[Rd] stats glm Response Format Ambiguity

Hello, Could there be clarification added to glm's documentation? In contrast, glmnet leaves no ambiguity about what it expects for response. glm: y: is a vector of observations of length n glmnet: y: For family="binomial" should be either a factor with two levels, or a two-column matrix of co

Re: [Rd] Changes in the survival package (long)

Good day, It is impressive to see such sustained package maintenance. -- Dr. Dario Strbenac Bioinformatics Research Associate School of Mathematics and Statistics, University of Sydney Camperdown N.S.W. 2050, Australia __

Re: [Rd] confint Attempts to Use All Server CPUs by Default

Hello, It is from the stats package and applied to the output of logistic regression as implemented by glm with setting family = "binomial". So, it is a base package and not an add-on CRAN package. I shall recommend linking to FlexiBLAS to our system administrator.

[Rd] confint Attempts to Use All Server CPUs by Default

Hello, Would a less resource-intensive value, such as 1, be a safer default CPU value for confint? I noticed excessive CPU usage on a I.T. administrator-managed server which was being three-quarters used by another staff member when the confidence interval calculation in an R Markdown document

[Rd] Subset has No Examples for Vector Data

Hello, Could the documentation page for subset gain an example of how to use it for something other than a data frame or matrix? I arrived at > random <- LETTERS[rpois(100, 10)] > subset(table(random), x > 10) named integer(0) I expected a part of the table to be returned rather than an empty v

[Rd] save.image Non-responsive to Interrupt

Hello, Could save.image() be redesigned so that it promptly responds to Ctrl+C? It prevents the command line from being used for a number of hours if the contents of the workspace are large. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia

[Rd] Combinations and Permutations

Good day, In utils, there is a function named combn. It would seem complementary for utils to also offer permutations because of how closely mathematically related they are to each other. Could permutations be added to save on a package dependency if developing a package? -

[Rd] Data Frame Conversion and Table Input

Good day, as.data.frame is documented on ?table and on ?as.data.frame (for list and matrix inputs). For inputs of list type and matrix type, there is an argument optional, which allows preservation of column names. If the input is a table, there is no such option. Could the API be made consiste

Re: [Rd] [External] svd For Large Matrix

Good day, Ah, I was confident it wouldn't be environment-specific but it is. My environment is R version 4.1.0 (2021-05-18) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 LAPAC

[Rd] svd For Large Matrix

Good day, I have a real scenario involving 45 million biological cells (samples) and 60 proteins (variables) which leads to a segmentation fault for svd. I thought this might be a good example of why it might benefit from a long vector upgrade. test <- matrix(rnorm(4500*60), ncol = 60) test

Re: [Rd] dgTMatrix Segmentation Fault

Good day, Thanks to handy hints from Martin Morgan, I ran R under gdb and checked for any numeric overflow. We pinpointed the cause: (gdb) info locals i = 0 j = 10738 m = 20 n = 5 ans = 0x5b332790 aa = 0x5b3327c0 There is a line of C code in dgeMatrix.c for (i = 0; i < m; i++) a