How to Load Packages in R Automatically

How to load packages in R automatically?

Put library(foo) in your .Rprofile file or set R_DEFAULT_PACKAGES: see ?Rprofile ...

In particular (because ?Rprofile is long and potentially intimidating):

If you want a different set of packages than the default ones when you
start, insert a call to ‘options’ in the ‘.Rprofile’ or
‘Rprofile.site’ file. For example, ‘options(defaultPackages =
character())’ will attach no extra packages on startup (only the
‘base’ package) (or set ‘R_DEFAULT_PACKAGES=NULL’ as an environment
variable before running R). Using ‘options(defaultPackages = "")’ or
‘R_DEFAULT_PACKAGES=""’ enforces the R system default.

Since you probably do want all of the default packages loaded, and then extra ones in addition (rather than, say, not loading some of the default packages), you can either put

library("mypackage1")
library("mypackage2")
[etc.]

or using options(defaultPackages=...):

options(defaultPackages=c(getOption("defaultPackages"),
       "mypackage1","mypackage2", ... [etc.]))

in your .Rprofile to append your desired packages to the standard defaults.

edit (copied from comment) re getting this to work in Rstudio:
http://rstudio.org/docs/using/workspaces suggests that Rstudio executes .Rprofile and then "Performs the other actions described in R Startup [ http://stat.ethz.ch/R-manual/R-patched/library/base/html/Startup.html ]" (which is the same as ?Rprofile). It is ambiguous whether it looks at Rprofile.site or not.

edit #2: according to comment below, it does work with a recent version of Rstudio.

How to load packages automatically when opening a project in RStudio

I presume you want to say that you have to reload all of the packages that were loaded in the workspace previously. That's not an error, that's by design.

If you want to load some packages at startup in a project, you can do so by creating a file called .Rprofile in the project directory, and specify whatever code you want RStudio to run when loading the project.

For example:

cat("Welcome to this project.\n")
require(ggplot2)
require(zoo)

would print a welcome message in the console, and load ggplot2 and zoo every time you open the project.

See also http://www.rstudio.com/ide/docs/using/projects

Elegant way to check for missing packages and install them?

Yes. If you have your list of packages, compare it to the output from installed.packages()[,"Package"] and install the missing packages. Something like this:

list.of.packages <- c("ggplot2", "Rcpp")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

Otherwise:

If you put your code in a package and make them dependencies, then they will automatically be installed when you install your package.

How to load packages automatically when opening a project in RStudio

I presume you want to say that you have to reload all of the packages that were loaded in the workspace previously. That's not an error, that's by design.

If you want to load some packages at startup in a project, you can do so by creating a file called .Rprofile in the project directory, and specify whatever code you want RStudio to run when loading the project.

For example:

cat("Welcome to this project.\n")
require(ggplot2)
require(zoo)

would print a welcome message in the console, and load ggplot2 and zoo every time you open the project.

See also http://www.rstudio.com/ide/docs/using/projects

Loading R packages automatically while preserving the portability of my code

After discussing this question on Software Engineer Stackexchange, I decided to use Imports:magrittr as the smallest and most widely used package that loads all of my custom package dependencies.

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