[R] R in batch mode: cannot mkdir R_TempDir
Dear all, I am trying to run a simple R script in batch mode on a cluster. Running a simple test script with "R CMD BATCH test.R test.Rout" works fine, but as soon as I submit the very same command to the queue and the job gets sent to a node, the following error is written to test.Rout: Fatal error: cannot mkdir R_TempDir I set the environment variables TEMP, TMP and TMPDIR to /tmp/ and I also make sure that all environment variables are set on the nodes. Running the R command "tempdir()" on a node returns something like "/tmp/RtmpadvdoQ". I also made sure that the /tmp/ directory is readable and writable on all nodes. I know that this question might be more cluster-specific (I'm running scientific linux) than R specific and my example is hard to reproduce. However, maybe someone encountered similar problems. Is it maybe possible to specify the tempdir in an argument to R CMD BATCH? Many thanks in advance, Hannes -- View this message in context: http://r.789695.n4.nabble.com/R-in-batch-mode-cannot-mkdir-R-TempDir-tp4649503.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] multi-panel figure: overall title for each row
Dear all,
I have a 3x2 plot and in addition to the title of the individual plots I
would like to have an overall title
for each row. I managed to get an overall title for the whole plot matrix
with mtext:
par(mfrow=(c(3,2)), mar=c(6.4,4.5,4.2, 1.8), oma=c(0,0,3,0))
for (i in 1:6)
barplot(sample(1:10,5), main=paste("Plot #",i))
mtext("Overall Title Row 1", outer=TRUE)
but I cannot put an overall title in the middle above the titles of the
plots in the second or third row.
If I use mtext within the loop, I can only add another title above an
individual plot.
I hope someone can help me, many thanks in advance
Hannes
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[R] splitting a vector
Hello, I have a vector with positive integer numbers, e.g. > numbers <- c(1,2,1,2,3,4,5) and want to split the vector whenever an element in the vector is smaller or equal to its predecessor. Hence I want to obtain two vectors: c(1,2) and c(1,2,3,4,5). I tried with which(), but it is not so elegant: > numbers[1:(which(numbers<=numbers[1])[2]-1)] > numbers[which(numbers<=numbers[1])[2]:length(numbers)] Sure I can do it with a for-loop, but that seems a bit tedious for that small problem. Does maybe anyone know a simple and elegant solution for this? I'm searching for a general solution, since my vector may change and maybe be split into more than two vectors, e.g. give five vectors for c(1,1,2,3,4,5,1,2,3,2,3,4,5,6,4,5). Many thanks in advance, Hannes -- View this message in context: http://r.789695.n4.nabble.com/splitting-a-vector-tp4638675.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] convex nonnegative basis vectors in nullspace of matrix
Hi the solution with linear programming works very well! Even if I take more 'realistic' matrices with dimensions of about 25x60, the calculation of the basis goes well (if I increase the number of iterations to 1000). Meanwhile I also found an algorithm for an exact calculation of the extreme rays of the cone (Appendix in http://www.sciencedirect.com/science/article/pii/S0022519300910737). When I have time I will try to implement this solution as well and compare the performances, but the one I have now works fine in my application. Many thanks, Hannes -- View this message in context: http://r.789695.n4.nabble.com/convex-nonnegative-basis-vectors-in-nullspace-of-matrix-tp4548822p4552371.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] convex nonnegative basis vectors in nullspace of matrix
Dear all, I want to explore the nullspace of a matrix S: I currently use the function Null from the MASS package to get a basis for the null space: > S = matrix(nrow=3, ncol=5, c(1,0,0,-1,1,1,1,-1,-1,0,-1,0,0,0,-1)); S > MASS::Null(t(S)) My problem is that I actually need a nonnegative basis for the null space of S. There should be a unique set of convex basis vectors spanning a vector space in which each vector v satisfies sum (S %*% v) == 0 and min(v)>=0. Is there maybe an R function that can calculate that for me? I would appreciate any help, Thanks in advance, Hannes -- View this message in context: http://r.789695.n4.nabble.com/convex-nonnegative-basis-vectors-in-nullspace-of-matrix-tp4548822p4548822.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] single, double or no quotes in expression
Many thanks, "parse" is exactly what I was looking for!! Hannes -- View this message in context: http://r.789695.n4.nabble.com/single-double-or-no-quotes-in-expression-tp4475247p4475475.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] single, double or no quotes in expression
Dear all,
I am confused about how to create an expression. I use a package (rsbml)
which uses expressions and seems to make a difference if there is a quote
around the expression or not.
For example, package works with expressions such as
> expression(A + B)
but not with
> expression("A + B")
I now have a set of math expressions represented as strings, something like
this:
> rhs_eq<- c("0", "A + B", "B * (2+C)")
and want to make expressions without quotes out of it.
I tried
> lapply(lapply(rhs_eq, as.symbol), as.expression)
which only turns the double quotes into single quotes, but does not remove
the quotes.
I also played around with as.formula, as.name, quote and enquote, but had no
success.
Does anyone know about quotes in the expression data type?
Thanks in advance,
Hannes
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