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If/when you want to go into R packaging in more depth, see Hadley Wickham’s book R Packages.
littleforecast <- function(data, nyears=10){
fit <- forecast::auto.arima(data)
fc <- forecast::forecast(fit, h = nyears)
ggplot2::autoplot(fc)
class(fit) <- c("foo", class(fit))
return(fit)
}
#' Prints foo object
#'
#' prints a foo object returned from littlefunction().
#'
#' @param x foo object
#' @param ... Not used
#' @method print foo
#' @export
print.foo <- function(x, ...) {
cat("Hello there")
}
#' Plots foo object
#'
#' Plots foo object.
#'
#' @param x An foo object.
#' @param ... Not used.
#' @method plot foo
#' @export
plot.foo <- function(x, ...) {
plot(1:10)
}
roxygen2 (and the the ‘Build and Install’ step) will create the help files that users access with `?function.name.
The same man files are also used to create a package manual, e.g. package help file
And it generates the navigation page for all the documentation
help(package="forecast")
The man files are also used by pkgdown to make a website version of your documentation. Here is an example of a pkgdown-generated webpage for the FIT R package r4MAS.
install.packages("roxygen2")
Set the Project Build Options to use Roxygen
Tools > Project Options… > Build Tools > then check the checkbox “Generate documentation with Roxygen”. Then click “Configure”. Check the box at the bottom for “Install and Restart”.
Make sure your DESCRIPTION file has these lines:
Roxygen: list(markdown = TRUE)
RoxygenNote: <some number>
Roxygen comments with #'
are put at the top of your
function, in the same file. They have a standard format and standard
sections. There is a bit of customization you can do, but the following
basic form will cover 95% of your needs. Read
this for more details.
#' @title Short title
#'
#' @description
#' Description should be one paragraph. Put details in details.
#'
#' @details
#' Optional if you want to add more detais.J
#'
#' @param param.name1 Describe all your function arguments
#' @param param.name2 Describe all your function arguments
#'
#' @examples
#' # provide some examples of how to use your function
#' hello()
#'
#' @seealso List relevant other functions [littleforecast()].
#'
#` @references
#' List references
#' @export
yourfunction <- function(param.name1, param.name2){}
@title
and @description
can be left off
(not the text, just the @…. part), but title text should be in line 1,
then a blank line (#’ only), and then the description text. The only
required elements are @title
, @description
,
and @param
(defining the function arguments).
@export
means that your function is added to your
NAMESPACE so is not hidden. Just include this for now.
hello()
First remove the old hello.Rd
file from the man folder.
That is there because when we created our new package using RStudio’s
template, we didn’t select ‘use Roxygen’ so it added a manually created
help (i.e. Rd) file for us in the man folder. Now we are going to use
Roxygen, so we need to remove that file.
Copy and paste this to the top of hello.r
in the R
folder. Replace all the comments at the top with these lines.
#' Hello World!
#'
#' Prints a the classic first program greeting. It takes no arguments.
#'
#' @examples
#' hello()
#' @export
To build the documentation, click ‘Install and Restart’ from the Build tab.
Once your package is reloaded (library(MyPackage)
appears on the command line), you can type ?hello
to get
the help info.
When you update the documentation or add new documentation, rebuild the help files using the ‘Install and Restart’ button on the Build tab. Note, with the default Project Options, RStudio does not remake the documentation when you click ‘Install and Restart’. You have to change that by going to Tools > Project Options > Build Tools and then clicking ‘Configure’ next to ‘Generate documentation with Roxygen’ and then clicking the box next to ‘Install and Restart’.
If you use BibTex you can insert references by citation in your help files.
inst
folder if you don’t have oneREFERENCES.bib
3 Add refs to that
in BibTex format.Imports
in your
DESCRIPTION file and add RdMacros: Rdpack
to your
DESCRIPTION file.\insertRef{Waltonetal1998}{MyPackage}
Example of a reference in REFERENCES.bib
@article{Waltonetal1998,
title={The development and operational application of nonlinear algorithms for the measurement of sea surface temperatures with the NOAA polar-orbiting environmental satellites},
author={Walton, CC and Pichel, WG and Sapper, JF and May, DA},
journal={Journal of Geophysical Research: Oceans},
volume={103},
number={C12},
pages={27999--28012},
year={1998},
publisher={Wiley Online Library}
}
Add the citation to your Rd file with
\insertRef{Waltonetal1998}{MyPackage}
Install the packages. I’ll use {usethis} to make things easier.
install.packages("usethis")
install.packages("pkgdown")
usethis::use_pkgdown()
pkgdown::build_site()
Let’s get this up on GitHub using GitHub Pages. Go to Settings on your repo and scroll down to ‘GitHub Pages’.
The NMFS Fisheries Integrated Toolbox has a branded template that you can use pkgdown template.
Remembering to run {pkgdown::build.site()} every time you change code is both a hassle and unnecessary. Today, we use GitHub Actions to do that for us.
These are put in a .github/workflows
folder in your
GitHub repo. Here
is an example.
That looks hard! Oh we don’t write that code. You just copy a template. Talk to someone who uses these to get tips.
You should stick with a uniform style guide to make your code easier to follow. I use the tidyverse style guide with the styler R package. styler has an RStudio Addin which does all the work of styling my code for me. Install the package, restart RStudio, and then go to Tools > Addins > Browse Addins. Scroll down to styler, and select the file(s), you want to style.
Spell-checking all your code. Use an RStudio add-in or {usethis} package.
Just use the RStudio Check in the Build tab. You’ll have many issues (most likely). Plug away at each one until you pass with no errors or warnings. Don’t ignore Notes either. They are sometimes more serious than the errors and warnings.
If R asks you to update packages, and then proceeds to fail at installation because of a warning that a package was built under a later R version than you have on your computer, use
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS=TRUE)
Run Check from the Build tab regularly.
It is best not to put this off too long or else you’ll create a lot more work for yourself as you track down one warning or error after another.
Don’t let yourself suffer trying to figure out what the warnings and errors mean.
Most are simple namespace issues that are easy to fix once you know how. Ask someone who builds packages. The NMFS R UG Group Chat is a good place.
::
somewheredontrun{}
to make code that won’t run. Horribly, it
can be really hard to actually not run this code, so make sure the code
is correct. If you are showing bad code, then you’ll need to comment it
out.donttest{}
. It is hard to get this respected when
you run check. If you have donttest{}
in your examples
you’ll need to get some help.These are the most common things I run into or want to do with my packages.
@Depends These
packages that will be loaded when your package is loaded. So if you have
gplot2 in @Depends, like
above, then the user automatically can use ggplot2
functions without issuing the command library(ggplot2)
.
@Imports Are required
for the package functions, but the user will not have access to the
functions without calling library(...)
. In your package,
you will use ::
to access the functions from the packages
on the @Imports line. Most of your
package dependencies will be here.
To limit the number of headaches that users face when trying to install your package, use as few packages on your @Depends and @Imports lines in DESCRIPTION file as possible. If your package does not need the package to work, then put the package on @Suggests.
I have R packages that are mainly for my personal use. I use the
package to make sure I have access to the various packages that I’ll be
using. So for example, if I am doing work on my sardine papers, I have
set of packages that I use. When I issue the command
library(SardineForecast)
a bunch of packages are loaded.
This makes it handy for me, but all those dependencies makes it a huge
hassle to install the package from GitHub for my collaborators (and even
a hassle for me to install from GitHub). Huge Hassle. Invariable one of
the 15 packages that I need will itself have a dependency that won’t
load and then I have to debug that. If I need collaborators, who are on
different operating systems and various versions of R to install it,
it’s a suffer-fest.
For my MARSS package, I have only 3 non-base dependencies in the @Imports line and nothing on the @Depends line besides R. The imports are KFAS, mvtnorm, and nlme. Then on the @Suggests line, I have a bunch of packages that are used in the vignettes. MARSS is easy to install from GitHub (though it is also hosted on CRAN).
What should you put on your Depends and Imports lines?
First off, when you are starting, don’t worry too much about this. Just add packages that are needed as you work on your functions.
ALWAYS use ::
to use functions from other packages
in your package functions. Seriously. You will save yourself so many
headaches down the road by being able to search for
xyzpackage::
to find all that packages functions. Why?
Trust me, one day you will want to swap out packages or remove
dependencies. Note, this can be a hassle with functions like
ggplot()
which use functions within their calls and you
have to use ::
everywhere. Like so
ggplot2::ggplot(df) +
ggplot2::geom_point(ggplot2::aes(gp, y))
Arg. Another example is say a GAM call:
mgcv::gam(a ~ mgcv::s(b), data=df)
But this is just for your package functions. In your scripts, you’d
probably use a library()
call.
Never ever use library()
in a function! Use
xyzfunction::function
. Sure use library()
in
your scripts, but never in a package function. When you add a function
from a new package to your function, add those packages to @Depends or @Imports in your DESCRIPTION file as you go
along.
Every so often check that you don’t have packages on @Depends and @Imports that you don’t use. Just do a Edit >
Find in Files… search for xyzpackage::
to find out if you
are still using xyzpackage
.
How do you know if you forgot a dependency or forgot a
::
somewhere? Two ways:
library(yourpackagename)
and try
your functions. Things will fail if you have a package in @Imports but forgot a ::
somewhere.You should stick with a uniform style guide to make your code easier to follow. I use the tidyverse style guide with the styler R package. styler has an RStudio Addin which does all the work of styling my code for me. Install the package, restart RStudio, and then go to Tools > Addins > Browse Addins. Scroll down to styler, and select the file(s), you want to style.
Doing this in RStudio is easy. See rmarkdown vignette chapter and Hadley’s vignette chapter for more info.
Manually
---
fences.Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Or use a helper function:
devtools::use_vignette("my-vignette")
or
usethis::use_vignette("MyNewPackage")
Open your vignette file and click the Knit button.
Once you have your vignettes in the vignettes
folder,
you’l like to be able to build them and have them appear when you type
browseVignettes("MyNewPackage")
. This will not work. In
fact, RStudio seems to actively hinders this workflow.
Vignettes can take a long time to build and by default when R builds
a package from source (which is what Install and Restart on the build
tab does), it does not re-make your vignettes. You can make RStudio
re-make your vignettes in the vignettes
folder (if the Rmd
file changes) using Tools > Project Options > Build Tools >
Generate documentation with Roxygen > Configure and clicking the
vignettes check-box. But this will not get your vignettes loaded when
you click Install and Restart on the Build tab
(browseVignettes()
still won’t work).
So how does R know about your vignettes when it is building from
source (i.e. from Install and Restart in the Build tab in RStudio)? It
needs the vignette files (.Rmd, .R and .html) in the
inst/doc
folder. How do you get them there? You have to put
them there.
That’s easy. I’ll just put them there whenever I change or add
vignettes. Unfortunately, the default RStudio default behavior is to
delete the whole inst/doc
folder whenever you click Check
(package) in the Build tab. It’s happening because the default is to use
devtools::check()
and there is no way to set
devtools::check(vignettes=FALSE)
. To stop RStudio from
deleting inst/doc
on package checking, uncheck the
use devtools package functions if available
box. You may
also want to add --no-manual
to the R CMD Check options box
since that is the default for devtools::check()
.
This is my vignette workflow:
vignette
folder and add vignette Rmds to it
using the R Markdown vignette template in RStudio.inst
folder in my package at the base level
(same level as the R folder).inst/doc
folder.tools::buildVignettes(dir = ".", tangle=TRUE)
dir.create("inst/doc")
file.copy(dir("vignettes", full.names=TRUE), "inst/doc", overwrite=TRUE)
Once your vignette files are in inst/doc
, Install and
Restart button will add the vignettes to your package and
install_github()
will have them too.
Careful, RStudio Check
in the Build tab will
delete the inst/doc
folder and not recreate it. So
always check that inst/doc
not been trashed and
uncheck the use devtools package functions
checkbox on the Build > More > Configure Build Tools… window. You
will most likely also want to add --no-manual
to the
R CMD check additional options
box.
If/when you want to go into R packaging in more depth, work through the material from this R package workshop material. You’ve seen much of this material so it should be somewhat familiar. See also Hadley Wickham’s book R Packages. I like this reference too http://www.danieldsjoberg.com/writing-R-packages/#1