diff --git a/R_usage.md b/R_usage.md index 05de97c..77b7e14 100644 --- a/R_usage.md +++ b/R_usage.md @@ -2,28 +2,37 @@ R Programming in HPC ==================== ## What is R? -R is a programming language and a software environment for statistical computing and graphics techniques. This is widely used now a days by statisticians and data miners for developing software tools required for data analysis. The R language is primarily derived from the S language developed at Bell Laboratories in 1975. R provides various tools and techniques for linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering etc. More history and documentation of R are available at this [link](https://cran.r-project.org/manuals.html) +R is a programming language and a software environment for statistical computing and graphics techniques. This is widely used nowadays by statisticians and data miners for developing software tools required for data analysis. The R language is primarily derived from the S language developed at Bell Laboratories in 1975. R provides various tools and techniques for linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. More history and documentation of R are available at this [link](https://cran.r-project.org/manuals.html) ## How to run R? -First login to one of the CARC machines via SSH. +First, login to one of the CARC machines via SSH. -`ssh -X user@machine_name.alliance.unm.edu` +`ssh user@machine_name.alliance.unm.edu` -Once logged into the machine, you have to load the module which has R program files. +Once logged into the machine, load the default version of R provided by the CARC machine with: -`module load r-3.5.0-gcc-4.8.5-python2-khqxja7` +`module load r` + +If you would like to see all available versions of R, run: + +`module spider r` + +To also load a specific version of R, use: + +`module load r/` + +Note: Some versions of R may have compiler dependencies and require a compiler module such as GCC to be loaded first. If these dependencies are needed, the module system will display an error message when attempting to load the R module that includes a `module spider r/` command that will help identify the required modules. After loading the R module, begin R programming by typing -`R` +`srun --pty R` -This will shows +This will show ```bash -R version 3.5.0 (2018-04-23) -- "Joy in Playing" -Copyright (C) 2018 The R Foundation for Statistical -Computing -Platform: x86_64-pc-linux-gnu (64-bit) +R version 4.4.0 (2024-04-24) -- "Puppy Cup" +Copyright (C) 2024 The R Foundation for Statistical Computing +Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. @@ -40,17 +49,18 @@ Type 'demo()' for some demos, 'help()' for on-line help, or Type 'q()' to quit R. ``` -This means the R module is loaded and you are ready to use R for your research +This means the R module is loaded, and you are ready to use R for your research ## Running a sample script example.R -Let us look a sample script, example.R which will print "Hello World" +Let us look at a sample script called "example.R" which will print "Hello World". The script looks like ```bash +# example.R # Program to print Hello World print('Hello World') ``` -In order to execute this script, type +Before running the script, make sure you have exited the R interpreter (indicated by the `>` prompt) by typing `q()` and returning back to the Linux command line. In order to execute this script, type `Rscript example.R` @@ -58,22 +68,23 @@ This will give an output of `[1] "Hello World"` -If you want to generate samples from a normal distribution, you can use the `rnorm()` function. Let's make some change to the example.R script. +If you want to generate samples from a normal distribution, you can use the `rnorm()` function. Let's make some changes to the example.R script. ```bash # Program to print Hello World and to generate normal random numbers print('Hello World') -#Calling the rnorm() function to generate three random numbers from a -normal distribution with mean 5 and a standard deviation of 5 +# Calling the rnorm() function to generate three random numbers from a +# normal distribution with mean 5 and a standard deviation of 5 rnorm(3,mean=5,sd=5) ``` -Execute the script again and the look at the new output. +Execute the script again and look at the new output. ```bash [1] "Hello World" [1] 3.744463 7.954163 3.363275 -``` \ No newline at end of file +``` +