It is my first experience in writing an R-package. I used roxygen2 by following the instructions given in this link http://kbroman.org/pkg_primer/
Everythig is working fine except few things.. there could be a simpler solution to solve the issues, but I am not finding clues what I am doing wrong. I hope someone here in this blog can give a solution to solve my issues.
First issue is about {\code\link{function-name}} in roxygen2:
In .R script I inlcuded this line:
#' #seealso \code{\link{s2a}}
After documenting (generating .Rd files) there is no hyperlink to s2a ,
in documentation s2a shows like a normal text not like hyperlink..
export(s2a) is listed out in NAMESPACE.
Is there any other place i need to modify ?
Second issue is about data():
I saved the dataset in .Rdata format and placed in the data/ in package directory. I also created the .R script in R/ as like following steps here http://kbroman.org/pkg_primer/pages/data.html
In DESCRIPTION file LazyData: true .
but when I type data(shh) in R console gives a warning message
data(shh)
Warning message:
In data(shh) : data set ‘shh’ not found
Any ideas is of great help:)
It's been a while since you asked this, but I was having the exact same problem with hyperlinks in documentation not appearing correctly, so for anyone who might be having a similar problem: Are you possibly viewing the development documentation? The links don't seem to work there. (You'll know this is the case if you see Using development documentation for your_function_name in your console output when you run ?your_function_name.)
The links should appear in the non-development documentation. To generate this you can try building and reloading your package, for instance by following the steps here: http://r-pkgs.had.co.nz/man.html#man-workflow-2
Related
Cross posted from: https://community.rstudio.com/t/link-to-r6-method-from-separate-package-in-help-pages-and-pkgdown/134702
I'm currently writing an R package and would like to link to the help page for an R6 method in a separate package. The page I want to link to is here: https://mc-stan.org/cmdstanr/reference/model-method-sample.html, and there is an .Rd file for the method as well (https://github.com/stan-dev/cmdstanr/blob/master/man/model-method-sample.Rd). Finally, I can also access the help page from R directly with ?cmdstanr::`model-method-sample`.
However, when I try to add a link to my own help page using the normal link to another package syntax described here, [cmdstanr::`model-method-sample`], I get this error:
Warning: Link to unknown topic: cmdstanr::`model-method-sample`
I feel like there must be some way to link to this help page, given that it definitely exists and has an .Rd page, but I haven't found a solution yet. Has anyone else run into this problem or know the solution?
I think you (or Roxygen) are using the wrong syntax for the link. According to Writing R Extensions, the Rd syntax should be:
\link[cmdstanr]{model-method-sample}
I'm not sure how to generate this from Roxygen, but it appears to work as-is if I put it in Roxygen comments.
If you want the link with different text, the syntax is
\link[cmdstanr:model-method-sample]{link text}
I was getting this error when running devtools::document but had no idea how to troubleshoot. The file that popped up on my installed package when I entered ?MyPackage-package did not match the text in MyPackage-package.R at all. I initially suspected it might have been from adding the awesome citation functionality from RDpack, but this was not the culprit. How did I go about ultimately fixing the problem?
The error resulted from incorrect formatting in my PackageName-package.R file.
I had heavily edited the file created by usethis::use_package_doc(), and added all of my roxygen comments Below the default content added by usethis. After looking at the documentation for merTools, I saw that it was ok to have the stuff I understand to be important for roxygen2 to make the .Rd files after and not before all the other roxygen comments.
After moving the stuff created by usethis::use_package_doc() (and not just the NULL line; that was already at the end) to the bottom of the .R file, everything seemed to render fine and this error disappeared.
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 am trying to use the R function dmvnorm (found in the mvtnorm package) in Sublime Text 3. I installed it and ran my code in RStudio, so I know the code is fine. In sublime, I entered:
install.packages('mvtnorm',repos='http://cran.us.r-project.org')
library(mvtnorm)
It looked as though it worked, but when I ran my code it said:
Error: could not find function "dmvnorm"
I'm using a Mac and my hunch is this is somehow related to specifying the path in Preferences -> Package Settings -> Sublime REPL -> Settings - User. The current path displayed as part of the error reads:
[path: /usr/bin:/bin:/usr/sbin:/sbin]
Thanks!
I had a hard time with this recently as well. I'm very new to R so I'm not sure this is the best answer, but to hold you off until someone gives a better one, did you include library('package.name') in the file (in sublime)? require('package.name') also works, but this appears not to be best practice for reasons described, e.g., here.
I hope this helps!
The help page of the news() R function says:
it is attempted to read its news in structured form from files
‘inst/NEWS.Rd’, ‘NEWS’ or ‘inst/NEWS’ (in that order).
Doing so and installing the package, we get (under windows) a link to the NEWS file at the top of the html page open by the command help(package=packagename). For an example, assuming you have installed party, you can try
help(package="party")
This works however only with files named NEWS. When we provide instead a NEWS.Rd file, there is no link to the news. Try
help(package="survival")
Is there a way to get this link when we provide a NEWS.Rd file?
Thanks for your help.
The problem has been solved since R 3.0.0.
It seems, however, that a series of the Rd formatting code such as \code{} for example are ignored when rendering the NEWS.Rd in html.