similar to: pnorm

You may want to look into using the log option to qnorm e.g., in round figures: > log(1e-300) [1] -690.7755 > qnorm(-691, log=TRUE) [1] -37.05315 > exp(37^2/2) [1] 1.881797e+297 > exp(-37^2/2) [1] 5.314068e-298 Notice that floating point representation cuts out at 1e+/-308 or so. If you want to go outside that range, you may need explicit manipulation of the log values. qnorm()

I agree with many the sentiments about the wisdom of computing very small p-values (although the example below may win some kind of a prize: I've seen people talking about p-values of the order of 10^(-2000), but never 10^(-(10^8)) !). That said, there are a several tricks for getting more reasonable sums of very small probabilities. The first is to scale the p-values by dividing the

>>>>> William Dunlap via R-devel >>>>> on Sun, 23 Jun 2019 10:34:47 -0700 writes: >>>>> William Dunlap via R-devel >>>>> on Sun, 23 Jun 2019 10:34:47 -0700 writes: > include/Rmath.h declares a set of 'logspace' functions for use at the C > level. I don't think there are core R functions that call

Hello, Well, try it: p <- .Machine$double.eps^seq(0.5, 1, by = 0.05) z <- qnorm(p/2) pnorm(z) # [1] 7.450581e-09 1.228888e-09 2.026908e-10 3.343152e-11 5.514145e-12 # [6] 9.094947e-13 1.500107e-13 2.474254e-14 4.080996e-15 6.731134e-16 #[11] 1.110223e-16 p/2 # [1] 7.450581e-09 1.228888e-09 2.026908e-10 3.343152e-11 5.514145e-12 # [6] 9.094947e-13 1.500107e-13 2.474254e-14 4.080996e-15

Hi again, I realised it is useful to replicate the warnings locally without relying on CRAN automatic check; instead of R(-devel) CMD check --as-cran package_version.tar.gz one can use R CMD check --configure-args="" and in my case the WARNINGS were initially given with https://www.stats.ox.ac.uk/pub/bdr/gcc9/README.txt and those specification might as well used in --configure-args

Hi All, I wonder if there should be one character for quote= in read.table, i.e., > args(read.table) function (file, header = FALSE, sep = "", quote = "\"'", dec = ".", ... I have a file containing the following lines, 08248-GOTERM 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process 08279-GOTERM 3'-phosphoadenosine

Dear R-developers, I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes, Gene,SNP,prot,log10p YWHAE,13:62129097_C_T,1433E,7.35 YWHAE,4:72617557_T_TA,1433E,7.73 Both read.cv() and readr::read_csv() consider prot(ein) name as (possibly confused by

?s 11:46 de 16/04/2024, jing hua zhao escreveu: > Dear R-developers, > > I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes, > > Gene,SNP,prot,log10p > YWHAE,13:62129097_C_T,1433E,7.35 > YWHAE,4:72617557_T_TA,1433E,7.73 >

On 28.05.2018 11:07, G?bor Cs?rdi wrote: > stdin() is not the same as file("stdin"), see the note in ?stdin. In particular stdin() works in an interactive session but not when R -f / Rscript is used, since it does not wait for the user to input anything: $ R -f readLines.R R version 3.5.0 (2018-04-23) -- "Joy in Playing" Copyright (C) 2018 The R Foundation for Statistical

No, that will make it even worse since you'll be declaring a lot more memory that you actually have. The real problem is that you're ignoring the truncation, so you probably want to use something like if (snprintf(tempname, sizeof(tempname), "%s.%d", of1name, j) >= sizeof(tempname)) Rf_error("file name is too long"); BTW: most OSes systems have a path limits that

I had trouble with some tests for the survival suite last night that I cannot explain. Framework: Ubuntu Linux, R2.11. For testing survival I have a separate directory and Makefile. I pull everything into the local .RData, no packages, library, or namespace. (It's easier to add test modifications to a routine in a chain of calls). A test of survreg + psline would fail because

Dear R-developers, I would appreciate any insights over compiling R 3.4 with Intel MKL -- I have been successful until R 3.3.3 but now it stops complaining about pcre though it worked without Intel MKL as follows, ./configure LDFLAGS=-L/genetics/data/software/lib CFLAGS=-fPIC -I/genetics/data/software/include --enable-R-shlib I have used, export MKL_NUM_THREADS=15 export

>>>>> jing hua zhao >>>>> on Mon, 24 Jun 2019 08:51:43 +0000 writes: > Hi All, > Thanks for all your comments which allows me to appreciate more of these in Python and R. > I just came across the matrixStats package, > ## EXAMPLE #1 > lx <- c(1000.01, 1000.02) > y0 <- log(sum(exp(lx))) > print(y0) ## Inf

Gene names being misinterpreted by spreadsheet software (read.csv is no different) is a classic issue in bioinformatics. It seems like every practitioner ends up encountering this issue in due time. E.g. https://pubmed.ncbi.nlm.nih.gov/15214961/ https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7 https://www.nature.com/articles/d41586-021-02211-4

On our Scientific Linux 6, there is gcc --version gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17) and later version (a symbolic at HOME to the system directory), export MKL=/home/jhz22/11.3.3.210/mkl export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MKLROOT/lib/intel64 ./configure --prefix=/home/jhz22 LDFLAGS=-L/home/jhz22/lib CPPFLAGS=-I/home/jhz22/include \ --enable-R-shlib --with-lapack \

Hi Peter, Rui, Chrstophe and Gabriel, Thanks for your inputs -- the use of qnorm(., log=TRUE) is a good point in line with pnorm with which we devised log(p) as log(2) + pnorm(-abs(z), lower.tail = TRUE, log.p = TRUE) that could do really really well for large z compared to Rmpfr. Maybe I am asking too much since z <-20000 >

include/Rmath.h declares a set of 'logspace' functions for use at the C level. I don't think there are core R functions that call them. /* Compute the log of a sum or difference from logs of terms, i.e., * * log (exp (logx) + exp (logy)) * or log (exp (logx) - exp (logy)) * * without causing overflows or throwing away too much accuracy: */ double Rf_logspace_add(double

Dear r-devel members, I tried to build R packages on a PC running Windows XP but experience problems. However, it is ok when there is no inst directory in a package. Any help would be appreciated. The following is an example, C:\work>R CMD check VR_7.2-19.tar.gz * checking for working latex ... OK * using log directory 'C:/work/VR.Rcheck' * using R version 2.1.1, 2005-06-20 *

Hi All, Thanks for all your comments which allows me to appreciate more of these in Python and R. I just came across the matrixStats package, ## EXAMPLE #1 lx <- c(1000.01, 1000.02) y0 <- log(sum(exp(lx))) print(y0) ## Inf y1 <- logSumExp(lx) print(y1) ## 1000.708 and > ly <- lx*100000 > ly [1] 100001000 100002000 > y1 <- logSumExp(ly) > print(y1) [1] 100002000

I found the following strange behavior using qnorm() and pnorm(): > x<-8.21;x-qnorm(pnorm(x)) [1] 0.0004638484 > x<-8.22;x-qnorm(pnorm(x)) [1] 0.01046385 > x<-8.23;x-qnorm(pnorm(x)) [1] 0.02046385 > x<-8.24;x-qnorm(pnorm(x)) [1] 0.03046385 > x<-8.25;x-qnorm(pnorm(x)) [1] 0.04046385 > x<-8.26;x-qnorm(pnorm(x)) [1] 0.05046385 > x<-8.27;x-qnorm(pnorm(x))