I do have a *.r file where I order it to coduct a Chi Square of Independence and write it to an html file. It's working fine but I'd like to add a graph.
Doing by hand in R with linecommands works perfectly, but the exact same commands do not work in the *.r file but i want it to do it automatically.
mat1 <-matrix(c(12,3,2,12),nrow=2,byrow=T)
attach(mat1)
png('independence.png')
barplot(mat1,beside=TRUE)
dev.off()
Is there an additional command necessary?
kind regards
If you have an error in a script with no try or tryCatch, then entrie script fails. By trying to attach a matrix, you throw an error with the message:
Error in attach(mat1) :
'attach' only works for lists, data frames and environments
So you should pay more attention to the error messages in interactive mode, and if you are planning to use .r files for production you should learn to use error handling routines in R. The `attach function is a common source of new user errors, although this error is not particularly common. The more common errors with its use involve regression functions where the authors of the functions are expecting entire objects, usually dataframes, to be passed to a data argument.
Related
I'm trying to test a function of mine with the testthat package. The function is supposed to create an excel file, and I want to test if that excel file exists and contains the things it's supposed to contain. I tried running the function to create a simple mockup excel file and then reading in the output again, but that seems to not do anything, I'm guessing because of the localized testing environment. I also feel like writing code outside of the tests is not a good idea since it gave me a warning message about it.
Is there a way to test an external output with testthat that I don't know about? I'm new to unit testing and this package so any help would be appreciated.
I actually solved this myself by accident: code run in test_that DOES produce output, just in the test folder. I could read it from there and then test.
I have just started to learn to code on R, so I apologize for the very simple question. I understand it is best to type your code in as a Script so you can edit and save it. However, when I try to make an object in the script section, it does not work. If I make an object in the console, R saves the object and it appears in my environment. I am typing in a very simple code to try a quick exercise on rolling dice:
die <- 1:6
But it only works in the console and not when typed as a script. Any help/explanation appreciated!
Essentially, you interact with R environment differently when running an .R script via RScript.exe or via console with R.exe, Rterm, etc. and in GUI IDEs like RGui or RStudio. (This applies to any programming language with interactive compilers not just R).
The script does save thedie object in R environment but only during the run or lifetime of that script (i.e., from beginning to end of code lines). Your code line is simply an assignment of object. You do nothing with it. Apply some function, output results, and other actions in that script to see.
On the console, the R environment persists interactively until you quit it with q(). So assigned objects remains for lifetime of your console session. After assigning, you can afterwards apply function, output results, or other actions in line by line calls.
Ultimately, scripts gathers all line by line code in advance of run for automated execution without relying on user to supply lines. Imagine running 1,000 lines of code with nested if/then or for/while loops, apply functions on console! Therefore, have all your R coding needs summarily handled in scripts.
It is always better to have the script, as you say, you can save edit correct, without having to rewrite the code to change a variable or number.
I recommend using Rstudio, it is very practical and will help you to program more efficiently and allows you to see, among other things, the different objects that you have created.
I need to understand an R script. Since I did not use R until now, I try to understand the script step by step. At the beginning of the script command line arguments (input files) are passed with commandArgs(). I know that one can access additional arguments for an R script with commandArgs().
But I just cannot figure out how to run a script with arguments in the interactive mode, so that I can print all variables used in the script later on. For example source("script.R") does not seem to take arguments.
My apologies if I am just not capable of using the right search query...
I think you're misunderstanding the use of commandArgs - it's for getting the arguments supplied when run through the command line... not the interpreter. If you just want to "supply arguments" when sourcing a file then just put those into the global namespace (just create the variables you want to use). Using source is almost just like copying the script and pasting it into the interpreter.
I am new to R and have been trying to use JRI. Through JRI, I have used the "eval()" function to get certain results. If I want to execute an R script, I have used "source()". However I am now in a situation where I need to execute a script on continuously incoming data. While I can still use "source()", I don't think that would be an optimal way from a performance perspectve.
What I did was to read the entire R script into memory and then try and use "eval()" passing the script - but this does not seem to work. I have ensured that the script has been correctly loaded into memory - that is because if I write this script (loaded into the memory) into a file and source this newly created file, it does produce the expected results.
Is there a way for me to not keep sourcing the same file over and over again and execute it from memory? Each of my data units are independent and have to be processed independently and as soon as they become available. I cannot wait to collect a bunch of data units and then pass them on to the R script.
I have searched a lot and not found anything related to this. Any pointers which could help me in this direction would be really helpful.
The way I handled this is as below -
I enclosed the entire script into a function.
I sourced the script file (which now contains the function) at the start of the execution of my program.
The place where I was sourcing the file, I am now just calling the function which contains the script itself i.e. -
REXP result = rengine.eval("retVal<-" + getFunctionName() + "()");
Here, getFunctionName() gives me the name of the name of the function which contains the script.
Since this is loaded into the memory and available, I do not have to source the script file every time I want to execute the script. Any arguments being passed to the script are done as env. variables.
This seems to be a workaround, but solves my problem. Any better options are welcome.
I am creating an R package, and found it useful to break parts of the logic in one file into internal helper functions, which I define in the same file. I have sort of a special case where my function decides which helper function to use via match.fun(). Since they won't be useful to other functions or people, I don't want to put these in separate files, and I don't want to export them.
All my testthat cases pass using test_dir(). When I don't export these functions, my testthat cases fail during R CMD check.
"object 'helperfunction1' of mode 'function' was not found", quote(get(as.character(FUN),
mode = "function", envir = envir)))
After looking at this post, I am able to get things to work if I explicitly export or add export entries to NAMESPACE, but again I don't want to export these.
Is there a better way to do this and doesn't require me to export? (I'll admit that the source of the issue may be match.fun() and am open to other ways of calling functions at runtime.)
From memory it wasn't clear in the documentation last time I read it (it may have changed), but it will work correctly (without having to export) so long as everything is in the right directories:
You should have a file:
tests/run-all.R
That looks like:
library(testthat)
library(myPackage)
test_package("myPackage")
Then your individual test files should be in the directory inst/tests
These will be run when you do R CMD check, otherwise you can call test_package("myPackage") in R manually.