How do I ensure R / Rcpp code is reproducible ("distributable")? - r

I've written some R code for a dissertation, relying on some external packages (e.g., plyr and reshape) and writing a couple relatively simple inline C++ functions using inline and RcppArmadillo.
I would like to ensure it can be performed "as is" on computers others than my own (Win64), for research reproducibility purposes.
My question: suppose I included code for installing the required packages, would the RcppArmadillo (and Rcpp and inline) packages be sufficient to be able to compile the functions written in RcppArmadillo, or would the end user need to change system paths for compilation on his Windows machine? If not, is it possible/recommended to saved the compiled functions from my end and included in the R code I'm shipping?
Also, in the unlikely case that the code should be run some time later (say, a couple of years), is it suffient to include a full R installation with the relevant packages in their current version to make the code "future-proof"?
I hope the question is clear.

I think you mean your code to be "distributable" and "executable by someone else" which is a looser requirement. Being "reproducible" implies that the previous question is a true, and adds the restriction that the results are identical (up to the an epsilon of your choice).
And the usual answer for 'how can I let others run my R code' is to create a package.
For Rcpp-related code, we have an entire vignette devoted to building your own package with your Rcpp-using cod. The vignette is called 'Rcpp-package'.

Related

What is the difference between :: and library? [duplicate]

I'm writing some R functions that employ some useful functions in other packages like stringr and base64enc. Is it good not to call library(...) or require(...) to load these packages first but to use :: to directly refer to the function I need, like stringr::str_match(...)?
Is it a good practice in general case? Or what problem might it induce?
It all depends on context.
:: is primarily necessary if there are namespace collisions, functions from different packages with the same name. When I load the dplyr package, it provides a function filter, which collides with (and masks) the filter function loaded by default in the stats package. So if I want to use the stats version of the function after loading dplyr, I'll need to call it with stats::filter.
This also gives motivation for not loading lots of packages. If you really only want one function from a package, it can be better to use :: than load the whole package, especially if you know the package will mask other functions you want to use.
Not in code, but in text, I do find :: very useful. It's much more concise to type stats::filter than "the filter function from the stats package".
From a performance perspective, there is a (very) small price for using ::. Long-time R-Core development team member Martin Maechler wrote (on the r-devel mailing list (Sept 2017))
Many people seem to forget that every use of :: is an R
function call and using it is inefficient compared to just using
the already imported name.
The performance penalty is very small, on the order of a few microseconds, so it's only a concern when you need highly optimized code. Running a line of code that uses :: one million times will take a second or two longer than code that doesn't use ::.
As far as portability goes, it's nice to explicitly load packages at the top of a script because it makes it easy to glance at the first few lines and see what packages are needed, installing them if necessary before getting too deep in anything else, i.e., getting halfway through a long process that now can't be completed without starting over.
Aside: a similar argument can be made to prefer library() over require(). Library will cause an error and stop if the package isn't there, whereas require will warn but continue. If your code has a contingency plan in case the package isn't there, then by all means use if (require(package)) ..., but if your code will fail without a package you should use library(package) at the top so it fails early and clearly.
Within your own package
The general solution is to make your own package that imports the other packages you need to use in the DESCRIPTION file. Those packages will be automatically installed when your package is installed, so you can use pkg::fun internally. Or, by also importing them in the NAMESPACE file, you can import an entire package or selectively importFrom specific functions and not need ::. Opinions differ on this. Martin Maechler (same r-devel source as above) says:
Personally I've got the impression that :: is
much "overused" nowadays, notably in packages where I'd strongly
advocate using importFrom() in NAMESPACE, so all this happens
at package load time, and then not using :: in the package
sources itself.
On the other hand, RStudio Chief Scientist Hadley Wickham says in his R Packages book:
It's common for packages to be listed in Imports in DESCRIPTION, but not in NAMESPACE. In fact, this is what I recommend: list the package in DESCRIPTION so that it’s installed, then always refer to it explicitly with pkg::fun(). Unless there is a strong reason not to, it's better to be explicit.
With two esteemed R experts giving opposite recommendations, I think it's fair to say that you should pick whichever style suits you best and meets your needs for clarity, efficiency, and maintainability.
If you frequently find yourself using just one function from another package, you can copy the code and add it to your own package. For example, I have a package for personal use that borrows %nin% from the Hmisc package because I think it's a great function, but I don't often use anything else from Hmisc. With roxygen2, it's easy to add #author and #references to properly attribute the code for a borrowed function. Also make sure the package licenses are compatible when doing this.

R: When to use package::function() vs function()? [duplicate]

I'm writing some R functions that employ some useful functions in other packages like stringr and base64enc. Is it good not to call library(...) or require(...) to load these packages first but to use :: to directly refer to the function I need, like stringr::str_match(...)?
Is it a good practice in general case? Or what problem might it induce?
It all depends on context.
:: is primarily necessary if there are namespace collisions, functions from different packages with the same name. When I load the dplyr package, it provides a function filter, which collides with (and masks) the filter function loaded by default in the stats package. So if I want to use the stats version of the function after loading dplyr, I'll need to call it with stats::filter.
This also gives motivation for not loading lots of packages. If you really only want one function from a package, it can be better to use :: than load the whole package, especially if you know the package will mask other functions you want to use.
Not in code, but in text, I do find :: very useful. It's much more concise to type stats::filter than "the filter function from the stats package".
From a performance perspective, there is a (very) small price for using ::. Long-time R-Core development team member Martin Maechler wrote (on the r-devel mailing list (Sept 2017))
Many people seem to forget that every use of :: is an R
function call and using it is inefficient compared to just using
the already imported name.
The performance penalty is very small, on the order of a few microseconds, so it's only a concern when you need highly optimized code. Running a line of code that uses :: one million times will take a second or two longer than code that doesn't use ::.
As far as portability goes, it's nice to explicitly load packages at the top of a script because it makes it easy to glance at the first few lines and see what packages are needed, installing them if necessary before getting too deep in anything else, i.e., getting halfway through a long process that now can't be completed without starting over.
Aside: a similar argument can be made to prefer library() over require(). Library will cause an error and stop if the package isn't there, whereas require will warn but continue. If your code has a contingency plan in case the package isn't there, then by all means use if (require(package)) ..., but if your code will fail without a package you should use library(package) at the top so it fails early and clearly.
Within your own package
The general solution is to make your own package that imports the other packages you need to use in the DESCRIPTION file. Those packages will be automatically installed when your package is installed, so you can use pkg::fun internally. Or, by also importing them in the NAMESPACE file, you can import an entire package or selectively importFrom specific functions and not need ::. Opinions differ on this. Martin Maechler (same r-devel source as above) says:
Personally I've got the impression that :: is
much "overused" nowadays, notably in packages where I'd strongly
advocate using importFrom() in NAMESPACE, so all this happens
at package load time, and then not using :: in the package
sources itself.
On the other hand, RStudio Chief Scientist Hadley Wickham says in his R Packages book:
It's common for packages to be listed in Imports in DESCRIPTION, but not in NAMESPACE. In fact, this is what I recommend: list the package in DESCRIPTION so that it’s installed, then always refer to it explicitly with pkg::fun(). Unless there is a strong reason not to, it's better to be explicit.
With two esteemed R experts giving opposite recommendations, I think it's fair to say that you should pick whichever style suits you best and meets your needs for clarity, efficiency, and maintainability.
If you frequently find yourself using just one function from another package, you can copy the code and add it to your own package. For example, I have a package for personal use that borrows %nin% from the Hmisc package because I think it's a great function, but I don't often use anything else from Hmisc. With roxygen2, it's easy to add #author and #references to properly attribute the code for a borrowed function. Also make sure the package licenses are compatible when doing this.

when is R's `ByteCompile` counter-productive?

The R docs describe the ByteCompile field in the "DESCRIPTION file" section as:
The ‘ByteCompile’ logical field controls if the package code is to be byte-compiled on installation: the default is currently not to, so this may be useful for a package known to benefit particularly from byte-compilation (which can take quite a long time and increases the installed size of the package)
I infer the only detrimental side-effects to byte-compiling are (a) time-to-install and (b) installation size. I haven't found a package that takes too long during installation/byte-compiling, and the general consensus is that GBs are cheap (for storage).
Q: When should I choose to not byte-compile packages I write? (Does anybody have anecdotal or empirical limits beyond which they choose against it?)
Edit: As noted in the comments of an older question, the rationale that debugging is not possible with byte-compiled code has been debunked. Other related questions on SO have discussed how to do it (either manually with R CMD INSTALL --byte-compile ... or with install.packages(..., type="source", INSTALL_opts="--byte-compile")), but have not discussed the ramifications of or arguments against doing so.
I have yet to find a downside for byte-compiling, other than the ones you mention: slightly increased file size and installation time.
In the past, compiling certain code could cause slow-down but in recent versions of R (version >3.3.0), this doesn't seem to be a problem.

Stealing methods and data from other R packages

I am currently developing an R package that make use of different datasets from other R packages. As a result, my package has a large number of dependencies, and the user is required to install various unrelated packages in order for my package to work.
I would prefer to copy these datasets to my own package and give proper credit in the documentation, but is there a problem with that?
And what about simple functions from other packages? For example, I need the Matern function from the fields package, and it seems much simpler to just copy that function to my own package instead of having a dependency on a whole package full of unrelated functionality.
Why not just ask the authors/maintainers of those packages for their permission or thoughts on the matter? They may know something that the rest of us don't about how the functions are implemented and how easy they are to copy.
Two different people asked me if they could include a function from my package in theirs, they explained why they wanted to and what they were doing and I agreed that having the user install my whole package for just the 1 function would be overkill and gave them my blessing (and the original source code) to include the functions in their packages (technically due to the license they did not need my permission). Now when I update either of the functions, I also send the updated source code to those 2 authors so that they can keep their copy up to date if they want to.

Is it a good practice to call functions in a package via ::

I'm writing some R functions that employ some useful functions in other packages like stringr and base64enc. Is it good not to call library(...) or require(...) to load these packages first but to use :: to directly refer to the function I need, like stringr::str_match(...)?
Is it a good practice in general case? Or what problem might it induce?
It all depends on context.
:: is primarily necessary if there are namespace collisions, functions from different packages with the same name. When I load the dplyr package, it provides a function filter, which collides with (and masks) the filter function loaded by default in the stats package. So if I want to use the stats version of the function after loading dplyr, I'll need to call it with stats::filter.
This also gives motivation for not loading lots of packages. If you really only want one function from a package, it can be better to use :: than load the whole package, especially if you know the package will mask other functions you want to use.
Not in code, but in text, I do find :: very useful. It's much more concise to type stats::filter than "the filter function from the stats package".
From a performance perspective, there is a (very) small price for using ::. Long-time R-Core development team member Martin Maechler wrote (on the r-devel mailing list (Sept 2017))
Many people seem to forget that every use of :: is an R
function call and using it is inefficient compared to just using
the already imported name.
The performance penalty is very small, on the order of a few microseconds, so it's only a concern when you need highly optimized code. Running a line of code that uses :: one million times will take a second or two longer than code that doesn't use ::.
As far as portability goes, it's nice to explicitly load packages at the top of a script because it makes it easy to glance at the first few lines and see what packages are needed, installing them if necessary before getting too deep in anything else, i.e., getting halfway through a long process that now can't be completed without starting over.
Aside: a similar argument can be made to prefer library() over require(). Library will cause an error and stop if the package isn't there, whereas require will warn but continue. If your code has a contingency plan in case the package isn't there, then by all means use if (require(package)) ..., but if your code will fail without a package you should use library(package) at the top so it fails early and clearly.
Within your own package
The general solution is to make your own package that imports the other packages you need to use in the DESCRIPTION file. Those packages will be automatically installed when your package is installed, so you can use pkg::fun internally. Or, by also importing them in the NAMESPACE file, you can import an entire package or selectively importFrom specific functions and not need ::. Opinions differ on this. Martin Maechler (same r-devel source as above) says:
Personally I've got the impression that :: is
much "overused" nowadays, notably in packages where I'd strongly
advocate using importFrom() in NAMESPACE, so all this happens
at package load time, and then not using :: in the package
sources itself.
On the other hand, RStudio Chief Scientist Hadley Wickham says in his R Packages book:
It's common for packages to be listed in Imports in DESCRIPTION, but not in NAMESPACE. In fact, this is what I recommend: list the package in DESCRIPTION so that it’s installed, then always refer to it explicitly with pkg::fun(). Unless there is a strong reason not to, it's better to be explicit.
With two esteemed R experts giving opposite recommendations, I think it's fair to say that you should pick whichever style suits you best and meets your needs for clarity, efficiency, and maintainability.
If you frequently find yourself using just one function from another package, you can copy the code and add it to your own package. For example, I have a package for personal use that borrows %nin% from the Hmisc package because I think it's a great function, but I don't often use anything else from Hmisc. With roxygen2, it's easy to add #author and #references to properly attribute the code for a borrowed function. Also make sure the package licenses are compatible when doing this.

Resources