I am working on an R GUI with the shiny package.
In the GUI, I am trying to create tooltips for multiple functions which are provided through other R-packages.
So my idea was to parse the necessary information for the tooltips from the documentation (help-files) of the respective packages.
So, for example, one such tooltip might be to show the description text from the help files.
My current problem is that I can't find any way to parse the output of the R help into a string or other type of variable that I can then further process.
For example:
?sum
opens a help page with the description:
sum returns the sum of all the values present in its arguments.
Now if i try something like:
capture.output(?sum)
paste(?sum)
I won't get any helpful results.
Is there a way to directly parse a help file into a string etc.?
Thanks for your help ;)
Just to give a quick summary of the solution that was given to me in the comment by Nate: I wrote a short method to extract a help file by package- and method-name.
library(tools)
getMethodHelp <- function(packageName, methodName){
db <- Rd_db(packageName)
return(db[[paste0(methodName,".Rd")]])
}
And maybe a usage example:
getMethodHelp("base","sum")
Returns the helpfile of the sum function from the base-package.
Hope this helps someone in the future....
Related
I have a somewhat niche question that I'm hoping someone can answer for me or help me find a work-around to:
I've written a script in R that will run an ImageJ macro for sets of images I produce as a part of my workflow.
Because this is work that I may publish at some point or may be used by other researchers in the lab after me, I like to keep a copy of the R script and ImageJ macro within each dataset's folder as I sometimes modify the script a little for a certain series of images and this makes it very clear which version of code I used to process which set of images.
I am somewhat new to coding so I'm slowly trying to make this piece of code more streamlined and to have fewer places within the script that need to be modified each time I copy it to a new datafile, which is where I'm running into an issue.
In the script, I call the macro using the following code:
macro <- function(i) {
system2('/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx', args=c('-batch "/Users/xxxx/yyyy/zzzz/current experiment/ImageJ Macro.ijm"', i))
}
For each new project I need to edit the filepath manually. I would love a way to define a variable at the beginning of the script which could be passed into the arguments as a string, but I can't figure out how to do it.
I've tried creating a variable just for the filepath, but R can't recognize a variable as part of the string that includes '-batch...'
I've also tried creating a variable containing the entire string that needs to be passed to args, but that doesn't work either. Here's what I coded for that attempt:
ImageJMacro <- paste(getwd(),"/ImageJ Macro.ijm",sep="")
batch1 = sprintf('-batch "%s"', ImageJMacro)
batchline = sprintf("'%s'", batch1)
As you can see, I had to do this in two steps because the single quotes outside of double quotes was giving an error. I thought this would work because when I run:
cat(batchline)
The string looks correct, but when passed into the arguments clause of the system command like so:
macro <- function(i) {
system2('/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx', args=c(batchline, i))
}
it still throws an error.
Any ideas? Other solutions I should try? Thanks in advance for your help, I appreciate it!
Editing to add additional clarification as requested by #rmagn0:
ImageJ is an image analysis software which allows you to write 'macros', hard-coded scripts of repetitive analyses and apply them across many images. I'm not including the ImageJ macro code here because it's not relevant to my question. Suffice it to say that it expects to receive a string argument input, which it then parses out into several components used in the image processing. These string components are parsed out using an asterisk as a delimiter as described in this stack overflow: Calling an ImageJ Macro from R
I am trying to use R to pass a list of arguments to my ImageJ macro, one for each data file I need analyzed, as demonstrated in the code above. Note on above: I named the function in R 'macro', but it is really just calling the command line instance of my ImageJ macro.
If I were to run one instance of the list in the command line, it would look like this:
Contents/MacOS/ImageJ-macosx -batch "/Users/xxxx/yyyy/zzzz/current experiment/ImageJ Macro.ijm" ImageName.tif*Xcoord*Ycoord*/Users/xxxx/yyyy/zzzz/InputDirectory*/Users/xxxx/yyyy/zzzz/OutputDirectory*Suffix
I'm trying to modify a CRAN package. From what I understand, they use a C interface using .Call().
So I made changes in the C code (can't do it anywhere else since it's in a loop) but I need to ask the user to input an integer.
I read the "Writing R extension" doc and found out that you need to use specific functions as Rprintf() instead of printf().
But I can't seem to find a way to replace scanf() so how can we ask for an input?
And finally is Rprintf() supposed to print in the R console because it is what I'd want but I can't find where it is printed?
Edit:
I'm unable to try it right now but it may seem that using capture_output() may work to get the Rprintf() output. Therefore the only remaining issue would be the scanf() :)
Thanks a lot!
I've been struggling to get the example code for a function working using devtools::check(), because the data required for the example is not in .RData format. Unfortunately, the way the function is written, .RData cannot be loaded and work properly. The function takes in a list of filenames and performs an action on them collectively.
Therefore, example code must be written in a way that check() is able to access a folder and list the files therein. Using the function on my own computer, I input
setwd("/Users/mydirectory")
myfilelist <- list.files(pattern = "mypattern")
output <- myfunction(myfilelist, ...)
and everything is groovy. But this doesn't work with devtools because #examples doesn't know how to access subdirectories on my computer. check() pulls the following error:
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
This is almost undoubtedly because check() doesn't know where to look for the data. I'd like it to look toward github to access the online data repository.
I found this brief conversation regarding a similar roxygen-related problem, but overall I haven't seen much advice on how to work through it. I think that perhaps this issue starts to get a little closer to my situation, but here the user failed to export a function, rather than bind data to an example.
I don't think I'm looking for a pull function (though the end goal is to pull data...), does anyone have advice moving forward? I have the data stored in the inst/extdata folder on github, so while I don't really have something reproducible for you all I'm hoping you might have some thoughts.
Edit: I worked around the problem using #alistaire's advice below, and guiding the roxygen to the package directory (updated on github) and also using \dontrun{}. However, I am leaving the question unanswered for now because I think accessing data stored in github should still be somehow possible and we haven't yet addressed that.
I am fitting a GLMM and I had seen some examples where is used the function: overdisp_fun, defined in glmm_funs.R, but I don't know which package contain them or how can I call it from R, can somebody help me?
Thanks,
If you google for glmm_funs.R, you'll find links to the script (eg here: http://glmm.wdfiles.com/local--files/trondheim/glmm_funs.R).
You can save the file on your local machine, then call it in your R session with source("path to file/glmm_funs.R").
You will then be able to use the functions contained in the script, including overdisp_fun().
You can think of it a little bit like loading a package, except the functions are just presented in a script.
I am a newbie to R.
I can successfully load my dataset into R-Studio, and I can see my dataset in the workspace.
When I run the command summary(mydataset), I get the expected summary of all my variables.
However, when I run
data(mydataset)
I get the following warning message:
In data(mydataset) : data set ‘mydataset’ not found
I need to run the data() command as recommended in the fitLogRegModel() command, which is part of the PredictABEL package.
Does anybody have a hint on how I can specify mydataset as working dataset?
You don't need to use the data command. You can just pass your data to the function
riskmodel <- fitLogRegModel(data=mydataset, cOutcome=2,
cNonGenPreds=3:10, cNonGenPredsCat=6:8,
cGenPreds=c(11, 13:16), cGenPredsCat=0)
The example uses data(ExampleData) so that it can make data that is in the package available to you. Since you already have your data, you don't need to load it.
An alternative, although it has its drawbacks, is to use attach(mydataset). You can then refer to variables without a mydatdataset$ prefix. The main drawback, as far as I know (although I'd welcome the views of more expert R users) is that if you modify a variable after attaching, it is then not part of the dataset. This can cause confusion and lead to "gotchas". In any case, many expert R users counsel against the use of attach.