7486ac",
".n c #a4b2d4",
".o c #ccd2e4",
".p c #9caacc",
".q c #8c9ac4",
".r c #848eac",
".s c #444e64",
".t c #949acc",
".u c #bcc2ec",
".v c #dce2e4",
".w c #b4bad4",
".x c #5c6674",
".y c #d4daec",
".z c #9ca2d4",
".A c #acbae4",
".B c #7c82a4",
".C c #6c769c",
".D c #d4d2d4",
".E c #8c92c4",
".F c #7c8eac",
".G c #a4b2dc",
".H c #545664",
".I c #8c92ac",
".J c #8c8e94",
".K c #949abc",
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".M c #7c86ac",
".N c #747ea4",
".O c #242a34",
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".R c #6c6e7c",
".S c #7482b4",
".T c #9c9aa4",
".U c #b4bedc",
".V c #dcdedc",
".W c #94a6d4",
".X c #8496c4",
".Y c #acb2cc",
".Z c #ccd2f4",
".0 c #8c9ad4",
".1 c #848ebc",
".2 c #949ed4",
".3 c #9ca6dc",
".4 c #7c8abc",
".5 c #7482a4",
".6 c #3c3a3c",
".7 c #9ca6bc",
".8 c #747a8c",
".9 c #acaebc",
"#. c #8496b4",
"## c #c4cadc",
"#a c #545e84",
"#b c #747aa4",
"#c c #64728c",
"#d c #ccd6ec",
"#e c #9caadc",
"#f c #8c9ecc",
"#g c #949ec4",
"#h c #bcc6f4",
"#i c #9ca6cc",
"#j c #8c96c4",
"#k c #8c96bc",
"#l c #5c6274",
"#m c #7c8ab4",
"#n c #4c4e6c",
"#o c #9c9ea4",
"#p c #acb6d4",
"#q c #acaeb4",
"#r c #848694",
"#s c #3c465c",
"#t c #bcbecc",
"#u c #545e7c",
"#v c #d4dee4",
"#w c #6c7aa4",
"#x c #94a2dc",
"#y c #8492cc",
"#z c #7486b4",
"#A c #646a84",
"#B c #9caad4",
"#C c #8c9acc",
"#D c #848eb4",
"#E c #4c4e54",
"#F c #bcc6e4",
"#G c #5c668c",
"#H c #d4deec",
"#I c #7c82ac",
"#J c #6c7a9c",
"#K c #a4aac4",
"#L c #d4d6dc",
"#M c #a4b2e4",
"#N c #545674",
"#O c #b4bac4",
"#P c #8c96b4",
"#Q c #c4c6cc",
"#R c #7c86b4",
"#S c #2c2e3c",
"#T c #bcc2d4",
"#U c #ccced4",
"#V c #6c727c",
"#W c #c4cedc",
"#X c #4c526c",
"#Y c #747eac",
"#Z c #9ca2c4",
"#0 c #8c8a94",
"#1 c #dcdee4",
"#2 c #94a6dc",
"#3 c #8496cc",
"#4 c #acb2d4",
"#5 c #848ec4",
"#6 c #dcdef4",
"#7 c #7482ac",
"#8 c #949ecc",
"#9 c #9ca6d4",
"a. c #8c96cc",
"a# c #5c627c",
/* pixels */
"................................................",
"................................................",
".....d.y#H#v.j#v.j#v.y#v#v.j.j#W#F#p............",
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".....Y#y.m.k#8.x.............Y#m.4.2.z.H.T......",
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".....Y.X#7a.#j.b#C.p.c#..N.C.K#W#r.O.6.D........",
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".....Y#j#7.W.u.i.6.f#X#A#j#2#e#X#T..............",
".....Y#y.m.k#8#l......#O#G#j#f.F.w..............",
".....Y#y#I#x#8#l.........9.N.l#R.1#J#Q..........",
".....Y#5#z.k#8#l........#O#c#D#5#5.b.I.V........",
"....#4.l#R.k.t#l...........9.N.l#3.E.C.g........",
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".....Y.1.c.U.K.i..............#G#m.n#p.r.i......",
"....#t.8#V#A.R.e...............h.8.R.R.R.#.a....",
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"................................................"
};

40
.emacs.d/elpa/ess-20160208.453/etc/icons/switch_ess.xpm Normal file
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@@ -0,0 +1,40 @@
/* XPM */
static char *switch_ess[]={
"24 24 13 1",
". c None s backgroundToolBarColor",
"a c #000000",
"e c #131313",
"# c #1532ed",
"d c #313131",
"k c #434343",
"j c #535353",
"h c #707070",
"b c #878787",
"i c #949494",
"g c #a0a0a0",
"f c #bfbfbf",
"c c #c3c3c3",
"........................",
"........................",
"........................",
"........................",
"..###...................",
"..###...................",
"..###...................",
"..###.aaaab.cdedc.cdedc.",
"..###.af....ag....ag....",
"..###.af....ba....ba....",
"..###.aaad...fah...fah..",
"..###.af.......ga....ga.",
"..###.af....i..jk.i..jk.",
"..###.aaaak.jeej..jeej..",
"..###...................",
"..###...................",
"..###...................",
"..###...........#.......",
"..###...........##......",
"..#################.....",
"..##################....",
"...################.....",
"................##......",
"................#......."};

112
.emacs.d/elpa/ess-20160208.453/etc/icons/switchr.xpm Normal file
View File

@@ -0,0 +1,112 @@
/* XPM */
static char *rt4[]={
"24 24 85 2",
"Qt c None s backgroundToolBarColor",
".V c #14162c",
".A c #1c263c",
"#d c #24263c",
".K c #242e44",
".H c #2c3244",
"#o c #2c3644",
".Q c #34364c",
".Z c #3c3e54",
".N c #3c4264",
".q c #444664",
".p c #444a64",
"#. c #444e64",
".r c #4c4e6c",
".w c #4c566c",
"#m c #545e74",
"#j c #546284",
".B c #54628c",
"#e c #5c6284",
".4 c #5c6a9c",
"#k c #646a8c",
"#p c #646e8c",
".5 c #646e9c",
".S c #647294",
".b c #647a94",
".c c #6c769c",
".h c #6c7aa4",
".3 c #6c7ea4",
".k c #747ea4",
".O c #7482b4",
".u c #7482bc",
".i c #7486b4",
".X c #7c82a4",
".d c #7c86a4",
".g c #7c86ac",
"#b c #7c86b4",
".E c #7c86bc",
"#h c #7c8abc",
".L c #7c8ac4",
".a c #7c8eb4",
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".# c #848ebc",
".2 c #8492b4",
".m c #8492bc",
".l c #8492c4",
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".v c #8c92c4",
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"QtQt.x.x.xQtQt.m.E.F.G.HQtQtQtQtQtQt.m.I.J.rQtQt",
"QtQt.x.x.xQtQt.#.i.t.s.KQtQtQtQtQtQt.D.L.M.NQtQt",
"QtQt.x.x.xQtQt.#.O.y.P.QQtQtQtQtQt.R.S.T.U.VQtQt",
"QtQt.x.x.xQtQt.#.i.t.W.FQtQtQtQtQt.X.Y.U.ZQtQtQt",
"QtQt.x.x.xQtQt.#.i.m.0.1.t.2.3.4.5.6.7.VQtQtQtQt",
"QtQt.x.x.xQtQt.#.i.l.8.9.Q#.##.P#a.GQtQtQtQtQtQt",
"QtQt.x.x.xQtQt.##b.t#c#dQtQtQt#e#f#g.SQtQtQtQtQt",
"QtQt.x.x.xQtQt.##h.t#i.KQtQtQtQt#b.m#h.aQtQtQtQt",
"QtQt.x.x.xQtQt.#.O.t#i.KQtQtQtQt#j.#.l.l#kQtQtQt",
"QtQt.x.x.xQtQt.F.O.y.s.HQtQtQtQtQt#b.l#l.##mQtQt",
"QtQt.x.x.xQtQt.##b.F#n#oQtQtQtQtQt#j.F#f.m#pQtQt",
"QtQt.x.x.xQtQt.#.t#q#r.KQtQtQtQtQtQt.i#s#q.YQtQt",
"QtQt.x.x.xQtQtQtQtQtQtQtQtQtQtQt.xQtQtQtQtQtQtQt",
"QtQt.x.x.xQtQtQtQtQtQtQtQtQtQtQt.x.xQtQtQtQtQtQt",
"QtQt.x.x.x.x.x.x.x.x.x.x.x.x.x.x.x.x.xQtQtQtQtQt",
"QtQt.x.x.x.x.x.x.x.x.x.x.x.x.x.x.x.x.x.xQtQtQtQt",
"QtQtQt.x.x.x.x.x.x.x.x.x.x.x.x.x.x.x.xQtQtQtQtQt",
"QtQtQtQtQtQtQtQtQtQtQtQtQtQtQtQt.x.xQtQtQtQtQtQt",
"QtQtQtQtQtQtQtQtQtQtQtQtQtQtQtQt.xQtQtQtQtQtQtQt"};

32
.emacs.d/elpa/ess-20160208.453/etc/icons/switchs.xpm Normal file
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@@ -0,0 +1,32 @@
/* XPM */
static char *switchs[]={
"24 24 5 1",
". c None",
"# c #000000",
"c c #1532ed",
"b c #838383",
"a c #ce3000",
"........................",
"........###.aaa.bbb.....",
"........###.aaa.bbb.....",
"........###.aaa.bbb.....",
"..ccc...................",
"..ccc...aaa.bbb....bbb..",
"..ccc...aaa.bbb....bbb..",
"..ccc...aaa.bbb....bbb..",
"..ccc...................",
"..ccc...bbb....bbb.aaa..",
"..ccc...bbb....bbb.aaa..",
"..ccc...bbb....bbb.aaa..",
"..ccc...................",
"..ccc......bbb.aaa.###..",
"..ccc......bbb.aaa.###..",
"..ccc......bbb.aaa.###..",
"..ccc...................",
"..ccc...........c.......",
"..ccc...........cc......",
"..ccccccccccccccccc.....",
"..cccccccccccccccccc....",
"...cccccccccccccccc.....",
"................cc......",
"................c......."};

25
.emacs.d/elpa/ess-20160208.453/etc/in-string-bug-ex.Rnw Normal file
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@@ -0,0 +1,25 @@
% From: Richard Morrisroe <richie.morrisroe@gmail.com>
% To: <ess-help@r-project.org>
% Subject: Re: [ESS] noweb file and assignment key
% Date: Tue, 30 Oct 2012 20:57:32 +0000
\documentclass{article}
\begin{document}
<<packages, echo=FALSE, results=hide>>=
i.can.haz.assginment <- TRUE
@
Now, we will introduce an extraneous apostrophe, for no reason '
<<test2>>=
aa <- _2 #ess-smart-underscore-no-longer-works
@
'
<<test3, echo=TRUE, results=verbatim >>=
nowitdoes <- cat("Note the apostrophe above which closes the earlier one\n")
@
\end{document}

72
.emacs.d/elpa/ess-20160208.453/etc/other/S-spread/README Normal file
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@@ -0,0 +1,72 @@
spread We have designed and constructed an interactive spreadsheet
interface to S/Splus that maintains the complete power and
generality of the S language. At user level, the interface
behaves like the popular spreadsheet programs available for
personal computers: one or more S data objects (matrices or
three-way arrays) are displayed on the screen. The user
graphically (with mouse or cursor motion) identifies a cell
for review, and possible updating, of its contents. Macros
containing arbitrary S expressions can be associated with
the entire spread.frame or one of its cells. The
spreadsheet is designed in a modular fashion with
device-specific methods for the display and updating of
spreadsheet objects. We include methods for two devices:
the generic S graphics device and a character based device
using the emacs 19 environment.
Richard M. Heiberger (rmh@astro.ocis.temple.edu)
Magnus Mengelbier (magnus@astro.ocis.temple.edu)
The interface is described in
\item Heiberger, Richard M., and Magnus Mengelbier (1995, to appear)
``Design of a Spreadsheet Interface for S,''
{\it Proceedings of the American Statistical Association},
Section on Statistical Graphics.
This is placeholder announcement. The files will be
available on statlib after one more level of testing.
Files in this distribution:
README Abstract, file listing, and setup instructions.
sprd3d.how Instructions for spread.frame users.
sprd-emc.s S for emacs driver
sprd-grd.s S for class="grade"
sprd-spr.s S for class="spread" This is the primary set of functions.
sprd-txt.s S for graphics device driver based on text() command.
sprd-int.el emacs lisp file
Load this file into emacs 19 each time you start a
spread.frame session.
gradexmp.s S example
Setup Instructions
The emacs spreadsheet interface for S consists of four S files
"sprd-*.s" and one emacs lisp file "sprd-int.el".
1. Create a new directory to store the four S files "sprd-*.s" and one
emacs lisp file "sprd-int.el". I use "/disk5/rmh/sprd3d/". You might
wish to place it under the directory where you store other S/Splus
libraries.
2. Make a new .Data, "/disk5/rmh/sprd3d/.Data", start S/Splus, and
source the four sprd-*.s files:
> source("sprd-emc.s")
> source("sprd-grd.s")
> source("sprd-spr.s")
> source("sprd-txt.s")
> q()
3. The directory /disk5/rmh/sprd3d/ should now be treated as a
library directory and should not be further touched. All further work
using the spread.frames should be done in a different directory.
4. See the file sprd3d.how for user instructions. You may look at
the file "gradexmp.s" for an example.

337
.emacs.d/elpa/ess-20160208.453/etc/other/S-spread/S-spread.el Normal file
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;; spreadsheet in S, S-mode or stand-alone
;; Richard M. Heiberger
;; 1996
;; S-mode
;; Load this file from a running *S* window after starting S/Splus with M-x S
;; or
;; stand-alone
;; Load this file from the dired window in which .Data exists.
;(set-variable 'buffers-menu-max-size nil)
(defvar spread-directory (concat "/tmp/" (make-temp-name "spr"))
"Directory in which to store ascii spreadsheet displays.")
(defvar spread-command-file (concat spread-directory "/*command*")
"File through which S will communicate with emacs.")
(defvar spread-directory-p nil
"predicate value non-nil when directory has been defined.")
(defun print-find-emacs nil "display spread.frame from minibuffer" (interactive)
(spread-print-find (read-string "spread.frame: ") t))
(defun emacs-rc nil "" (interactive)
(emacs-cell "1")
)
(defun emacs-macro nil "" (interactive)
(emacs-cell "2")
)
(defun emacs-macro-control-text nil "" (interactive)
(emacs-cell "4")
)
(defun emacs-macro-print-text nil "" (interactive)
(emacs-cell "5")
)
(defun emacs-cell (result-type) "" (interactive)
(setq spread-name (buffer-name))
(setq r (count-lines 1 (point)))
(setq c (current-column))
(set-buffer S-buffer)
(spread-insert
(format "emacs.cell('%s', %s, %s, %s)"
spread-name r c result-type
)
)
(save-excursion
(set-buffer "*command*")
(revert-t-t)
(goto-char (point-min))
(setq beg (point)) (end-of-line)
(if (equal result-type "4")
(progn
(setq command (buffer-substring beg (point)))
(set-buffer S-buffer)
(spread-insert command)
)
(setq command (read-string "> " (buffer-substring beg (point))))
(set-buffer S-buffer)
(spread-insert command)
(spread-insert "invisible(assign(.Active, x))")
(spread-print-find spread-name nil)
(goto-line r)(forward-char c)
))
)
(defun spread-insert (spread-command) "" (interactive)
(goto-char (point-max))
(insert spread-command)
(comint-send-input)
(accept-process-output spread-process)
)
(defun revert-t-t nil "revert-buffer with no questions asked"
(interactive)
(revert-buffer t t)
)
(defun revert-t-t-read-only nil "revert-buffer, no questions, read-only"
(interactive)
(revert-buffer t t)
(setq buffer-read-only t)
)
(defvar spread-mode-map nil "Keymap for Spread mode.")
(if spread-mode-map
nil
(setq spread-mode-map (make-sparse-keymap))
(define-key spread-mode-map "\C-cv" 'revert-t-t-read-only)
(define-key spread-mode-map "\C-m" 'emacs-rc)
(define-key spread-mode-map "\C-cc" 'emacs-macro)
(define-key spread-mode-map "\C-cs" 'emacs-macro-control-text)
(define-key spread-mode-map "\C-cp" 'emacs-macro-print-text)
(define-key spread-mode-map "f" 'emacs-print-find-emacs)
(define-key spread-mode-map [mouse-2] 'spread-mouse-print-find-emacs)
(define-key spread-mode-map [mouse-3] 'spread-mouse-rc)
)
(defun spread-mouse-rc (event) "move point then enter"
(interactive "e")
(mouse-set-point event)
(emacs-rc)
)
(defun spread-mouse-print-find-emacs (event) "move point then find file"
(interactive "e")
(mouse-set-point event)
(emacs-print-find-emacs)
)
(defun spread-mode () "Major mode for spreadsheets.\\{spread-mode-map}"
(interactive)
(kill-all-local-variables)
(make-local-variable 'beg)
(make-local-variable 'command)
(use-local-map spread-mode-map)
(setq mode-name "Spread")
(setq major-mode 'spread-mode)
(if (equal (buffer-name) ".Registry") (spread-highlight-macro))
(setq buffer-read-only t)
)
;; from dired.el L547
; (put-text-property (point)
; (save-excursion
; (dired-move-to-end-of-filename)
; (point))
; 'mouse-face 'highlight)
;
;; (put-text-property (point) (mark) 'mouse-face 'highlight)
(defun spread-highlight-macro nil
"highlight spread.frame names for mouse access"
(interactive)
(save-excursion
(goto-char (point-min))
(search-forward "**macro**")(forward-char)
(toggle-read-only -1)
(while (progn
(setq beg (point))(end-of-line)
(not (= beg (point)))
)
(put-text-property beg (1-(point)) 'mouse-face 'highlight)
(forward-char)
)
(toggle-read-only 1)
)
(save-buffer)
)
(defun emacs-print-find-emacs nil "" (interactive)
(beginning-of-line)
(setq beg (point)) (end-of-line) (backward-char)
(setq spread-name (buffer-substring beg (point)))
(spread-print-find spread-name nil)
)
(defun find-spread-frame-directory nil
"Locate directory in which spread.frame functions are stored."
(list-command-history)
(set-buffer "*Command History*")
(goto-char (point-min))
(search-forward "(load-file ")
(goto-char (1+ (match-end 0)))(setq beg (point))
(end-of-line)(search-backward "/")
(goto-char (match-end 0))
(setq spread-frame-directory
(expand-file-name (buffer-substring beg (point))))
(kill-buffer "*Command History*")
)
(defvar inferior-spread-mode nil
"Non-nil if using inferior-spread-mode as a minor mode of some other mode.")
(make-variable-buffer-local 'inferior-spread-mode)
(put 'inferior-spread-mode 'permanent-local t)
(or (assq 'inferior-spread-mode minor-mode-alist)
(setq minor-mode-alist (append minor-mode-alist
(list '(inferior-spread-mode " spread")))))
(defvar inferior-spread-mode-map nil)
(if inferior-spread-mode-map
nil
(setq inferior-spread-mode-map (make-sparse-keymap))
(define-key inferior-spread-mode-map "\C-cv" 'revert-t-t)
(define-key inferior-spread-mode-map "\C-cr" 'print-find-emacs))
(or (assq 'inferior-spread-mode minor-mode-map-alist)
(setq minor-mode-map-alist
(cons (cons 'inferior-spread-mode inferior-spread-mode-map)
minor-mode-map-alist)))
(defun inferior-spread-mode (&optional arg)
"Toggle Inferior Spread mode.
With arg, turn Inferior Spread mode on if arg is positive, off otherwise."
(interactive "P")
(setq inferior-spread-mode
(if (null arg) (not inferior-spread-mode)
(> (prefix-numeric-value arg) 0)))
(if inferior-spread-mode
(progn
(set-process-filter spread-process 'comint-output-filter)
(set-variable 'comint-output-filter-functions
'(spread-output-filter
comint-postoutput-scroll-to-bottom))
(set-variable 'comint-scroll-to-bottom-on-output "this")
(set-variable 'comint-scroll-show-maximum-output t)
(force-mode-line-update))
(message "Don't know how to turn off Inferior Spread mode")))
(defun spread-process ()
"Start stand-alone S process to run spread."
(comint-run S-program)
(setq spread-process (get-buffer-process (current-buffer)))
(setq comint-prompt-regexp shell-prompt-pattern)
(if (not(file-writable-p ".Data/.Audit"))
(accept-process-output spread-process))
(accept-process-output spread-process)
spread-process
)
(defun spread-output-filter (str)
"detect errors in S output"
(if (or
(string-match "Dumped" str)
(string-match "Error" str)
)
(progn
(switch-to-buffer-other-window S-buffer)
(comint-show-maximum-output)
(set-variable 'quit-flag t); beeps and writes "quit" in the message area
)
)
)
(defun spread-print-find (spread-name update-Registry)
"Place SPREAD-NAME in foreground of S-buffer (*S* or *Splus*),
update .Registry and revert buffer when UPDATE-REGISTRY is t,
print all views of spread.frame associated with SPREAD-NAME in .Registry
to /tmp/spr***** directory, and find or revert all views into emacs buffers."
(interactive)
(set-buffer S-buffer)
(spread-insert
(format "print.find.emacs('%s', update.Registry=%s)"
spread-name (if update-Registry "T" "F")))
(if update-Registry
(save-excursion (spread-find-file ".Registry")))
(spread-print-sprds)
(switch-to-buffer spread-name)
)
(defun spread-print-sprds () "Display in buffers all views of spread.frame"
(interactive)
(save-excursion
(set-buffer "*command*")
(revert-t-t)
(goto-char (point-min))
(while (< (point) (point-max))
(set-buffer "*command*")
(setq beg (point)) (end-of-line)
(setq spread-name-i (buffer-substring beg (point)))
(save-excursion (spread-find-file spread-name-i))
(forward-line)))
)
(defun spread-find-file (spread-name) "Display one view of spread.frame"
(interactive)
(switch-to-buffer spread-name)
(if (buffer-file-name)
(revert-t-t-read-only)
(kill-buffer spread-name)
(find-file (concat spread-directory "/" spread-name))
)
(spread-mode)
)
(defun spread-start () "load emacs spread.frame handler"
(if (equal major-mode 'inferior-S-mode)
(progn
(setq spread-mode "S-mode")
(setq S-buffer (current-buffer)))
(if (equal major-mode 'dired-mode)
(progn
(setq spread-mode "stand-alone")
(setq S-program (read-string "Splus or S? " "Splus"))
(setq S-buffer (concat "*" (file-name-nondirectory S-program) "*"))
(if (not (get-buffer S-buffer))
(get-buffer-create S-buffer))
(if (get-buffer-process S-buffer) (set-variable 'quit-flag t)))
(set-variable 'quit-flag t)))
(setq spread-home-directory default-directory)
(find-spread-frame-directory)
(if (not spread-directory-p)
(progn (make-directory spread-directory)
(setq spread-directory-p t)))
(set-buffer S-buffer)
(cd spread-home-directory)
(setq spread-process
(if (equal spread-mode "stand-alone")
(spread-process)
(get-buffer-process (current-buffer))))
(inferior-spread-mode 1)
(spread-insert
(format "assign('.spread.Data',attach('%s.Data'),frame=0)"
spread-frame-directory))
(spread-insert
(format "emacs.start('%s')" spread-directory))
(find-file spread-command-file)
(spread-find-file ".Registry")
)
;; start it up
(spread-start)

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.emacs.d/elpa/ess-20160208.453/etc/other/S-spread/S-spread.elc Normal file
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30845
.emacs.d/elpa/ess-20160208.453/etc/other/S-spread/asaprc.ps Normal file
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18
.emacs.d/elpa/ess-20160208.453/etc/other/S-spread/gradexmp.s Normal file
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@@ -0,0 +1,18 @@
who <- c(
"Aaaaa",
"Bbbbb",
"Cccc",
"Zzzzzzz",
"maximum")
what <- c("1a","1b","1c","1d","1e","1f","1g",
"1h","2a","2b","2c")
x <- matrix(0, length(who), length(what),
dimnames=list(who,what))
x["maximum",] <- c(5,5,6,4,20,6,16,8,10,10,10)
section.7 <- as.grade(x)

280
.emacs.d/elpa/ess-20160208.453/etc/other/S-spread/sprd-emc.s Normal file
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#-*-Fundamental-*-
col.spacing <- function(x)
{
rn.w <- if (length(dimnames(x)[[1]]) > 0) max(nchar(dimnames(x)[[1]]))
else nchar(as.character(nrow(x)))+3
col.w <- apply(x, 2, function(x) nchar(format(x))[1])
dn.w <- if (length(dimnames(x)[[2]]) > 0) nchar(dimnames(x)[[2]])
else nchar(as.character(ncol(x)))+3
col.w <- ifelse( col.w > dn.w , col.w, dn.w)
cumsum(c(rn.w,col.w)+1)
}
emacs.expr <- function(x, i, j=i[2], result.type)
# 1. emacs.rc
# 2. emacs.macro
# 3. emacs.macro.text(deparse.result=T) #default for index.value
# 4. emacs.macro.text(deparse.result=F)
# 1. assign expression to cell or to macro
# 2. evaluate macro expression
# 3. retrieve macro expression
# 4. construct control.text() expression from macro name
# 5. construct print.text() expression from macro name
{
# i and j are integer scalars
if (missing(j)) {j <- i[2] ; i <- i[1]}
if ((.Active == .Active.buffer) && (length(dim(x)) > 2))
stop("Must use rectangular slice, not 3d buffer")
if (i <= nrow(x) && result.type==1)
return(expr.rc(x, c(i, j)))
if (!inherits(x, "spread")) stop("Not a spread.frame")
mm <- (nrow(x)+1):(nrow(x)+2+length(macro(x)))
bb <- mm[length(mm)]+(1:(2+length(before(x))))
aa <- bb[length(bb)]+(1:(2+length(after(x))))
find.expr <- function(type.x, kk, type, result.type)
{
if (kk>0) {
iv <- index.value(names(type.x), kk,
!((result.type == 4) || (result.type == 5)))
switch(result.type,
paste(type, "(x)[", iv, "] <- expression(",
expr.value(type.x[kk],1), ")"),
paste("x <- eval.spread(x, ", type, "(x)[", iv, "] )" ),
deparse(eval(parse(text=paste(type, "(x)[", iv, "]")))[[1]]),
paste(iv, "<- control.text(", iv, ")"),
paste(iv, "<- print.text(", iv, ")")
)
}
else if (result.type==1) paste(type, "(x)[\"\"] <- expression()")
else NULL
}
k <- match(i, mm, 0)
if (k) return(find.expr(macro(x), k-2, "macro", result.type))
k <- match(i, bb, 0)
if (k) return(find.expr(before(x), k-2, "before", result.type))
k <- match(i, aa, 0)
if (k) return(find.expr(after(x), k-2, "after", result.type))
}
cell.rc.emacs <- function(x, e.r, e.c)
{
x.r <- ifelse(e.c == 0, e.r, e.r-1)
x.c <- sum(e.c >= col.spacing(x))
c(row=x.r, col=x.c)
}
print.update.emacs <- function(x, ...,
file=paste(.spread.directory, .Active.buffer, sep="/"))
{
sink(file)
print(x, ...)
xs <- get(.Active)
if (inherits(xs, "spread"))
{
print.spread.macro(xs, macro)
print.spread.macro(xs, before)
print.spread.macro(xs, after)
}
sink()
invisible(x)
}
print.spread.macro <- function(x, macro)
{
cat("\n**", as.character(substitute(macro)), "**\n", sep="")
ne <- names(macro(x))
if (length(ne))
for (i in 1:length(ne))
cat(index.value(ne,i,F),"\n")
}
as.two.way.array <- function(x, subs=parse(text=.Active.buffer)[[1]][-(1:2)])
{
if (length(dim(x))==2) return(x)
# This is designed for 3 way arrays with
# two missing and one specified dimension.
# If the drop parameter exists, it is over-ridden.
subs$drop <- NULL
which.subs <- (sapply(subs,length)==0)
dnx <- dimnames(x)[which.subs]
dimnames(x) <- NULL
dim(x) <- dim(x)[which.subs]
dimnames(x) <- dnx
x
}
fg <- function( sprdname=.Active )
# sprdname = character name, possibly subscripted
{
if (is.na(match(sprdname, names(macro(.Registry))))) {
macro(.Registry)[sprdname] <- sprdname
assign(".Registry", .Registry, where=1 )
}
assign(".Active.buffer", sprdname, frame=0 )
assign(".Active", find.names(sprdname), frame=0 )
assign("x", eval(parse(text=.Active)), where=1 )
assign("x.buffer", where=1,
if (.Active.buffer==.Active) x
else as.two.way.array(eval(parse(text=.Active.buffer))))
invisible(sprdname)
}
control.emacs <- function(x)
{
#this is a fake function
#emacs does the work
# control.emacs never gets called when emacs is in control.
# RET in spread window puts old command in minibuffer:
# emacs sends
# emacs.cell('spreadname', e.r, e.c, result.type)
# emacs reads the file written by the above and
# asks the user to revise it in the minibuffer.
# RET in minibuffer puts revised command in S buffer,
# and causes the revised command to be executed, updating the spreadsheet.
# emacs issues
# invisible(assign(.Active, x))
# to place the object in x into the object named in .Active
# emacs issues
# print.find.emacs('spreadname', update.Registry=F)
# to update all buffers showing views of the object named in .Active
# When S gets control back, the command has been executed and the
# spreadsheet has been updated
}
#emacs usage
#load-file S-spread.el
#In the *S* buffer, type ^Cr to place a spread.frame or 2-way or 3-way array
# into a spread.frame buffer.
#In the spread.frame buffer, type RET to update a cell.
#In the minibuffer, revise the cell and type RET to update the object and
# the display.
#If there is a timing problem and the display is not updated,
# then type ^Cv in the spread buffer.
find.sprds <- function(sprdname, reg.names=names(macro(.Registry)))
{
reg.names[find.names(reg.names) == find.names(sprdname)]
}
find.names <- function(reg.names)
{
prn <- parse(text=reg.names)
for (i in 1:length(prn))
if (mode(prn[[i]]) != "name") reg.names[i] <- prn[[i]][[2]]
reg.names
}
print.sprds.emacs <- function(sprdname)
{
fssn <- find.sprds(sprdname)
fssn2 <- fssn
for(i in fssn2) {
fg(i)
print.update.emacs(x.buffer)
}
cat(paste(fssn, collapse="\n"), "\n", sep="", file=.spread.command.file)
invisible(fg(sprdname))
}
print.update.emacs.3d <- function(object)
{
object.name <- as.character(substitute(object))
dobject <- dim(object)
if (length(dobject) != 3) stop("3-way array required")
fg(object.name)
n3 <- dimnames(object)[[3]]
if (is.null(n3)) n3 <- seq(length=dobject[3])
else n3 <- paste("\"", n3, "\"", sep="")
for (i in n3) {
fg(paste( object.name, "[,,", i, "]", sep="" ))
print.update.emacs(x.buffer)
}
invisible(object)
}
emacs.start <- function(spread.directory)
{
assign('.spread.directory', spread.directory, frame=0)
if (!exists('.Registry', 1))
assign(".Registry", where=1, as.spread(matrix(".Registry")))
assign(".spread.command.file", frame=0,
paste(spread.directory, "*command*", sep="/"))
fg(".Registry")
print.update.emacs(.Registry)
invisible(".Registry")
}
print.find.emacs <- function(spread=.Active, update.Registry=T)
{
fg(spread)
if (update.Registry) {
fg(".Registry")
print.update.emacs(.Registry)
fg(spread)
}
print.sprds.emacs(spread)
invisible(spread)
}
emacs.cell <- function(spread, e.r, e.c, result.type)
{
fg(spread)
cell.rc <- cell.rc.emacs(x.buffer, e.r, e.c)
.Options$width <- 1000
if (result.type==1 && cell.rc[1] <= nrow(x.buffer)) {
cell.rc <- cell.sub.emacs(x, cell.rc)
cell.expr <- expr.rc(x, cell.rc)
}
else
cell.expr <- emacs.expr(x, cell.rc, result.type=result.type)
cat(cell.expr, '\n', sep='', file=.spread.command.file)
}
cell.sub.emacs <- function(x, i, j=i[2])
{
# i and j are integer scalars
if (missing(j)) {j <- i[2] ; i <- i[1]}
if (i==0 && j==0) stop("non-zero row or column required")
if ((length(dim(x)) == 2)) {
acpab <- c("","")
positions <- 1:2
}
else if (.Active == .Active.buffer)
stop("Must use rectangular slice, not 3d buffer")
else {
pab <- parse(text=.Active.buffer)
acpab <- as.character( pab[[1]][-(1:2)] )
positions <- (1:length(acpab))[sapply(acpab, nchar) == 0]
}
di <- index.value(dimnames(x)[[positions[1]]], i)
dj <- index.value(dimnames(x)[[positions[2]]], j)
acpab[positions[1]] <- di
acpab[positions[2]] <- dj
acpab
}

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as.grade <- function(x)
{
if (inherits(x,"grade")) return(x)
if (match("sum",dimnames(x)[[2]],0) == 0) {
dx <- dim(x)
dnx <- dimnames(x)
if (length(dim(x)) == 2) {
if (length(dnx) != 2) dimnames(x) <- list(NULL, 1:dx[2])
tmp <- cbind(x,sum=0)
}
if (length(dim(x)) == 3) {
dimnames(x) <- NULL
tmp <- aperm(x,c(1,3,2))
dim(tmp) <- c(dim(tmp)[1]*dim(tmp)[3], dim(tmp)[2])
tmp <- cbind(tmp, sum=0)
dim(tmp) <- (dx + c(0,1,0))[c(1,3,2)]
tmp <- aperm(tmp,c(1,3,2))
if (length(dnx) != 3) dnx <- list(NULL, 1:dx[2], NULL)
dnx[[2]] <- c(dnx[[2]], "sum")
dimnames(tmp) <- dnx
}
if (length(dim(x)) > 3) stop("grade requires 2d or 3d")
}
x <- as.spread(tmp)
sum.col <- match("sum",dimnames(x)[[2]],0)
tmp.expr <- paste(
"x[,",
sum.col,
if (length(dim(x))==3) ",",
"] <- apply(x[,",
-sum.col,
if (length(dim(x))==3) ",",
"],",
deparse(if (length(dim(x))==3) c(1,3) else 1),
",sum)"
)
after(x)["sum"] <- parse(text=tmp.expr)
class(x) <- c("grade", class(x))
update.spread(x)
}
expr.rc.grade <- function(x, acpab)
{
if (sapply(acpab,nchar)[[2]] == 0) {
j <- -match("sum", dimnames(x)[[2]], 0)
acpab[2] <- j
}
expr.rc.default(x,acpab)
}

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;; spreadsheet in S
;; Richard M. Heiberger
;; 1995
;; Load this file from the dired window in which .Data exists.
;; This file does not work with S-mode. Use S-spread.el for S-mode.
(set-variable 'buffers-menu-max-size nil)
(defvar spread-directory (concat "/tmp/" (make-temp-name "spr"))
"Directory in which to store ascii spreadsheet displays.")
(defvar spread-command-file (concat spread-directory "/*command*")
"File through which S will communicate with emacs.")
(defvar spread-directory-p nil
"predicate value non-nil when directory has been defined.")
(defun print-find-emacs nil "display spread.frame from minibuffer" (interactive)
(spread-print-find (read-string "spread.frame: ") t))
(define-key global-map "\C-cr" 'print-find-emacs)
(defun emacs-rc nil "" (interactive)
(emacs-cell "1")
)
(defun emacs-macro nil "" (interactive)
(emacs-cell "2")
)
(defun emacs-macro-control-text nil "" (interactive)
(emacs-cell "4")
)
(defun emacs-macro-print-text nil "" (interactive)
(emacs-cell "5")
)
(defun emacs-cell (result-type) "" (interactive)
(setq spread-name (buffer-name))
(setq r (count-lines 1 (point)))
(setq c (current-column))
(set-buffer S-buffer)
(spread-insert
(format "emacs.cell('%s', %s, %s, %s)"
spread-name r c result-type
)
)
(save-excursion
(set-buffer "*command*")
(revert-t-t)
(goto-char (point-min))
(setq beg (point)) (end-of-line)
(if (equal result-type "4")
(progn
(setq command (buffer-substring beg (point)))
(set-buffer S-buffer)
(spread-insert command)
)
(setq command (read-string "> " (buffer-substring beg (point))))
(set-buffer S-buffer)
(spread-insert command)
(spread-insert "invisible(assign(.Active, x))")
(spread-print-find spread-name nil)
(goto-line r)(forward-char c)
))
)
(defun spread-insert (spread-command) "" (interactive)
(goto-char (point-max))
(insert spread-command)
(comint-send-input)
(accept-process-output spread-process)
)
(defun revert-t-t nil "revert-buffer with no questions asked"
(interactive)
(revert-buffer t t)
)
(defun revert-t-t-read-only nil "revert-buffer, no questions, read-only"
(interactive)
(revert-buffer t t)
(setq buffer-read-only t)
)
(define-key global-map "\C-cv" 'revert-t-t)
(defvar spread-mode-map nil "Keymap for Spread mode.")
(if spread-mode-map
nil
(setq spread-mode-map (make-sparse-keymap))
(define-key spread-mode-map "\C-cv" 'revert-t-t-read-only)
(define-key spread-mode-map "\C-m" 'emacs-rc)
(define-key spread-mode-map "\C-cc" 'emacs-macro)
(define-key spread-mode-map "\C-cs" 'emacs-macro-control-text)
(define-key spread-mode-map "\C-cp" 'emacs-macro-print-text)
(define-key spread-mode-map "f" 'emacs-print-find-emacs)
(define-key spread-mode-map [mouse-2] 'spread-mouse-print-find-emacs)
(define-key spread-mode-map [mouse-3] 'spread-mouse-rc)
;; (define-key spread-mode-map [double-mouse-1] 'spread-mouse-rc) ;doesn't work
(define-key spread-mode-map [menu-bar spread]
(cons "Spread" (make-sparse-keymap "Spread")))
; (define-key spread-mode-map [menu-bar spread spread-macro]
; '("macro" . spread-macro))
(define-key spread-mode-map [menu-bar spread spread-before]
'("before" . spread-before))
(define-key spread-mode-map [menu-bar spread spread-after]
'("after" . spread-after))
(define-key spread-mode-map [menu-bar spread spread-macro]
(cons "Macro" (make-sparse-keymap "sprdtwo")))
(define-key spread-mode-map [menu-bar spread spread-macro display]
'("after" . spread-display))
; (define-key spread-mode-map [mouse-2] 'emacs-menu-print-find-ww)
)
(defun spread-mouse-rc (event) "move point then enter"
(interactive "e")
(mouse-set-point event)
(emacs-rc)
)
(defun spread-mouse-print-find-emacs (event) "move point then find file"
(interactive "e")
(mouse-set-point event)
(emacs-print-find-emacs)
)
(defun spread-mode () "Major mode for spreadsheets.\\{spread-mode-map}"
(interactive)
(kill-all-local-variables)
(make-local-variable 'beg)
(make-local-variable 'command)
(use-local-map spread-mode-map)
(setq mode-name "Spread")
(setq major-mode 'spread-mode)
(if (equal (buffer-name) ".Registry") (spread-highlight-macro))
(setq buffer-read-only t)
)
;; from dired.el L547
; (put-text-property (point)
; (save-excursion
; (dired-move-to-end-of-filename)
; (point))
; 'mouse-face 'highlight)
;
;; (put-text-property (point) (mark) 'mouse-face 'highlight)
(defun spread-highlight-macro nil
"highlight spread.frame names for mouse access"
(interactive)
(save-excursion
(goto-char (point-min))
(search-forward "**macro**")(forward-char)
(toggle-read-only -1)
(while (progn
(setq beg (point))(end-of-line)
(not (= beg (point)))
)
(put-text-property beg (1-(point)) 'mouse-face 'highlight)
(forward-char)
)
(toggle-read-only 1)
)
(save-buffer)
)
(defun emacs-print-find-emacs nil "" (interactive)
(beginning-of-line)
(setq beg (point)) (end-of-line) (backward-char)
(setq spread-name (buffer-substring beg (point)))
(spread-print-find spread-name nil)
)
(defun find-spread-frame-directory nil
"Locate directory in which spread.frame functions are stored."
(list-command-history)
(set-buffer "*Command History*")
(goto-char (point-min))
(search-forward "(load-file ")
(goto-char (1+ (match-end 0)))(setq beg (point))
(end-of-line)(search-backward "/")
(goto-char (match-end 0))
(setq spread-frame-directory
(expand-file-name (buffer-substring beg (point))))
)
(defun inferior-spread-mode ()
"Major mode for running spread.frames under S/Splus."
(comint-run S-program)
(setq comint-prompt-regexp shell-prompt-pattern)
(setq major-mode 'inferior-spread-mode)
(setq mode-name "Inferior Spread")
(setq mode-line-process '(":%s"))
(setq spread-process (get-buffer-process (current-buffer)))
(set-process-filter spread-process 'comint-output-filter)
(set-variable 'comint-output-filter-functions
'(spread-output-filter
comint-postoutput-scroll-to-bottom)
)
(set-variable 'comint-scroll-to-bottom-on-output "this")
(set-variable 'comint-scroll-show-maximum-output t)
(if (not(file-writable-p ".Data/.Audit"))
(accept-process-output spread-process))
(accept-process-output spread-process)
)
(defun spread-output-filter (str)
"detect errors in S output"
(if (or
(string-match "Dumped" str)
(string-match "Error" str)
)
(progn
(switch-to-buffer-other-window S-buffer)
(comint-show-maximum-output)
(set-variable 'quit-flag t); beeps and writes "quit" in the message area
)
)
)
;(put 'spread-region 'menu-enable 'mark-active)
;(put 'spread-validate-region 'menu-enable 'mark-active)
;(put 'spread-print 'menu-enable '(stringp spread-print-file))
;(put 'spread-alt-print 'menu-enable '(stringp spread-print-file))
;(put 'spread-view 'menu-enable '(stringp spread-print-file))
;(put 'spread-recenter-output-buffer 'menu-enable '(get-buffer "*spread-shell*"))
;(put 'spread-kill-job 'menu-enable '(spread-shell-running))
(defun emacs-menu-print-find (spread-name) "" (interactive)
(spread-print-find spread-name nil)
)
(defun spread-print-find (spread-name update-Registry)
"Place SPREAD-NAME in foreground of S-buffer (*S* or *Splus*),
update .Registry and revert buffer when UPDATE-REGISTRY is t,
print all views of spread.frame associated with SPREAD-NAME in .Registry
to /tmp/spr***** directory, and find or revert all views into emacs buffers."
(interactive)
(set-buffer S-buffer)
(spread-insert
(format "print.find.emacs('%s', update.Registry=%s)"
spread-name (if update-Registry "T" "F")))
(if update-Registry
(save-excursion (spread-find-file ".Registry")))
(spread-print-sprds)
(switch-to-buffer spread-name)
)
(defun spread-print-sprds () "Display in buffers all views of spread.frame"
(interactive)
(save-excursion
(set-buffer "*command*")
(revert-t-t)
(goto-char (point-min))
(while (< (point) (point-max))
(set-buffer "*command*")
(setq beg (point)) (end-of-line)
(setq spread-name-i (buffer-substring beg (point)))
(save-excursion (spread-find-file spread-name-i))
(forward-line)))
)
(defun spread-find-file (spread-name) "Display one view of spread.frame"
(interactive)
(switch-to-buffer spread-name)
(if (buffer-file-name)
(revert-t-t-read-only)
(kill-buffer spread-name)
(find-file (concat spread-directory "/" spread-name))
)
(spread-mode)
)
(define-key spread-mode-map [menu-bar spread ww]
'("ww" . emacs-menu-print-find-ww))
(defun emacs-menu-print-find-ww () "" (interactive)
(emacs-menu-print-find "ww"))
(define-key spread-mode-map [menu-bar spread ww2]
'("ww2" . "\e\e (emacs-menu-print-find \"ww\")"))
(define-key spread-mode-map [menu-bar spread ww3]
'("ww3" . "\M-x eval-expression\C-m (emacs-menu-print-find \"ww\")"))
(defun spread-start () "load emacs spread.frame handler"
(if (not (equal major-mode 'dired-mode)) (set-variable 'quit-flag t))
(setq spread-home-directory (dired-current-directory))
(find-spread-frame-directory)
(kill-buffer "*Command History*")
(if (not spread-directory-p)
(progn (make-directory spread-directory)
(setq spread-directory-p t)))
(setq S-program (read-string "Splus or S? " "Splus"))
(setq S-buffer (concat "*" S-program "*"))
(if (not (get-buffer S-buffer))
(get-buffer-create S-buffer))
(if (get-buffer-process S-buffer) (set-variable 'quit-flag t))
(set-buffer S-buffer)
(cd spread-home-directory)
(inferior-spread-mode)
(spread-insert
(format "attach('%s.Data')" spread-frame-directory))
(spread-insert
(format "emacs.start('%s')" spread-directory))
(find-file spread-command-file)
(spread-find-file ".Registry")
)
;; start it up
(spread-start)

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#-*-Fundamental-*-
# Spreadsheet written in S
# The spreadsheet may be called anything.
# References to cells in the spreadsheet must be called "x".
# Updating is in column order.
# Version 3 classes and methods technology.
as.spread <- function(x)
{
if (is.spread(x)) return(x)
x <- as.array(x)
attr(x,"expr") <- as.expr(x, length=0)
attr(x,"macro") <- as.expr(x, length=0)
attr(x,"before") <- as.expr(x, length=0)
attr(x,"after") <- as.expr(x, length=0)
class(x) <- c("spread", class(x))
x
}
is.spread <- function(x)
inherits(x,"spread")
print.spread <- function(x, ..., quote=F)
{
if (inherits(x, "data.frame")) print.data.frame(x)
else {
class(x) <- class(x)[-match("spread",class(x))]
print.array(x, ..., quote=quote)
}
invisible(x)
}
"[.spread"<-
function(x, ..., drop = F)
{
# Note: We do not retain the spread class!
# If we did, the subscripts on the expr() and macros() would be wrong
#
NextMethod("[", drop=drop)
}
"[.expr" <- function(x, ... , drop=F)
{
# Note: We do retain the expr class.
# The primary use is for printing, so we want the original subscripting.
z <- NextMethod("[", drop=drop)
class(z) <- class(x)
z
}
update.spread <- function(object, ..., force=F)
{
if (force) object <- eval.spread(object, NULL, force=force)
if (length(before(object)))
object <- eval.spread(object, before(object))
if (length(expr(object)))
object <- eval.spread(object, force=force)
if (length(after(object)))
object <- eval.spread(object, after(object))
object
}
eval.spread <- function(object, e, force=F)
{
x <- object
class(x) <- class(x)[-match("spread",class(x))]
if (force) {
.Options$warn <- -1
tmp <- as.numeric(as.matrix(x))
if (!any(is.na(tmp))) x <- tmp
}
if (missing(e)) {
if (inherits(x,"data.frame")) {
e <- expr(object)
if (force)
for (j in 1:ncol(x)) for (i in 1:nrow(x))
x[[i,j]] <- eval(e[i,j])
else
for (j in 1:ncol(x)) for (i in 1:nrow(x)) {
eij <- e[i,j]
if(is.language(eij)) x[[i,j]] <- eval(eij)
}
}
else {
i <- 0
if (force)
for (ei in expr(object))
{i <- i+1; x[i] <- eval(ei)}
else
for (ei in expr(object))
{i <- i+1; if(is.language(ei)) x[i] <- eval(ei)}
}
}
else eval(e)
class(x) <- class(object)
x
}
#usage: x <- macro.eval(x, i)
macro.eval <- function(object, i)
eval.spread(object, macro(x)[i])
"[[<-.spread" <- function(...) do.call("[<-.spread", list(...))
"[<-.spread" <- function(object, ..., value)
{
x <- object
expr(x) <- expression()
class(x) <- NULL
e <- expr(object)
l.e <- length(e)
i.a.v <- is.atomic(substitute(value))
n.cells <- prod(dim(x[..., drop=F]))
if (l.e == 0) {
if (n.cells != 1 || i.a.v )
x[...] <- eval(substitute(value))
else {
e <- as.expr(object)
l.e <- length(e)
}
}
if (l.e != 0) {
if (n.cells != 1) {
e.s.v <- eval(substitute(value, sys.parent()))
x[...] <- e.s.v
e[...] <- e.s.v
}
else {
e[[...]] <- substitute(value)
x[[...]] <- eval(e[[...]])
}
}
attributes(x) <- attributes(object)
class(x) <- class(object)
expr(x) <- e
update.spread(x)
}
print.expr <- function(e, ..., replace.string=F) {
replace <- as.logical(replace.string)
if (length(e) == 0) {
if (replace) cat(replace.string, "<- ")
print(expression())
}
else if (is.null(dim(e))) {
ne <- names(e)
for (i in 1:length(e)) {
nei <- index.value(ne, i)
if (replace) cat(replace.string)
cat(paste("[", nei, "] ", sep=""))
if (replace) cat("<- expression(")
cat(e[i])
if (replace) cat(")")
cat("\n")
}
}
else {
dn <- dimnames(e)
if (is.null(dn)) dn <- list()
for (i in 1:length(dim(e))) {
if (is.null(dn[[i]])) dn[[i]] <- 1:dim(e)[i]
}
dnn <- outer(dn[[1]], dn[[2]], paste, sep=",")
if (length(dn) > 2)
for (i in 3:length(dn))
dnn <- outer(dnn, dn[[i]], paste, sep=",")
for (i in seq(length=length(e))) {
if (replace) cat("x")
cat(paste("[", dnn[i], "] ", sep=""))
if (replace) cat("<-")
cat(paste(" ", e[i], "\n", sep=""))
}
}
invisible(e)
}
as.expr <- function(x, ...) UseMethod("as.expr")
as.expr.default <- function(x, length.x=prod(dim(x))) {
e <- vector(mode="expression", length=length.x)
x <- unclass(x)
if (length.x > 0) {
e <- array(e, dim(x), dimnames(x))
e[] <- x[]
# for (i in 1:length(e)) e[i] <- x[i]
}
class(e) <- "expr"
e
}
as.expr.data.frame <- function(x, length.x=prod(dim(x))) {
e <- vector(mode="expression", length=length.x)
if (length.x > 0) {
e <- array(e, dim(x), dimnames(x))
u.x <- unclass(x)
for (j in 1:ncol(x)) {
uxj <- as.matrix(u.x[[j]])
for (i in 1:nrow(x))
e[i,j] <- uxj[i,1]
}
}
class(e) <- "expr"
e
}
expr <- function(x)
attr(x,"expr")
# "expr<-" is used only when value is a matrix the size of x, or to update
# a subscripted piece of x. It is not a user function.
# Currently used only in "[<-.spread".
"expr<-" <- function(x, value)
{
attr(x,"expr") <- value
x
}
"before<-" <- function(x, value)
{
attr(x,"before") <- value
class(attr(x,"before")) <- "expr"
x
}
"macro<-" <- function(x, value)
{
attr(x,"macro") <- value
class(attr(x,"macro")) <- "expr"
x
}
"after<-" <- function(x, value)
{
attr(x,"after") <- value
class(attr(x,"after")) <- "expr"
x
}
before <- function(x)
attr(x,"before")
macro <- function(x)
attr(x,"macro")
after <- function(x)
attr(x,"after")
expr.rc <- function(x, ...) UseMethod("expr.rc")
expr.rc.default <- function(x, acpab)
{
subs <- paste("[", paste(acpab, collapse=","), "]")
if (length(expr(x))==0) {
x.expr <- paste("x.value(x",subs,")",sep="")
value <- eval(parse(text=x.expr))
}
else {
e.expr <- paste("expr.value(expr(x)", subs, ", x", subs, ")")
value <- eval(parse(text=e.expr))
}
paste("x", subs, " <- ", value, sep="")
}
x.value <- function(x) {
value <-
if (length(x)==1)
as.vector(as.matrix(x[[1]]))
else if (inherits(x,"data.frame"))
lapply(x, function(x) as.vector(as.matrix(x)))
else
as.vector(x)
deparse(value)
}
expr.value <- function(e, x) {
if (inherits(x,"data.frame") &&
(dim(e)[2]>1 || inherits(x[[1]],"factor")))
value <- deparse(lapply(e, function(x) as.vector(as.matrix(x))))
else {
value <- paste(e, collapse=",")
if (length(e) > 1) value <- paste("c(", value, ")", sep="")
}
value
}
index.value <- function(dn, i, deparse.result=T) {
if (i==0) {i <- 0; mode(i) <- "missing"}
if (is.numeric(i) && i>0 && length(dn)) i <- dn[i]
if (deparse.result) deparse(as.vector(i))
else as.vector(i)
}
as.numeric.spread <- function(x)
{
.Options$warn <- -1
tmp <- as.numeric(unclass(x))
tmp <- ifelse(is.na(tmp), 0, tmp)
attributes(tmp) <- attributes(x)
tmp
}
all.numeric <- function(x) {
.Options$warn <- -1
!any(is.na(as.numeric(x)))
}

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# prspread is based on prmatrix
prspread <-
function(x, rowlab = character(0), collab = character(0), quote = T, right = F,
spread.name=deparse(match.call()[["x"]]) )
{
d <- dim(x)
dnames <- dimnames(x)
if(is.null(dnames))
dnames <- list(rowlab, collab)
else {
if(!missing(rowlab))
dnames[[1]] <- as.character(rowlab)
if(!missing(collab))
dnames[[2]] <- as.character(collab)
}
if(length(dnames[[1]]) == 0)
dnames[[1]] <- paste("[", 1:d[1], ",]", sep = "")
else if(length(dnames[[1]]) != d[1])
stop("rowlab is wrong length")
if(length(dnames[[2]]) == 0)
dnames[[2]] <- paste("[,", 1:d[2], "]", sep = "")
else if(length(dnames[[2]]) != d[2])
stop("collab is wrong length")
cbind(c(spread.name,dnames[[1]]), rbind(dnames[[2]], as.matrix(x)))
}
row.ch <- function(x, d=dim(x))
array(1:d[1], d, dimnames(x))
col.ch <- function(x, d=dim(x))
array(rep.int(1:d[2], rep.int(d[1], d[2])), d, dimnames(x))
print.text <- function(x, screen.n, cex=1,
spread.name=deparse(match.call()[["x"]]), clear=T, ...)
{
x.pr <- prspread(x, spread.name=spread.name)
if (!missing(screen.n)) screen(screen.n)
usr <- c(0, ncol(x.pr), 0, nrow(x.pr)) - .5
par(usr=usr)
par(plt=c(0,1,0,1))
if (clear)
polygon(usr[c(1,2,2,1)],usr[c(3,3,4,4)], den=-1,col=0,xaxt="s",yaxt="s")
text(x=as.vector(col.ch(x.pr)-1),
y=as.vector(nrow(x.pr)-row.ch(x.pr)), x.pr, cex=cex, ...)
box()
invisible(x)
}
text.update.spread <- function(xij, row.i, col.j, screen.n, cex=1, x)
{
if (!missing(screen.n)) {screen(screen.n, new=F); par(plt=c(0,1,0,1))}
y <- nrow(x)-row.i
clear.text(x=col.j, y=y)
text(x=col.j, y=y, xij, cex=cex)
box()
invisible(x)
}
cell.rc.text <- function(nrow.x, n=1, type="n")
{
xy <- locator(n, type)
c(row=nrow.x-round(xy$y), col=round(xy$x))
}
clear.text <- function(x,y)
polygon(x-.5+c(0,1,1,0), y-.5+c(0,0,1,1), den=-1, col=0, border=F,
xaxt="s", yaxt="s")
print.update.text <- function(x, ..., x.old, screen.n, cex=1,
spread.name=deparse(match.call()[["x"]]))
{
if(missing(x.old)) return(invisible(print.text(x, screen=screen.n,
cex=cex, spread.name=spread.name)))
if (!missing(screen.n)) {screen(screen.n, new=F); par(plt=c(0,1,0,1))}
diff.x <- as.vector(x != x.old)
xx <- col(x)[diff.x]
yy <- nrow(x)-row(x)[diff.x]
for (i in seq(along=xx)) clear.text(xx[i], yy[i])
box()
text(x=xx, y=yy, as.vector(unlist(x))[diff.x], cex=cex)
invisible(x)
}
control.text <- function(x, screen.n, cex=1,
spread.name=deparse(match.call()[["x"]]))
{
#This is a real function that does its own work
if (!missing(screen.n)) {screen(screen.n, new=F); par(plt=c(0,1,0,1))}
x.old <- x[,]
rc <- cell.rc.text(nrow(x))
command <- expr.rc(x, rc)
cat("> ", command, "\n", sep="", file="")
eval(parse(text=readline()))
if (!missing(screen.n)) {screen(screen.n, new=F); par(plt=c(0,1,0,1))}
print.update.text(x, x.old=x.old, cex=cex, spread.name=spread.name)
# print.text(x, cex=cex, spread.name=spread.name)
invisible(x)
}
#text usage
# device() # for example, x11(), or motif(), or win.graph()
# x <- my.spread # copy my.spread to x
##loop
# print.text(x) # work with x
# x <- control.text(x, screen) # screen is optional
##end loop
# my.spread <- x # copy revised x back to my.spread

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The emacs spread.frame device handler
Richard M. Heiberger
There are two variants in the usage of this emacs spread.frame device
handler. Both use the same command file: S-spread.el. One variant is
stand-alone. The other works with S-mode. Both are written in emacs
19.29 to use the comint.el package. They will not work in emacs 18.
A. Stand-alone Usage
1. Create a .Data subdirectory in the directory you will be using, say
`myclass' and `myclass/.Data'. Get into the dired buffer of the
directory `myclass'. Any other buffer will cause the terminal to beep.
2. From the dired buffer enter (on my computer):
M-x load-file <RET> /disk5/rmh/sprd3d/S-spread.el
Edit the pathname for your computer. Any other buffer than the dired
buffer will cause the terminal to beep. You will be prompted "S or
Splus? ". "Splus" has been filled in as the default. Edit the
command name if necessary, inserting a full pathname if appropriate,
then hit carriage return.
This leaves the window showing the .Registry buffer in Spread mode. If
you previously had a .Registry in that directory, it appears in the
buffer. If you have never used the spread.frame handler in that
directory, then a new .Registry has been created for you.
You also have a buffer called *Splus* (or *S*) in Inferior Spread mode
in which Splus (or S) is running.
NOTES for Stand-alone Version
If you were previously running Splus in buffer *Splus* in Inferior Spread mode
and accidentally killed the Splus process (for example, with the q()
command), you are still using that buffer and the Splus process has been
restarted.
If you have a buffer named *Splus* not associated with a process, for
example a file you are editing, emacs will use that buffer for the
Inferior Spread mode.
If you have a running Inferior Spread process, a shell process, or any
other process, in a buffer named *Splus*, the terminal will beep.
B. S-mode Usage
1. Create a .Data subdirectory in the directory you will be using, say
`myclass' and `myclass/.Data'. Get into the dired buffer of the
directory `myclass' and start S-mode with M-x S.
2. From the *S* buffer that S-mode has started enter (on my computer):
M-x load-file <RET> /disk5/rmh/sprd3d/S-spread.el
Edit the pathname for your computer. Any other buffer than the *S* buffer
will cause the terminal to beep.
This leaves the window showing the .Registry buffer in Spread mode.
If you previously had a .Registry in that directory, it appears in the
buffer. If you have never used the spread.frame handler in that
directory, then a new .Registry has been created for you.
NOTES FOR BOTH VERSIONS
S/Splus thinks it is in charge and does not know about emacs. Emacs with
comint attempts to coordinate its timing with Splus by sending commands to
Splus with (comint-send-input) and waiting for their completion with
(accept-process-output). If for any reason an out-of-date display of a
buffer appears, use ^Cv to bring up the current display. If things
still look wrong, go to the *Splus* buffer and force a current display
with ^Cr. You will be requested to type the name of the object to be
displayed in the minibuffer. All buffers displaying views of that
object, and the .Registry buffer will be updated.
Either usage of the spread.frame functions and the command file
S-spread.el works with S Version 3, S Version 4, or Splus 3.3.
3. Start working in the .Registry buffer. Move to the macro section.
a. Do "f" or [mouse-2] on the name of the spread.frame you want to see.
Spread.frame names are listed in the macro section of the display.
b. If no names appear, then you must add them.
4. To add more spread.frames, for example the "xy" spread.frame, where the
"xy" spread.frame already exists in the .Data:
a. Move to the *Splus* buffer. Enter "^Cr".
b. The minibuffer will ask you for the name of a spread.frame.
c. Enter the name of the object (for example xy (no quotes))
or an expression for a 2-way rectangular slice (xy[,,2]) of a 3-way object.
d. The "xy" spread.frame will appear in the buffer.
5. To add a three-way spread.frame to the display from the *Splus* buffer
a. Create a 3-way array and make it a spread.frame:
xs <- as.spread(array(1:12,dim=c(2,3,2)))
b. Print it to the /tmp/spraxxxxx directory with:
print.update.emacs.3d(xs)
c. Move the cursor to the .Registry buffer. Place the cursor on the
.Registry entry and press RETURN twice. The names for the slices
will now appear in the **macro** section (if not, use ^Cv).
d. Place the cursor on each of the slices' names and press f.
e. The entire spread.frame can also be displayed by pressing "f"
or [mouse-2] on its name.
The window displaying the entire spread.frame is not active.
Pressing RETURN will beep.
f. The slices are active. Pressing RETURN on a cell entry will update
the entire spread.frame and the display of the slices. Pressing RETURN
on a macro keyword or a macro name in a slice buffer will activate the
display and update of the macro for the entire spread.frame.
6. Move between spread.frames with ^X o.
7. To edit a spread.frame, place the cursor on a cell and press ENTER
or [mouse-3]. The expression associated with the cell will be
displayed in the mini-buffer. Edit it and press ENTER. The
spread.frame in Splus will be updated, and all views of the object in
emacs buffers will be updated.
8. To execute a macro, place the cursor on the macro name and enter ^Cc.
Don't use print() or cat() in macros; sink() is in use.
The graphics device can be used for rectangular spread.frames, but does
not yet work with three-way spread.frames.
To use a graphics device for the spread.frame display (but no macros yet).
9. Open a graphics device: x11(), iris4d(), motif(), etc.
10. Add the names of the spread.frames to .Registry as described above.
11. To place a spread.frame in the graphics device, put the cursor on the
spread.frame name in the **macro** listing in .Registry, and press ^Cp
The minibuffer will display
> xy <- print.text( xy )
Press ENTER and the device will show the xy spread.frame.
12. To change a value in a spread.frame in the graphics device, put the
cursor on the spread.frame name in the **macro** listing in .Registry,
and press ^Cs
The minibuffer will display
> xy <- control.text( xy )
Press ENTER, move the cursor into the graphics window, and click when the
crosshair is on the cell you wish to change. Place the cursor in the *Splus*
buffer, move to the end of the buffer by pressing ESC > . You will see
the expression to be edited (prefixed with a ">") on the next to the last
line. Move the cursor to that line, edit the value, and press ENTER.
The graphics window will be updated.
13. You can edit any emacs buffer spread.frame by switching to its
buffer and pressing ENTER or [mouse-3] on the appropriate entry. You
can edit any spread.frame in the graphics device, by switching to the
.Registry buffer, confirming that the spread.frame is in the graphics
window (or putting it there with ^Cp), and then entering ^Cs on the
macro name in the .Registry buffer that matches the spread.frame.
14. There is an additional feature in the spread.frame interface that
is very useful for numerical rows or columns. When the cursor is
placed on the dimnames row or column, the entire column or row is made
available in the mini-buffer. Warning: expr() in the row or column
will be evaluated and will no longer be expr().
15. Character data. Character matrices work well as spread.frames.
16. Warning: character or factor columns in data.frames.
S likes to coerce character columns in data.frames to factors.
Updating an entire factor column, or an entire row containing factor
columns, may be dangerous because the revised values may not be in the
levels(). The entire column may be replaced with NA values. Updating
of individual character values is fine in character arrays that are
not data.frames, or in data.frames where the length(expr(x)) ==
prod(dim(x)). To get a character column into a data frame use
my.frame$char <- character.value # remains character
Using either
my.frame[,"char"] <- character.value # coerced to factor
my.frame <- cbind(my.frame,character.value) # coerced to factor
won't work. Either of those forms coerces the values to factor.

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modify the test with a change.
SJE: simple change.

4
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Xemacs: Rodney Sparapani -- no longer
Debian: Dirk Eddelbuettel <edd@debian.org>
RPM: Tom Moertel <tom@moertel.com>
SuSe: Detlef Steuer <steuer@hsu-hh.de>

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Package: pkg1
Type: Package
Title: A sample package for testing ESS
Version: 1.0
Date: 2014-01-20
Author: ESS Core
Maintainer: <yourfault@somewhere.net>
Description: A sample package for testing ESS
License: GPL-2

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export(D1tr)

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D1tr <- function(y, x = 1)
{
## Purpose: discrete trivial estimate of 1st derivative.
## ----------------------------------------------------------------------
## Arguments: x is optional; let's say we don't like "'"
## ----------------------------------------------------------------------
## Author: Martin Maechler, ~ 1990
n <- length(y)
if(length(x) == 1)
c(y[2] - y[1], 0.5 * (y[-(1:2)] - y[-((n-1):n)]), y[n] - y[n-1])/x
else {
## Here, already using non-matching apostrophes, but developer mode
## still seems to work ..
if(n != length(x)) stop("lengths' of x & 'y' must equal")
if(is.unsorted(x)) stop("'x' must be sorted !")
c(y[2] - y[1], 0.5 * (y[-(1:2)] - y[-((n-1):n)]), y[n] - y[n-1]) /
c(x[2] - x[1], 0.5 * (x[-(1:2)] - x[-((n-1):n)]), x[n] - x[n-1])
}
}

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\name{D1tr}
\alias{D1tr}
\title{Numerical Derivatives of (x,y) Data}
\description{
Compute the numerical derivatives of \eqn{f()} given
observations \code{(x[i], y ~= f(x[i]))}.
\code{D1tr} is the \emph{\bold{tr}ivial} discrete first derivative
using simple difference ratios.
This is \bold{far} from optimal and only kept here for reference.
}
\usage{
D1tr(y, x = 1)
}
\arguments{
\item{x,y}{numeric vectors of same length, supposedly from a model
\code{y ~ f(x)}. For \code{D1tr()}, \code{x} can have length one
and then gets the meaning of \eqn{h = \Delta x}.}
}
\value{
\code{D1tr()} returns a numeric vector of the length of \code{y}.
}
\author{Martin Maechler, in 1992 (for S).}
\seealso{\code{\link[sfsmisc]{D1D2}} which directly uses the 2nd
derivative of the smoothing spline; \code{\link{smooth.spline}}.
}
\examples{
set.seed(330)
x <- sort(runif(500, 0,10))
y <- sin(x) + rnorm(500)/100
f1 <- D1tr(x=x,y=y)
plot(x,f1, ylim = range(c(-1,1, f1)))
curve(cos(x), col=3, add= TRUE)
}
\keyword{smooth}

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}
{\info{\title Help}{\author Rodney Sparapani}{\creatim\yr2001\mo4\dy26\hr10\min22}{\operator Rodney Sparapani}{\revtim\yr2001\mo4\dy26\hr10\min25}{\printim\yr2004\mo1\dy27\hr10\min21}{\comment StarWriter}{\vern6450}}\deftab720
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\par \trowd\trqr\trrh863\trpaddft3\trpaddt0\trpaddfl3\trpaddl0\trpaddfb3\trpaddb0\trpaddfr3\trpaddr0\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx1105\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx2201\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx3308\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx4423\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx4958\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx6064\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx7180\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx8285\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx9401\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx9973\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx11079\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx12194\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx13300\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clbrdrr\brdrs\brdrw1\brdrcf1\clvertalt\cellx14400
\pard\intbl\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F1\line Help}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F2}
\par {\loch\f2\fs20\lang1033\i0\b0 Refresh}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F3\line Submit}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F4\line Program}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F5\line Log}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F6\line Listing}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F7\line Text}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F8\line Shell}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F9}
\par {\loch\f2\fs20\lang1033\i0\b0 View}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F10}
\par {\loch\f2\fs20\lang1033\i0\b0 Log-Toggle}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F11}
\par {\loch\f2\fs20\lang1033\i0\b0 File-type-2}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F12\line Graph}
\cell\row\pard \pard\plain \ltrpar\s1\ql\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\par {\loch\f2\fs20\lang1033\i0\b0 PC key definitions for PC/Mac keyboard}
\par
\par \trowd\trqr\trrh863\trpaddft3\trpaddt0\trpaddfl3\trpaddl0\trpaddfb3\trpaddb0\trpaddfr3\trpaddr0\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx1105\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx2201\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx3308\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx4423\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx4958\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx6064\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx7180\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx8285\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx9401\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx9973\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx11079\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx12194\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx13300\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clbrdrr\brdrs\brdrw1\brdrcf1\clvertalt\cellx14400
\pard\intbl\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F1\line Help}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F2}
\par {\loch\f2\fs20\lang1033\i0\b0 Refresh}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F3\line Shell}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F4\line Text}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F5\line Program}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F6\line Log}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F7\line Listing }
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F8\line Submit}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F9}
\par {\loch\f2\fs20\lang1033\i0\b0 View}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F10}
\par {\loch\f2\fs20\lang1033\i0\b0 Log-Toggle}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F11}
\par {\loch\f2\fs20\lang1033\i0\b0 File-type-2}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F12\line Graph}
\cell\row\pard \pard\plain \ltrpar\s1\ql\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\par {\loch\f2\fs20\lang1033\i0\b0 Unix key definitions for Thinkpad keyboard}
\par
\par \trowd\trqr\trrh863\trpaddft3\trpaddt0\trpaddfl3\trpaddl0\trpaddfb3\trpaddb0\trpaddfr3\trpaddr0\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx1588\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx3177\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx4768\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx5624\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx7212\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx8803\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx10408\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx11998\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx12823\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clbrdrr\brdrs\brdrw1\brdrcf1\clvertalt\cellx14400
\pard\intbl\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F2}
\par {\loch\f2\fs20\lang1033\i0\b0 Refresh}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F3\line Submit}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F4\line {\fs18 Program}}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F5\line Log}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F6\line Listing}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F7\line Text}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F8\line Shell}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F9}
\par {\loch\f2\fs20\lang1033\i0\b0 View}
\cell\row\pard \pard\plain \ltrpar\s1\ql\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\par {\loch\f2\fs20\lang1033\i0\b0 PC key definitions for Thinkpad keyboard}
\par
\par \trowd\trqr\trrh863\trpaddft3\trpaddt0\trpaddfl3\trpaddl0\trpaddfb3\trpaddb0\trpaddfr3\trpaddr0\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx1588\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx3177\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx4768\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx5624\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx7212\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx8803\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx10408\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx11998\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx12823\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clbrdrr\brdrs\brdrw1\brdrcf1\clvertalt\cellx14400
\pard\intbl\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F2}
\par {\loch\f2\fs20\lang1033\i0\b0 Refresh}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F3\line Shell}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F4\line Text}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F5}
\par \pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs18\langfe255\loch\f2\fs18\lang1033 {\loch\f2\fs18\lang1033\i0\b0 Program}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F6\line Log}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F7\line Listing}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F8\line Submit}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F9}
\par {\loch\f2\fs20\lang1033\i0\b0 View}
\cell\row\pard \pard\plain \ltrpar\s1\ql\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\par {\loch\f2\fs20\lang1033\i0\b0 Unix key definitions for Sun keyboard (cut out the numbered boxes and leave the dividers between F4/F5 and F8/F9)}
\par
\par
\par \trowd\trqr\trrh1070\trpaddft3\trpaddt0\trpaddfl3\trpaddl0\trpaddfb3\trpaddb0\trpaddfr3\trpaddr0\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx1105\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx2201\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx3308\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx4423\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx4958\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx6064\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx7180\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx8285\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx9401\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx9973\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx11079\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx12194\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx13300\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clbrdrr\brdrs\brdrw1\brdrcf1\clvertalt\cellx14400
\pard\intbl\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F1}
\par \pard\plain \intbl\ltrpar\s1\ql\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F2}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F3}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F4}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F5}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F6}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F7}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F8}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F9}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F10}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F11}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F12}
\cell\row\pard \pard\plain \ltrpar\s1\ql\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 Help Refresh Submit Program Log Listing Text Shell Viewtable Log-Toggle File-type-2 Viewgraph}
\par
\par {\loch\f2\fs20\lang1033\i0\b0 PC key definitions for Sun keyboard (cut out the numbered boxes and leave the dividers between F4/F5 and F8/F9)}
\par
\par
\par \trowd\trqr\trrh1070\trpaddft3\trpaddt0\trpaddfl3\trpaddl0\trpaddfb3\trpaddb0\trpaddfr3\trpaddr0\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx1105\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx2201\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx3308\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx4423\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx4958\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx6064\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx7180\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx8285\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx9401\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx9973\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx11079\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx12194\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clvertalt\cellx13300\clbrdrt\brdrs\brdrw1\brdrcf1\clbrdrl\brdrs\brdrw1\brdrcf1\clbrdrb\brdrs\brdrw1\brdrcf1\clbrdrr\brdrs\brdrw1\brdrcf1\clvertalt\cellx14400
\pard\intbl\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F1}
\par \pard\plain \intbl\ltrpar\s1\ql\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F2}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F3}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F4}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F5}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F6}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F7}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F8}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F9}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F10}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F11}
\cell\pard\plain \intbl\ltrpar\s1\qc\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 \line F12}
\cell\row\pard \pard\plain \ltrpar\s1\ql\rtlch\af2\afs20\lang255\ltrch\dbch\af2\afs20\langfe255\loch\f2\fs20\lang1033 {\loch\f2\fs20\lang1033\i0\b0 Help Refresh Shell Text Program Log Listing Submit Viewtable Log-Toggle File-type-2 Viewgraph}
\par }

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@@ -0,0 +1,283 @@
Stephen Eglen's notes on future changes to ESS -*- org -*-
* Problem with ESS infrastructure and Martin away? Email isg@math.ethz.ch
* ess-history-file
needs documenting and possibly updating:
From: Stephen Eglen <S.J.Eglen@damtp.cam.ac.uk>
To: Erik Iverson <eriki@ccbr.umn.edu>
Comments: In-reply-to Erik Iverson <eriki@ccbr.umn.edu>
message dated "Wed, 20 Apr 2011 09:36:26 -0500."
Date: Tue, 26 Apr 2011 09:01:29 +0100
Cc: Feng Li <m@feng.li>, ess-help@stat.math.ethz.ch
Subject: Re: [ESS] ESS and .Rhistory
Sender: ess-help-bounces@r-project.org
Dear Erik, Feng,
Thanks for this -- I was blissfully unaware about this persistence of
history across R sessions. Howabout if we change the semantics of
ess-history-file to be:
nil -- do not attempt to read/write a history file
t -- use the default naming scheme for loading the history
"some.string" -- use this value as the filename.
Stephen
> Feng,
>
> On 04/20/2011 09:00 AM, Feng Li wrote:
> > Dear list,
> >
> > I tried to change the ESS default R history to a permanent file so
> > that ESS does not generate .Rhistory everywhere. I tried both
> >
> > (setq ess-history-directory "~/.R/history")
> >
> > and
> >
> > (setq ess-history-file "~/.R/history/.Rhistory")
>
> If I recall correctly, it's because of the way the ess-history-file
> variable is set in the ESS code. The following works for me:
>
> (defun ei-no-rhistory ()
> (setq ess-history-file "/dev/null"))
>
> (add-hook 'inferior-ess-mode-hook 'ei-no-rhistory)
* completion of functions within buffers
From: Stephen Eglen <S.J.Eglen@damtp.cam.ac.uk>
To: ESS-help@stat.math.ethz.ch
Date: Tue, 22 Jun 2010 14:00:25 +0100
Cc: Stephen Eglen <S.J.Eglen@damtp.cam.ac.uk>
Subject: [ESS] request for comments: completion within .R buffers
Sender: ess-help-bounces@stat.math.ethz.ch
Rodney recently kindly polled ess-help, and a summary of the results can
be seen in the SVN sources at:
https://svn.r-project.org/ESS/trunk/rsn.txt
One thing that came up was (thanks Ista Zhan):
Function/variable completion in script files (maybe this already is
supposed to work, but for me completion only works in interactive
sessions).
Below is some suggested code to implement this, based on a hint from
Deepayan. If you press TAB at the start of the line, you still get
standard indentation, but if you are already typing something, e.g.
write.t
then hitting TAB will complete to write.table
Hitting TAB again, will then bring up a *Completions* window showing
(for me):
Possible completions are:
write.table
write.table0
I don't like the *Completions* window hanging around, but apart from
that, is that the sort of completion people would like? Erik Iverson
mentioned something related:
I think ESS is very feature complete at this point. The only thing
I've looked at that seems interesting is some sort of 'intellisense'
feature that uses R's built-in completion mechanism to temporarily
display available completions using something like company-mode,
autocomplete, or completion-ui. I had at one point something that
almost worked, but I believe the library it was built in,
company-mode, has now changed significantly.
but I've not explored those options.
Code/ideas welcome!
Stephen
----------------------------------------------------------------------
(defun ess-indent-or-complete (&optional whole-exp)
(interactive "P")
"Function bound to TAB key in R mode buffers.
If at the start of the line, or numeric prefix provided, call
`ess-indent-command', otherwise try to complete object at point."
(if (or whole-exp
(save-excursion
(skip-chars-backward " \t")
(bolp)))
(ess-indent-command whole-exp)
(ess-complete-object-name)))
(add-hook 'ess-mode-hook
'(lambda () (local-set-key "\t" 'ess-indent-or-complete)))
* ess-eldoc.el
** Switch to use R-mode-hook, rather than ess-mode-hook
** Document in the info node.
* Debugger
Would like to implement a debugger akin to Norm Matloff's work:
http://cran.r-project.org/web/packages/edtdbg/index.html
http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/
Norm posted that he had started work on ESS, but had to abandon it.
* Comint so slow? ess-eval-visibly-p should be t again.
Why is comint so slow when passing code line by line? Markus Triska
recently looked at this:
To: ess-help@stat.math.ethz.ch
connect(): No such file or directory
From: Markus Triska <markus.triska@gmx.at>
Date: Sun, 16 May 2010 13:59:57 +0200
Subject: Re: [ESS] ESS on Mac slower than R.app?
Sender: ess-help-bounces@stat.math.ethz.ch
Hi Rodney,
Rodney Sparapani <rsparapa@mcw.edu> writes:
> I think if you update to the latest version of ESS this problem will
> go away. See the previous discussion of a very similar GNU Emacs bug
> fix at https://stat.ethz.ch/pipermail/ess-bugs/2009q4/000584.html
I think ess-eval-visibly-p should remain true by default, as it is quite
useful. If you change the accept-process-output call in
ess-eval-linewise to:
(accept-process-output sprocess 0 timeout-ms)
(the difference being that you explicitly state to wait for input from
"sprocess"), the test case works instantly also with ess-eval-visibly-p.
All the best,
Markus
* Funny indentation if semicolon follows brace:
From: Stephen Eglen <S.J.Eglen@damtp.cam.ac.uk>
To: Paul Burkander <paul@burkander.com>
Comments: In-reply-to Paul Burkander <paul@burkander.com>
message dated "Sat, 04 Jun 2011 10:17:03 -0400."
Date: Mon, 06 Jun 2011 10:35:27 +0100
Cc: ess-help@r-project.org
Subject: Re: [ESS] ess-indent-exp follow OWN style?
Sender: ess-help-bounces@r-project.org
> I think it must be ess-electric-brace, and I think it warrants a bug report.
>
> The behavior is the same in R and Stata (though I don't know if it
> would ever come up in R)
>
> Typing any line (excluding comments) that ends in { sets the
> indentation of the next line to ess-indent-level
> Typing any line (excluding comments) that ends in {; sets the
> indentation of the next line to so that the first character is below
> the preceding semicolon.
>
> I know basically nothing about Lisp, otherwise I'd like to try to
> debug this thing.  It seems like an important replicable issue that
> warrants a bug report.
Thanks; I can see this behaviour in R mode. As I don't think its a
common idiom in R to write something like
for (i in seq) {;
...
I'm afraid its not high enough on my priority list to fix right now
(sorry, too many other things already need fixing in ESS), but
I will make a note of it. Is this biting other users?
Stephen
** is ess-electric-brace working okay? should reindent line?
* Handing the *ESS* buffer
Is the *ESS* buffer necessary for end users? If not, have a toggle to
switch it off.
From: Stephen Eglen <S.J.Eglen@damtp.cam.ac.uk>
Date: Mon, 6 Jun 2011 22:12:08 +0100
> Re: the *ESS* buffer, how much of a pain is it? I recall also
> finding it a bit offputting seeing this many years ago, and in all
> my years of developing ESS, I for one have yet to find reason of
> inspecting it! I imagine other developers may differ -- but one
> thing I could suggest to other core members is having a variable
> to inhibit this buffer?
This could be as simple as having a variable ess-dribble-buffer
which if nil, means that the buffer is not created, otherwise, the
variable contains (as a string) the name of the buffer to use, which
defaults to "*ESS*". It could even be " *ESS*" so that it doesn't
appear in buffer lists, but is there and will be included into
reports generated by ess-submit-bug-report.
* Add ess-r-versions-list
Subject: Re: [ESS] Customisation of ess-r-versions or ess-r-versions-list
From: John Maindonald <john.maindonald@anu.edu.au>
Date: Thu, 18 Aug 2011 10:19:44 +1000
Cc: ess-help@stat.math.ethz.ch
To: Stephen Eglen <S.J.Eglen@damtp.cam.ac.uk>
On 18/08/2011, at 5:38 AM, Stephen Eglen wrote:
>> Yes,
>> (setq ess-s-versions-list
>> '( ("R64" "/usr/bin/R64")
>> ("R32" "/usr/bin/R32")))
>> works. The buffer for R64 is however called *S+6*. No doubt there is
>> some variable that one can set that will fix this; I have not
>> investigated.
> I don't recall ever doing this for R, but this was quite a few years
> ago. Did it ever work for you in earlier versions of ESS?
The lines that I had commented out had 'ess-r-versions-list'. If this variable
has never been available, this would be something that I tried by analogy
with 'ess-s-versions-list' and never did work.
If 'ess-s-versions-list' is to stay, it would seem to be cleanest to have a
matching 'ess-r-versions-list' also, following the precedent of
'ess-s-versions' and 'ess-r-versions'. An advantage of this way of doing
things (an 'ess-r-versions-list'), for some users at least, is that it is explicit
about the command line statement that is invoked.
> One can have defvar in place of setq. Does it matter which one uses?
> Better to use setq -- as it will always update the value. By contrast:
>
> (defvar apple 1)
> (defvar apple 2)
>
> Evaluate both lines above, in order, and check "apple" -- it has the
> value 1.
>
> Stephen
John Maindonald email: john.maindonald@anu.edu.au
phone : +61 2 (6125)3473 fax : +61 2(6125)5549
Centre for Mathematics & Its Applications, Room 1194,
John Dedman Mathematical Sciences Building (Building 27)
Australian National University, Canberra ACT 0200.
http://www.maths.anu.edu.au/~johnm
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### Example modified from Paul Johnson's post to ESS-help, Nov.25, 2013
op <- options("max.print")
##' construct (random) character vector of length n, of about 10 characters each
mkCh <- function(n) {
if(getOption("max.print") <= n) options(max.print = n + 1) ## <-
if(n == 10) stop("error's message with apostrophe - work's in developer mode")
N <- pmin(26,pmax(1, rpois(n, 10)))
cbind(vapply(N, function(m) paste(sample(letters, m), collapse=""), ""))
}
set.seed(1)
y <- mkCh(9999)
system.time(print(y))
## R CMD BATCH slow-long-output.R && grep -A 1 -B 1 '^ *user *sys' slow-long-output.Rout
## user system elapsed
## 0.059 0.010 0.070 -- MM@lynne R CMD BATCH
## 0.040 0.014 12.762 -- MM@lynne(2015) ESS 15.09-1 [git: dd226e2027..]
## 0.027 0.027 1.945 -- MM@lynne(2015) ESS 14.09 [svn: 6041]
## 0.120 0.138 3.225 -- MM@lynne(2013-12) ESS 13.09-1 [svn: 5930]
##---
## 0.124 0.097 52.540 -- MM@lynne ESS svn r 5909; incl font-locking, tracebug
## 0.128 0.080 57.305 ditto
## 0.139 0.088 54.770 -- sfs@lynne ESS 13.09 (emacs 24.3.1 GTK+)
## --
## 0.102 0.075 4.685 -- MM@lynne ESS 5.14 (emacs 24.3.1 incl font-lock!)
## 0.091 0.078 4.683 -- " ESS 12.04-4 [rev. 4896 (2012-06-07)]
## 0.123 0.063 4.638 -- " ESS 12.09-2 [rev. 5395 (2013-01-10)]
## 0.117 0.118 3.358 -- " ESS 13.05 [rev. 5574 (2013-05-14)]
## ^^^^^ clearly a bit faster !
set.seed(23456)
y <- mkCh(50000)
system.time(print(y))
## user system elapsed
## 0.255 0.089 0.345 -- BATCH MM@lynne
## 0.035 0.138 27.935 -- MM@lynne(2015) ESS 15.09-1 [git: dd226e2027..]
## .... but sometimes also fast, or considerably slower:
## 0.049 0.112 1.037
## 0.036 0.129 103.253
## 0.157 0.107 11.356 -- MM@lynne(2015) ESS 14.09 [svn: 6041]
## 0.685 0.369 1664.557 -- MM@lynne ESS svn r 5909 ...
## 0.760 0.398 1643.608 -- ..@lynne ESS 13.09
## 0.590 0.510 33.349 -- " ESS 13.05 [rev. 5574 (2013-05-14)]
## 0.565 0.548 28.251 " "
## 0.598 0.450 27.804 " "
## Don't even think of trying this with ESS, currently:
y <- mkCh(200000)
system.time(print(y))
## user system elapsed
## 1.013 0.284 1.300 -- BATCH MM@lynne
options(op)