[Rd] write.csv (PR#7992)
The write.csv() function is currently implemented as
function (..., col.names=NA, sep=",", qmethod="double")
{
write.table(..., col.names=NA, sep=",", qmethod="double")
}
Surely, it should be
function (..., col.names=NA, sep=",", qmethod="double")
{
write.table(..., col.names=col.names, sep=sep, qmethod=qmethod)
}
so that the user arguments serve a purpose. This notion is reflected in
the implementation of read.csv(), for example, where sep=sep, quote=quote,
etc.
Arni
R 2.1.1pat 2005-07-04 on WinXP
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[Rd] SSD() documentation (PR#7993)
There are a couple of harmless typos in the documentation for the stats::SSD function, where "varianve" should be "variance" "followint" should be "following" Arni R 2.1.1pat 2005-07-04 on WinXP __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] yaxs in bxp() (PR#8072)
It would be easy to add 'yaxs' support to bxp(), which can aid visual comparison when the lower limit is zero. The two lines from boxplot.R that would change are: plot.window(ylim=c(0.5,n+0.5), xlim=ylim, log=log) to plot.window(ylim=c(0.5,n+0.5), xlim=ylim, xaxs=pars$yaxs, log=log) and plot.window(xlim=c(0.5,n+0.5), ylim=ylim, log=log) to plot.window(xlim=c(0.5,n+0.5), ylim=ylim, yaxs=pars$yaxs, log=log) Boxplots already respond to a global par(yaxs="i"), and I think users would appreciate support for the local graphical parameter as well. Thanks, Arni R 2.1.1-patched on WinXP __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] pch=NA in bxp.Rd (PR#8073)
I'd like to iterate my earlier request (#7737) to change the documentation
for bxp().
The argument outpch=" " needs to be replaced with outpch=NA in two places.
I actually wrote this part of the documentation myself at one point, but
have now realized that pch=NA and pch=" " are not the same:
x <- split(rlnorm(26e4), letters)
## NA generates small file
postscript("na.ps");boxplot(x,outpch=NA); dev.off()
## Space generates large file
postscript("space.ps"); boxplot(x,outpch=" "); dev.off()
Thank you,
Arni
R 2.1.1-patched on WinXP
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[Rd] bxp.Rd typo (PR#8153)
Hi. There's a minor typo in bxp.Rd: whiskco:l should be whiskcol: Cheers, Arni R 2.1.1pat on WinXP __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] pairs(oma) warnings (PR#8252)
Unlike R 2.1.1, version 2.2.0 generates warnings when an 'oma' argument as passed to pairs(): A <- rnorm(100) B <- rnorm(100) pairs(cbind(A,B))# no warning pairs(cbind(A,B), oma=c(6,8,10,12)) # warnings in R 2.2.0 I think pairs() should draw the plot quietly, without warnings. Can't see anything in the documentation indicating that an 'oma' argument should not be passed in this way. Thanks, Arni R 2.2.0pat on WinXP __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] weighted.mean uses zero when na.rm=TRUE (PR#14032)
The weighted.mean() function replaces NA values with 0.0 when the user specifies na.rm=TRUE: x <- c(101, 102, NA) mean(x, na.rm=TRUE) # 101.5, correct weighted.mean(x, na.rm=TRUE)# 67.7, wrong weighted.mean(x, w=c(1,1,1), na.rm=TRUE)# 67.7, wrong weighted.mean(x, w=c(1,1,1)/3, na.rm=TRUE) # 67.7, wrong The weights are normalized w<-w/sum(w) before removing the NA values, effectively replacing x[is.na(x)]<-0. This bug was introduced between versions 2.9.2 and 2.10.0. Thanks, Arni __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Alphanumeric tools::file_path_sans_ext() (PR#14050)
The file_path_sans_ext() function in the 'tools' package does not handle
alphanumeric file extensions correctly:
require(tools)
file_path_sans_ext("song.txt") # song, correct
file_path_sans_ext("song.mp3") # song.mp3, wrong
The help page states that "only purely alphanumeric extensions are
recognized", which I had expected. To fulfill this, the function body
should be
sub("([^.]+)\\.[[:alnum:]]+$", "\\1", x)
instead of the current definition:
sub("([^.]+)\\.[[:alpha:]]+$", "\\1", x)
Thanks,
Arni
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[Rd] Model frame when LHS is cbind (PR#14189)
The model frame shows the response and predictors in a data frame with
nicely labelled columns:
fm <- lm(wt~qsec+log(hp)+sqrt(disp), data=mtcars)
model.frame(fm) # ok
When the left hand side consists of more than one response, those response
variables still look good, inside a matrix:
fm <- lm(cbind(qsec,hp,disp)~wt, data=mtcars)
model.frame(fm)[[1]] # ok
A problem arises when some of the response variables are transformed:
fm <- lm(cbind(qsec,log(hp),sqrt(disp))~wt, data=mtcars)
model.frame(fm)[[1]] # ugh, missing column names
The model frame is useful for many things, even more so when all column
names are legible. Therefore I propose adding two new lines to
model.frame.default() between lines 371 and 372 in
R-patched_2010-01-12/src/library/stats/R/models.R:
varnames <- sapply(vars, deparse, width.cutoff = 500)[-1L]
variables <- eval(predvars, data, env)
NEW if (is.matrix(variables[[1L]]))
NEW colnames(variables[[1L]]) <- as.character(formula[[2L]])[-1L]
if (is.null(rownames) && (resp <- attr(formula, "response")) >
0L) {
With this fix, the above example returns legible column names:
fm <- lm(cbind(qsec,log(hp),sqrt(disp))~wt, data=mtcars)
model.frame(fm)[[1]] # nice column names
I hope the R development team can either commit this fix or improve it.
Thanks,
Arni
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[Rd] Matrix dimnames crash (PR#13361)
In Windows XP, the matrix() function crashes the program when 'dimnames' is an empty list: matrix(1:4, nrow=2, dimnames=list()) # R has encountered a problem and needs to close ... This bug is specific to WinXP, as Linux64 handles this situation more gracefully: matrix(1:4, nrow=2, dimnames=list()) Error in matrix(1:4, nrow = 2, dimnames = list()) : invalid type (environment) for 'dimnames' (must be a vector) Thanks, Arni R 2.8.0-patched on WinXP __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] boxplot ignores 'boxfill' (PR#9352)
The boxplot.default() function ignores argument 'boxfill' passed by user:
x <- rnorm(100)
boxplot(x, boxfill="blue")
boxplot(x, pars=list(boxfill="green"))
As the original creator of the 'boxfill' argument, I'd like to propose the
following change to the if(plot) clause in boxplot.R:
if(plot) {
if(is.null(pars$boxfill) && is.null(args$boxfill))
pars$boxfill <- col
do.call("bxp",
c(list(z, notch=notch, width=width, varwidth=varwidth,
outline=outline, log=log, border=border, pars=pars,
horizontal=horizontal, add=add, at=at), args[namedargs]))
invisible(z)
}
What I've done is (1) setting boxfill=col only when that is desired, (2)
named the 'width' list element to avoid confusion, and (3) rearranged the
list so it has the same order as args(bxp).
Thanks,
Arni
R 2.4.0-patched on WinXP
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