Packagage Mangement?

[leirbagflow]

Just tried to run global.R and need to install a few packages first. I recommend updating to something like the following for ease of use:

If a package is installed, it will be loaded. If any
are not, the missing package(s) will be installed
from CRAN and then loaded.

First specify the packages of interest
packages = c("tidyverse", "geomorph",
"phytools", "viridis")

Now load or install&load all

package.check <- lapply(
packages,
FUN = function(x) {
if (!require(x, character.only = TRUE)) {
install.packages(x, dependencies = TRUE)
library(x, character.only = TRUE)
}
}
)

https://vbaliga.github.io/verify-that-r-packages-are-installed-and-loaded/

[DaveParr]

This could be done via renv?

Additionally, potentially this should be a package itself?

Is it possible to get the original researchers to set up renve from their machines. This should give us the explicit package versions in use. Also we should have a note of the version of R this was originally designed to run against for full reproducibility.

[DaveParr]

I've started on this this morning, on a branch of my fork: https://github.com/DaveParr/CalCAT/tree/set-up-package

You can see the exact steps from the commits, but generally:

• Ran renv and made an renv.lock file
• Made a NAMESPACE and a DESCRIPTION
• run sinew to put boilerplate roxygen comments in all the functions
• took the liberty of adding myself as a contributor (as well as the listed original authors) in the description.

Let me know if this is useful/ if you would like a PR