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StateOfCalifornia / CalCAT

California Communicable diseases Assessment Tool
MIT License
225 stars 101 forks source link

Packagage Mangement? #6

Open leirbagflow opened 4 years ago

leirbagflow commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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:

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