[R] R CMD BATCH: unable to start device PNG
Dear r-helpers:
Any ideas how to avoid problem described below?
I am having the same problem when I run R remotly (not from cgi script);
somehow png device wants to talk to X11 and X11 complains...
Best regards,
Ryszard
error msg from batch R process (Linux/R-2.4.0) (executed on Apache server
from cgi script):
Error in X11(paste("png::", filename, sep = ""), width, height, pointsize,
:
unable to start device PNG
In addition: Warning message:
unable to open connection to X11 display ''
Execution halted
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[R] how to print table with more columns per row?
When printing a table it is broken at some point (depending how long are
the associated names)
>>> see example below.
Is there a way to control number of columns being printed for a given
chunk of the table?
Best regards,
Ryszard
> z5
AAA BBB CCC DDD EEE FFF GGG HHH
III
AAA1.00 -0.69 -0.54 -0.88 NA NA NA NA
-0.88
BBB -0.691.000.650.82 NA NA NA 1
0.83
CCC -0.540.651.000.49 NA NA NA NA
0.94
DDD -0.880.820.491.00 NA NA NA 1
0.90
EEE NA NA NA NA NA NA NA NA
NA
FFF NA NA NA NA NA NA NA NA
NA
GGG NA NA NA NA NA NA NA NA
NA
HHH NA1.00 NA1.00 NA NA NA 1
NA
III -0.880.830.940.90 NA NA NA NA
1.00
JJJ NA NA NA NA NA NA NA NA
NA
KKK0.050.210.11 -0.11 NA NA NA 1
NA
LLL0.73 -0.68 -0.16 -0.91 NA NA NA -1
-0.35
JJJ KKK LLL
AAA NA0.050.73
BBB NA0.21 -0.68
CCC NA0.11 -0.16
DDD NA -0.11 -0.91
EEE NA NA NA
FFF NA NA NA
GGG NA NA NA
HHH NA1.00 -1.00
III NA NA -0.35
JJJ NA NA NA
KKK NA1.000.24
LLL NA0.241.00
>
CONFIDENTIALITY NOTICE\ \ The information contained in this ...{{dropped}}
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[R] strange matrix behaviour: is there a matrix with one row?
Consider this: > y <- matrix(1:8, ncol=2) > is.matrix(y[-c(1,2),]) [1] TRUE > is.matrix(y[-c(1,2,3),]) [1] FALSE > is.matrix(y[-c(1,2,3,4),]) [1] TRUE It seems like an inconsistent behaviour: - with 2 or more rows we have a matrix - with 1 row we do not have a matrix and - with 0 rows we have a matrix again I just stumbled on this behaviour, because I had a problem with my program in which I have assumed that matrix with some rows removed is still a matrix, which seems to be mostly true, but it is not true if only one row is left. Comments? Suggestions? How to work around this problem - without to many "if" statements? Best regards, Ryszard __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to initialize random seed properly ?
Here is my best solution so far using $RANDOM in bash
or maybe somebody has "pure R" solution ?
#!/bin/bash
for i in 1 2; do
p=tmp$i
cat > $p.R << EOF
set.seed($RANDOM)
cat('rnorm(3) =', rnorm(3), '\n')
EOF
nice R CMD BATCH --no-save --no-restore $p.R $p.log &
done
sleep 3
grep rnorm tmp[12].log
Best regards,
Ryszard
Ryszard Czerminski/PH/[EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
06/09/2004 03:24 PM
To: [EMAIL PROTECTED]
cc:
Subject:[R] how to initialize random seed properly ?
I want to start R processes on multiple processors from single shell
script
and I want all of them to have different random seeds.
One way of doing this is
sleep 2 # (with 'sleep 1' I am often getting the same number)
...
set.seed(unclass(Sys.time()))
Is there a simpler way without a need to sleep between invoking
different R processes ?
Ryszard
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[R] how to initialize random seed properly ?
I want to start R processes on multiple processors from single shell script and I want all of them to have different random seeds. One way of doing this is sleep 2 # (with 'sleep 1' I am often getting the same number) ... set.seed(unclass(Sys.time())) Is there a simpler way without a need to sleep between invoking different R processes ? Ryszard __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R-1.9.0: Error in paste(ncomp, "LV's") : Argument "ncomp" is missing, with no default
Is it just my installation or bug in 1.9.0 ? The same thing works fine in 1.8.1 Best regards, Ryszard # R-1.9.0 library(pls.pcr) nr <- 8; ndim <- 2 x <- matrix(rnorm(nr*ndim), nrow=nr) y <- as.matrix(x[,1]) for (i in 2:ndim) y <- y + x[,i] y <- y + rnorm(length(y)) m <- pls(x,y,validation='CV') # Error in paste(ncomp, "LV's") : Argument "ncomp" is missing, with no default __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] how to pass extra parameters using call() or similar mechanism ?
I am trying to write a function, which would allow to call various methods
and would pass to them extra arbitrary parameters.
My first attempt was to use call() as illustrated below, but apparently
'...' cannot be used in such context.
How can this be achieved ?
Best regards,
Ryszard
> myfun <- function(method, x, ...) {
+ v <- eval(call(method, x, ...))
+ }
> method = 'sqrt'
> myfun('sqrt',2)
Error in eval(call(method, x, ...)) : ... used in an incorrect context
> eval(call(method, 2, ...))
Error in eval(call(method, 2, ...)) : ... used in an incorrect context
> eval(call(method, 2))
[1] 1.414214
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[R] row.names are dropped when extracting one column ?
Apparently row names are dropped when I extract single column from a data frame. Why this behaviour ? > y <- as.matrix(df[,1:2]); length(row.names(y)) [1] 324 > y <- as.matrix(df[,1:1]); length(row.names(y)) [1] 0 Best regards, Ryszard __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] problem with read.table
Any ideas why read.table complains about not correct number of elements in
line
while readLine/strsplit indicate that all lines have the same number of
elements ?
R
> tbl <- read.table('tmp', header = T, sep = '\t')
Error in scan(file = file, what = what, sep = sep, quote = quote, dec =
dec, :
line 32 did not have 27 elements
> lines <- readLines('tmp')
> v <- 1:length(lines)
> i <- 0; for (line in lines) { i <- i + 1; v[i] <- length(strsplit(line,
'\t')[[1]]) }
> v
[1] 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27
27 27
[26] 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27
27 27
[51] 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27
> sum((v - v[1])^2)
[1] 0
> length(strsplit(lines[32], '\t')[[1]])
[1] 27
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[R] prcomp: error code 17 from Lapack routine dgesdd
I am trying to use prcomp and I am getting this error: > p <- prcomp(xtr, retx = TRUE, center = TRUE, scale = TRUE, tol = NULL) Error in La.svd(x, nu, nv, method) : error code 17 from Lapack routine dgesdd > dim(xtr) [1] 301 2439 Does it mean that the matrix is to big ? R __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] tune(): how to specify a kernel ?
I would like to use tune() for tuning parameters for svm method, but it is
not clear
to me how to specify a kernel.
I am trying to use something like this:
> obj <- tune(svm, Species~., data = iris, ranges = list(kernel =
c('radial', 'linear')))
Error in pmatch(x, table, duplicates.ok) :
argument is not of mode character
but it generates an error.
Ryszard
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Re: [R] dist(x,y)
Hi Erin, CLARIFICATION: I am looking for function which can calculate distances between rows in two different matrices (not in the same matrix as dist). Of course I can get the desired result by using rbind() and fiddling with indices of the result, which I already did, but I wonder if there is a function (or some variant of dist), which does it directly ? Ryszard Erin Hodgess <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 01/06/2004 12:41 PM To: [EMAIL PROTECTED] cc: Subject:[R] dist(x,y) Hi Ryszard! There is a dist function in R. It's in the mva package. You can set the kind of distance that you want. Thanks, Erin mailto:[EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] dist(x, y) ???
Is there a function in R (similar to dist) which would calculate distances between rows in two different matrices ? Ryszard __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] problem with pls(x, y, ..., ncomp = 16): Error in inherit s( x, "data.frame") : subscript out of bounds
Help for pls says: > ?pls [...] Arguments: ... ncomp: the numbers of latent variables to be assessed in the modelling. Default is from one to the rank of 'X'. [...] so my assumption was (maybe wrong) that idea of ncomp parameter is to limit number of assessed variables. also, if called without crossvalidation it gives the same error: > m <- pls(x, y, ncomp = 16) Error in inherits(x, "data.frame") : subscript out of bounds R "Liaw, Andy" <[EMAIL PROTECTED]> 12/09/2003 12:50 PM To: Ryszard Czerminski/PH/[EMAIL PROTECTED], [EMAIL PROTECTED] cc: Subject:RE: [R] problem with pls(x, y, ..., ncomp = 16): Error in inherit s( x, "data.frame") : subscript out of bounds I don't know the details of pls (in the pls.pcr package, I assume), but if you use validation="CV", that says you want to use CV to select the best number of components. Then why would you specify ncomp as well? Andy > From: [EMAIL PROTECTED] > > When I try to use ncomp parameter in pls procedure I get > following error: > > > library(pls.pcr) > > m <- pls(x, y, validation = "CV", niter = 68, ncomp = 16) > Error in inherits(x, "data.frame") : subscript out of bounds > > Without ncomp parameter everything seems to work OK > > > dim(x) > [1] 68 116 > > dim(y) > [1] 68 1 > > m <- pls(x, y, validation = "CV", niter = 68) > > length(m$ncomp) > [1] 67 > > Ryszard > > __ > [EMAIL PROTECTED] mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > > __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] problem with pls(x, y, ..., ncomp = 16): Error in inherits(x, "data.frame") : subscript out of bounds
When I try to use ncomp parameter in pls procedure I get following error: > library(pls.pcr) > m <- pls(x, y, validation = "CV", niter = 68, ncomp = 16) Error in inherits(x, "data.frame") : subscript out of bounds Without ncomp parameter everything seems to work OK > dim(x) [1] 68 116 > dim(y) [1] 68 1 > m <- pls(x, y, validation = "CV", niter = 68) > length(m$ncomp) [1] 67 Ryszard __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] plotting to postscript: how to control line width ?
When I use
plot(..., type = "line") then ldw parameter makes a difference...
Because of large number of points overlapping I simply han an impression
before that I am getting thick line...
R
Ryszard Czerminski/PH/[EMAIL PROTECTED]
Sent by: [EMAIL PROTECTED]
11/25/2003 01:34 PM
To: [EMAIL PROTECTED]
cc:
Subject:[R] plotting to postscript: how to control line width ?
How to control line width ?
if I do:
> postscript("IC50-density.eps", width = 4.0, height = 3.0, horizontal =
FALSE, onefile = FALSE, paper = "special", title = "IC50 distribution")
> plot(d$x, d$y, xlab = "-log10(IC50)", ylab = "density")
> lines(d$x, d$y, lwd = 0.1)
> dev.off()
but whatever value I give for ldw parameter (e.g. 0.1 or 10) I am getting
the same line width ?!
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[R] plotting to postscript: how to control line width ?
How to control line width ?
if I do:
> postscript("IC50-density.eps", width = 4.0, height = 3.0, horizontal =
FALSE, onefile = FALSE, paper = "special", title = "IC50 distribution")
> plot(d$x, d$y, xlab = "-log10(IC50)", ylab = "density")
> lines(d$x, d$y, lwd = 0.1)
> dev.off()
but whatever value I give for ldw parameter (e.g. 0.1 or 10) I am getting
the same line width ?!
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[R] index of max value ?
Is there a function in R, which would return index of maximum value in a vector ? e.g. > v <- round(10*rnorm(8)) > v [1] 6 -3 -6 15 7 9 0 -19 > max(v) [1] 15 ??? index.max(v) ??? 4 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] column extraction by name ?
I have a data frame (df) with colums x, y and z. e.g. df <- data.frame(x = sample(4), y = sample(4), z = sample(4)) I can extract column z by: df$z or df[3] I can also extract columns x,y by: df[1:2] or by df[-3]. Is it possible to extract x,y columns in a "symbolic" fashion i.e. by equivalent of df[-z] (which is illegal) ??? Or alternativeley, is there an equivalent of "index" function, which would return index of the column given name ? Ryszard __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] svm in e1071 package: polynomial vs linear kernel
I am trying to understand what is the difference between linear and
polynomial kernel:
linear: u'*v
polynomial: (gamma*u'*v + coef0)^degree
It would seem that polynomial kernel with gamma = 1; coef0 = 0 and degree
= 1
should be identical to linear kernel, however it gives me significantly
different results for very simple
data set, with linear kernel significantly outperforming polynomial
kernel.
*** mse, r2 = 0.5, 0.9 for linear
*** mse, r2 = 1.8, 0.1 for polynomial
What am I missing ?
Ryszard
P.S.
Here are my results:
# simple cross validation function
cv.svm <- function(formula, data, ntry = 3, kernel = "linear", scale =
FALSE, cross = 3,
gamma = 1/(dim(data)-1), degree = 3) {
mse <- 0; r2 <- 0
for (n in 1:ntry) {
svm.model <- svm(formula , data = data, scale = scale, kernel =
kernel,
cross = cross)
mse <- mse + svm.model$tot.MSE
r2 <- r2 + svm.model$scorrcoeff
}
mse <- mse/ntry; r2 <- r2/ntry; result <- c(mse, r2)
cat(sprintf("cv.svm> mse, r2 = %5.3f %5.3f\n", mse, r2))
return (result)
}
# define data set
x1 <- rnorm(9); x2 <- rnorm(9)
df <- data.frame(y = 2*x1 + x2, x1, x2)
# invoke cv.svm() for linear and polynomial kernels few times
> r <- cv.svm( y ~ ., df, kernel = "polynomial", gamma = 1, degree = 1,
ntry = 32)
cv.svm> mse, r2 = 1.888 0.162
> r <- cv.svm( y ~ ., df, kernel = "polynomial", gamma = 1, degree = 1,
ntry = 32)
cv.svm> mse, r2 = 1.867 0.146
> r <- cv.svm( y ~ ., df, kernel = "polynomial", gamma = 1, degree = 1,
ntry = 32)
cv.svm> mse, r2 = 1.818 0.105
> r <- cv.svm( y ~ ., df, kernel = "linear", gamma = 1, degree = 1, ntry =
32)
cv.svm> mse, r2 = 0.525 0.912
> r <- cv.svm( y ~ ., df, kernel = "linear", gamma = 1, degree = 1, ntry =
32)
cv.svm> mse, r2 = 0.537 0.878
> r <- cv.svm( y ~ ., df, kernel = "linear", gamma = 1, degree = 1, ntry =
32)
cv.svm> mse, r2 = 0.528 0.913
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[R] problem with tune.svm
> rng <- list(gamma = 2^(-1:1), cost = 2^(2:4)) > rng $gamma [1] 0.5 1.0 2.0 $cost [1] 4 8 16 > obj <- tune.svm(pIC50 ~ ., data = data, ranges = rng) Error in tune(svm, train.x = x, data = data, ranges = ranges, ...) : formal argument "ranges" matched by multiple actual arguments Ay idea why ??? Ryszard [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] strange sprintf() behaviour ?
This is quite strange behaviour - at least for R-novice as myself
Consider this:
> testf <- function() { x <-2; sprintf("%s %f", "x =", x); return(x) }
> result <- testf()
> testf <- function() { x <-2; sprintf("%s %f", "x =", x) }
> result <- testf()
> testf()
[1] "x = 2.00"
Apparently adding return() statement and invoking function like this
"result <- testf()"
suppresses output from sprintf()
Output from print() is NOT suppressed:
> testf <- function() { x <-2; print(c("x =", x)) }
> result <- testf()
[1] "x =" "2"
> testf <- function() { x <-2; print(c("x =", x)); return(x) }
> result <- testf()
[1] "x =" "2"
Is there a way to use sprintf() inside a function ?
I guess I can say: print(sprintf()) - is it the only solution for this ?
R
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[R] print(), cat() and simple I/O in R
I am trying to produce rather mundane output of the form e.g.
pi, e = 3.14 2.718
The closest result I achieved so far with print() is:
> print (c(pi, exp(1)), digits = 3)
[1] 3.14 2.72
> print(c("pi, e =", pi, exp(1)), digits = 3)
[1] "pi, e =" "3.14159265358979" "2.71828182845905"
I understand that c() promotes floats to strings and this is why I get
what I get.
and with cat() (it apparently does not have equivalent of digits"
parameter)
> cat ("pi, e =", pi, exp(1), "\n")
pi, e = 3.141593 2.718282
Any pointers with respect how can I print what I want to print would be
greatly appreciated.
Ryszard
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[R] svm from e1071 package
I am starting to use svm from e1071 and I wonder how exactly crossvalidation is implemented. Whenever I run > svm.model <- svm(y ~ ., data = trainset, cross = 3) on my data I get dirrerent values for svm.model$MSE e.g. [1] 0.9517001 1.7069627 0.6108726 [1] 0.3634670 0.9165497 1.4606322 This suggests to me that data are scrambled each time - the last time I looked at libsvm python interface this is what was done. Is this the same here (I hope) ? R [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] how to remove NaN columns ?
I received a lot of good advice how to remove NaN columns - thank you all !!! The simplest mechanism to center/scale and remove NaN columns seems to be > xdata <- data.frame(A = 3:1, B = 1:3, rep(9, 3)) > xs <- scale(xdata) > mask <- sapply(as.data.frame(xs), function(x) all(is.nan(x))) > scaled.centered.x <- as.data.frame(xs)[!mask] > scaled.centered.x A B 1 1 -1 2 0 0 3 -1 1 Note that as.data.frame(xs) is important, because apparently xs from scale() function is not a data frame and if as.data.frame() is omitted in the code fragment above we get something like this > mask <- sapply(xs, function(x) all(is.nan(x))) > xs[!mask] 123 10 -1 -101 Maybe somebody more knowledgeable could give some explanation for this behavior. Ryszard [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] how to select random rows ?
How can I select random subsets (rows!) from a data set ? If I generate simple data set > a <- data.frame(x=1:2, y = NaN, z = 2:1) > a x y z 1 1 NaN 2 2 2 NaN 1 I can select random subsets (colums) very easily using sample function: > sample(a, 2) z y 1 2 NaN 2 1 NaN I expected that using transpose of a would do the same for rows, but I am getting rather unexpected outcome > sample(t(a), 1) 1 R [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] how to remove NaN columns ?
Nice!
I noticed that in generated structure it has two attributes
attr(,"scaled:center") and attr(,"scaled:scale")
How can I access them ?
R
Giovanni Petris <[EMAIL PROTECTED]>
10/24/2003 02:50 PM
Please respond to Giovanni Petris
To: Ryszard Czerminski/PH/[EMAIL PROTECTED]
cc: [EMAIL PROTECTED]
Subject:Re: [R] how to remove NaN columns ?
> > xs <- lapply(xdata, function(x){(x - mean(x))/sqrt(var(x))})
Incidentally, the function 'scale' does just that.
--
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[ ]
[ Giovanni Petris [EMAIL PROTECTED] ]
[ Department of Mathematical Sciences ]
[ University of Arkansas - Fayetteville, AR 72701 ]
[ Ph: (479) 575-6324, 575-8630 (fax) ]
[ http://definetti.uark.edu/~gpetris/ ]
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[R] How to avoid converting "_" to "." ?
It is minor thing, but how can I avoid converting "_" to "." ?
e.g. I have a data set "test.csv"
A,A_B,A_C,C,D
X,11,0,13,14
Y,21,0,23,24
and when I read it all underscores are converted to dots (:<)
> d <- read.csv("test.csv")
> d
A A.B A.C C D
1 X 11 0 13 14
2 Y 21 0 23 24
Ryszard
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[R] how to remove NaN columns ?
How can I remove columns with NaN entries ?
Here is my simple example:
> data <- read.csv("test.csv")
> xdata <- data[3:length(data)]
> xs <- lapply(xdata, function(x){(x - mean(x))/sqrt(var(x))})
> x <- data.frame(xs)
> x
C D EF
1 -0.7071068 NaN -0.7071068 -0.7071068
2 0.7071068 NaN 0.7071068 0.7071068
I am sure it is possible to remove column D (with NaN's) in some simple
fashion, using is.nan function
without explicitly looping through, and I am sure I was able to do it in
the past, but I cannot recall how.
Your help will be greatly appreciated.
Ryszard
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