I want to view the R source code with any comments included, to see how the author of the package is running his code, but I am unsure what command to use to see it. In particular, I am trying to see the source code for the bgp() function in the R tgp package. So far I have tried
library(tgp)
tgp::bgp
tgp:::bgp
but each of these commands shows only the source code with the comments stripped away.
That is offering you the parsed version of the code, but it strips out all the comments. The package sources are here: http://cran.r-project.org/src/contrib/tgp_2.4-9.tar.gz
The bgp code is in btgp.R in the R directory.
The general approach to finding the original source to a package on CRAN is to go to: https://cran.r-project.org/web/packages/available_packages_by_name.html
Related
I'm working on a project using programs r and Mplus. On Macs, the Mplus program doesn't allow you to load plots directly but it interfaces with r to do so. Sadly, I've followed the directions provided by the Mplus website but can't seem to locate the "source code" file that they casually refer to. I've searched my computer and the internet for an r file called "mplus.R" to no avail. Does anyone have experience with this?
Here are the two sources from Mplus I've been following:
https://www.statmodel.com/mplus-R/
http://www.statmodel.com/mplus-R/Mplus%20R%20tutorial.pdf
I've loaded the BiocManager package which is required to load the rhdf5 package but there are no functions for mplus listed in that second link. The answer must be in the mplus.R source code but I can't find it anywhere. Any help is much appreciated.
I found the source code right after sending off that question. I won't delete it incase someone might find this useful.
The mplus.R code required to view plots can be find in the first link posted in the question. It's under the section titled "The File mplus.R" but it must be copied and pasted into your r console or script and ran.
I get this warning
Non-standard file/directory found at top level:
‘data-raw’
when building my package, even there is the recommendation of creating this folder to create package data http://r-pkgs.had.co.nz/data.html#data-sysdata
Any comments on that or do I need a specific setting to get rid of this message.
When used, data-raw should be added to .Rbuildignore. As explained in the Data section of Hadley's R-Packages book (also linked in the question)
Often, the data you include in data/ is a cleaned up version of raw data you’ve gathered from elsewhere. I highly recommend taking the time to include the code used to do this in the source version of your package. This will make it easy for you to update or reproduce your version of the data. I suggest that you put this code in data-raw/. You don’t need it in the bundled version of your package, so also add it to .Rbuildignore. Do all this in one step with:
usethis::use_data_raw()
I'm developing an R package, and I'm trying to make a link from the manual of the package to its vignette (a pdf). I've make this in the R function code, and it works:
\link[=../doc/package.pdf]{package's User Manual}
The problem is that the devtools::check() complains with a warning, which also causes a delay in the process of revision when uploading to CRAN...
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'package.Rd':
'../doc/package.pdf'
Is there a better way of linking from man to vignette? or it is not correct to do so? As the pdf can contain more graphical information, it seems desirable to be able to link to it.
If you use pkgdown to make a website out of your package, then you can directly link to the url of the specific vignette.
Or you can just write
Run \code{vignette("NAME_OF_YOUR_VIGNETTE", package = "NAME_OF_YOUR_PACKAGE")} to see the corresponding vignette.
R noobie here.
I'm am trying to use a package that I download off of github using source_gist, but it appears that I need to re-download it every time I quit R (I'm using RStudio).
To clarify, the function that I'm using is part of plotrix package and is called barp. Someone made a modified version of it (called barp2) and put it up on github. That's what I want to use.
So my question is this: is there anyway to have this modified code saved inside the plotrix package, so I wouldn't have to download it every time?
I hope I'm explaining this correctly.
So, let's get some quick terminology straight: the function you're getting off of github isn't a package, it's just a single function. If it was a package, you could use devtools::install_github once and then load it with require() or library() like any other package.
A good solution isn't too different. Just go to the gist, copy the code, paste it into your R editor, and save it somewhere as a .R script file. Something like C:/path/to/barp2.R (adjusting, of course, based on where you actually want to keep it and based on your OS). Then you can read it locally using source("C:/path/to/barp2.R") instead of devtools::source_gist().
If you always want to load it, you could load plotrix and then source this file every time R starts with a couple lines in your R profile, see ?Startup as #BondedDust suggests for details on this.
Reading it off of github every time does have the advantage that, if the author fixes bugs or otherwise improves it, you'll always be using the up-to-date version. It has several disadvantages too: requiring an internet connection, losing access if the gist is deleted, or being unable to access old versions if the author changes it in a way you don't like. Keeping a copy of a version you like is a smart move.
I'm new to Rcpp and want to export some C++ class into R. I've install RcppExmples intending to learn some code snippet. But I didn't even know how to use it? help(RcppExamples) only to get:
Description:
This package shows some simple examples for the use of ‘Rcpp’.
Both the older ('classic') and new API are documented.
It can also serve as a working template to create packages that
use ‘Rcpp’ to interface C++ code or libraries.
Where can I get the examples?
The sources for the examples in the package are, well, in the package itself.
This is Rcpp. It works with C++ source code, and R code. You don't use this like a normal package, you create packages with it. From source.
Did you had a look at the manual? I think it's clear from this document. But the DESCRIPTION file says:
Note that the documentation in this package currently does not cover all the features in the package. It is not even close.
So I fear that's all you can get - besides looking at the source code.