Once I've seen a package supporting R program in which his documentation and reference manual was divided into chapters ( they were called by the consecutive letters of the alphabet ) so that an user could see that functions presented by that package are divided into groups.
Now I'm trying to do the same. I'm building package using roxygen2 package but can not deal with that problem.
Can any1 has any solution ? So in that case my documentation will be split to a file like this:
Group1:
funAX
funBX
funCX
Group2:
funAY
funBY
funCY
instead of
funAX
funAY
funBX
funBY
funCX
funCY
A name of package that provides that solution will also be helpful.
In the lattice package developers invented a way to order a documentation. They simply add letters in an alfabetic order to the beginning of a .Rd file. This order might suggest the way of passing thru the manual to optimize understanding. Manual is here.
Related
So, I'd like to reference one of my package vignettes inside the roxygen2 comments of a function but I'm having a hard time understanding how to do it.
More generally, how do we reference documents inside /inst/doc? E.g. I'd like to reference /inst/doc/mypdf.pdf inside the roxygen2 comments for myFunc. What would that look like? Is it even possible?
I just tell people to run the code that opens the vignette:
#' For more details see the help vignette:
#' \code{vignette("help", package = "mypkg")}
I know this is 4 years old...and hadley provided the answer...but I'd like to offer another option:
\href{../doc/help.html}{\code{vignette("help", package = "mypkg")}}
This gives a direct link to opening the vignette, and provides the code to show the user how to open it on their own.
Long story short:
My aim is to submit a R package developed with roxygen2 to CRAN, and I need to find some guidelines on writing and documenting hidden functions.
More details:
I am writing my first R package using roxygen2 in Rstudio. I have documented all the functions I wrote so far, so that my collaborators can easily understand their purpose before going into the details of the script. All the functions that are of no use to the user, but necessary to the package, are not exported in the namespace and eliminated from the package manual/index (#keywords internal). At the same time, my collaborators can still read their documentation using the help of Rstudio.
Eventually, I would like to remove the documentation of these "hidden functions" from the help because there is no reason to keep it. I was considering to follow a suggestion I found in other posts, that is changing #' with ## in the documentation created with roxygen2. However, I am not sure this is the correct procedure to implement, and if removing the documentation of a function in the help and the manual is compatible with CRAN requirements.
Can anyone point me to some guidelines related to this issue, or has any experience to share?
I have two data.sets (from the memisc package) all set for merge, and the merge goes through without error or warning, but the output is a data.frame, not a data.set. The command is:
datTS <- merge(datT1, datT2, by.x="ryear", by.y="ryear")
(Sorry I don't have a more convenient example with toy data handy.) The following pages seem to make it very clear that there should be a method built into memisc that properly merges the data.sets into one data.set:
http://rpackages.ianhowson.com/rforge/memisc/man/dataset-manip.html
https://github.com/melff/memisc/blob/master/pkg/R/dataset-methods.R
...but it just doesn't seem to be properly triggering on my machine (sorry also for my clumsy lingo). Note the similarity of my code and the example code from the very end of the first page I linked:
ds6 <- merge(ds1,ds5,by.x="a",by.y="c")
I've verified that I have the most recent versions of R, RStudio, memisc, and all dependencies. I've used a number of other memisc methods so far (within, transform, missing.values, etc.) without issue.
So my question is: what else does one need to do to get the merge function to properly produce a data.set when the source data are in data.set form, as per the memisc package? (There's no explicit addressing of this merge capability in the official package documentation.) Since the code in the second link above seems to provide the method for this, is there some workaround, at least, for installing and utilizing that code? Maybe there's just some separate "methods installation" I'm not aware of (but why would it be separate from the main package?).
The help page for pkg:memisc in the released version 0.97 does not describe a merge function method for data.sets. You are pointing us to the github version which may not be the one that has been released. You need to install the github version. See: https://github.com/melff/memisc/releases
What is the possible documentation available for R package? For example I try to understand sp package.
In addition to help(sp), what are the other functions for searching through help and documentation?
Getting help on a function that you know the name of
Use ? or, equivalently, help.
?mean
help(mean) # same
For non-standard names use quotes or backquotes; see An Introduction to R: Getting help with functions and features:
For a feature specified by special characters, the argument must be enclosed in double or single quotes, making it a “character string”: This is also necessary for a few words with syntactic meaning including if, for and function."
?`if`
?"if" # same
help("if") # same
There are also help pages for datasets, general topics and some packages.
?iris
?Syntax
?lubridate
Use the example function to see examples of how to use it.
example(paste)
example(`for`)
The demo function gives longer demonstrations of how to use a function.
demo() # all demos in loaded pkgs
demo(package = .packages(all.available = TRUE)) # all demos
demo(plotmath)
demo(graphics)
Finding a function that you don't know the name of
Use ?? or, equivalently, help.search.
??regression
help.search("regression")
Again, non-standard names and phrases need to be quoted.
??"logistic regression"
apropos finds functions and variables in the current session-space (but not in installed but not-loaded packages) that match a regular expression.
apropos("z$") # all fns ending with "z"
rseek.org is an R search engine with a Firefox plugin.
RSiteSearch searches several sites directly from R.
findFn in sos wraps RSiteSearch returning the results as a HTML table.
RSiteSearch("logistic regression")
library(sos)
findFn("logistic regression")
Finding packages
available.packages tells you all the packages that are available in the repositories that you set via setRepositories. installed.packages tells you all the packages that you have installed in all the libraries specified in .libPaths. library (without any arguments) is similar, returning the names and tag-line of installed packages.
View(available.packages())
View(installed.packages())
library()
.libPaths()
Similarly, data with no arguments tells you which datasets are available on your machine.
data()
search tells you which packages have been loaded.
search()
packageDescription shows you the contents of a package's DESCRIPTION file. Likewise news read the NEWS file.
packageDescription("utils")
news(package = "ggplot2")
Getting help on variables
ls lists the variables in an environment.
ls() # global environment
ls(all.names = TRUE) # including names beginning with '.'
ls("package:sp") # everything for the sp package
Most variables can be inspected using str or summary.
str(sleep)
summary(sleep)
ls.str is like a combination of ls and str.
ls.str()
ls.str("package:grDevices")
lsf.str("package:grDevices") # only functions
For large variables (particularly data frames), the head function is useful for displaying the first few rows.
head(sleep)
args shows you the arguments for a function.
args(read.csv)
General learning about R
The Info page is a very comprehensive set of links to free R resources.
Many topics in R are documented via vignettes, listed with browseVignettes.
browseVignettes()
vignette("intro_sp", package = "sp")
By combining vignette with edit, you can get its code chunks in an editor.
edit(vignette("intro_sp",package="sp"))
This answer already gives you a very comprehensive list.
I would add that findFn("some search terms") in package sos is extremely helpful, if you only have an idea/keywords of what you are looking for and don't already have a package or function in mind.
And also the task views on CRAN: not really a search process but a great place to wander as you wonder.
This thread contains many good suggestions. Let me add one more.
For finding which packages are loaded, plus extra goodies, ?sessionInfo is quite nice.
help(package="<package-name>") where of course <package-name> is the name of the package you want help for.
Often the same function name is used by several packages. To get help on a function from a specific package, use:
help(aggregate, package="stats")
help(aggregate, package="sp")
In the RStudio IDE you can click on any function name and press F1, which will directly open the associated function help text in its pane. Like you would have called help() or ?fun().
I am writing an R package names slidify. The main function in the package is also named slidify. When I run devtools::check, I get a warning that there is a conflict in the Rd files.
I don't want to rename the function, since it succintly conveys what the package is intended for. What is best practice in this situation? Should typing ? slidify lead to the function documentation or package documentation?
Any thoughts would be appreciated.
I'd make a "slidify-package.Rd" file, (or a "slidify-package.R" file with nothing but roxygen comment blocks)
?slidify should lead to the function documentation and slidify?package should lead to the package documentation, and both help pages should have a link to the other (in the seealso section, for example)