In R, one very neat feature is that the source code of functions is accessible as objects in the workspace.
Thus, if I wanted to know the source code of, for example, grep() I can simply type grep into the console and read the code.
Similarly, I can read the documentation for grep by typing ?grep into the console.
Question: How can I get the source code for the documentation of a function? In other words, where do I find the .rd files?
I find studying the source of well-written code an excellent way of learning the idioms. Now I want to study how to write documentation for some very specific cases. I have not been able to find the documentation files for any of the base R functions in my R installation. Perhaps I have been looking in the wrong place.
It seems you can extract the Rd sources from an installed R. I'm using R-devel (2011-09-05 r56942).
Get the database of Rd for the base package.
library(tools)
db <- Rd_db("base")
Search for "grep.Rd" in the names of the Rd DB, for example:
grep("grep.Rd", names(db), value = TRUE)
[1] "d:/murdoch/recent/R64/src/library/base/man/agrep.Rd"
[2] "d:/murdoch/recent/R64/src/library/base/man/grep.Rd"
Get just the Rd object for grep.
db[grep("/grep.Rd", names(db))]
$`d:/murdoch/recent/R64/src/library/base/man/grep.Rd`
\title{Pattern Matching and Replacement}
\name{grep}
\alias{grep}
\alias{grepl}
\alias{sub}
\alias{gsub}
\alias{regexpr}
\alias{gregexpr}
\alias{regexec}
\keyword{character}
\keyword{utilities}
\description{
\code{grep}, \code{grepl}, \code{regexpr} and \code{gregexpr} search
for matches to argument \code{pattern} within each element of a
character vector: they differ in the format of and amount of detail in
the results.
\code{sub} and \code{gsub} perform replacement of the first and all
matches respectively.
}\usage{
...
...
There are tools for getting the components from the Rd objects, so you can refine searching to keywords or name, see examples in ?Rd_db and try this.
lapply(db, tools:::.Rd_get_metadata, "name")
Related
In R you can search the documentation by typing a question mark ? or a double question mark ??. How do you search the manual for strings in the Julia REPL?
>?first
No documentation for ‘first’ in specified packages and libraries:
you could try ‘??first’
>??first
In the R console a browser window opens up:
In RStudio the page is opened within the IDE.
The help() function and ? help operator in R provide access to the
documentation pages for R functions, data sets, and other objects,
both for packages in the standard R distribution and for contributed
packages.
The help() function and ? operator are useful only if you already know the name of the function that you wish to use. Other ways to search include apropos and ??
The apropos() function searches for objects, including functions,
directly accessible in the current R session that have names that
include a specified character string.
The ?? operator is a synonym for help.search(). The help.search()
function scans the documentation for packages installed in your
library. The argument to help.search() is a character string or regular expression.
P.S. I intend to answer my own question.
Julia has similar interactive utilties. Julia's main search utility for docstrings is named apropos.
To search the documentation for information about "first" in Julia, you have apropos("first") or equivalently ?"first". Thus ?"first" is roughly equivalent to R's ??.
To search for functions and methods, you can type a singe question mark ?, just as with R. In the Julia REPL, as you type the question mark, the prompt changes to a question mark. If you type "first" it searches through strings, while if you type first without quote-marks, you get a search over variables exported by the modules currently loaded.
Illustration:
help?>"first"
# or equivalently:
julia>apropos("first")
help?>first
If you search for a string, case is ignored. If you want to search within the DataFrames module, type using DataFrames before searching.
This also works in Visual Studio Code and Atom:
I have a query.
There is a package in python called "Enchant"
Enchant is a module in python which is used to check the spelling of a word, gives suggestions to correct words. Also, gives antonym and synonym of words. It checks whether a word exists in dictionary or not.
In this module, we can define our own dictionary.
Can you tell me if there is a similar package available in R.
I checked hunspell but I am not able to define my own dictionary.
Can you please help me out
R has a spelling package. See https://cran.r-project.org/package=spelling. It doesn't provide synonyms and antonyms.
I need to extract the exact lines of the source that was parsed to create an R function, for use in coverage analysis. deparse is not accurate enough because in doing coverage analysis with package covr exact line numbers matter.
If there is a srcfile, I just need the filename. If there isn't, e.g. function was created in console, I need to create an equivalent temporary file that could have been, line by line, the source file for that function.
I see several function to extract src information from a function, like getsrcFilename or getSrcref, but none specifically to get the source code.
getSrclines looked promising, but doesn't take functions as arguments. I tried to use attributes to get to the srcref and get to the information that way, but it doesn't seem to be stored consistently -- clearly I am missing something.
Sometimes
attributes(body(cover.fun))$srcfile works and sometimes this attributes(attributes(cover.fun)$srcref)$srcfile) does, and in the srcref itself I found the source in srcfile$lines or srcfile$original$lines and of course these look just like experiments and not The Right Way to implement this.
I need something that takes care of functions created in a package, with source or interactively. If the filename is available, that's all I need, otherwise I need the source lines. Thanks
I recently learned R has a function called RShowDoc() that lets you specify and open package documentation and R help files.
I had fun with some examples but have been limited by document file names that I know. Is there a way to list all the available documents I could use with this function, something like ls().
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().