bbolker / mm_iowa2024

mixed models workshop for Iowa State *Conference On Applied Statistics In Agriculture And Natural Resources*

MM workshop for Iowa 2024

The friendly GitHub pages version of this repo is posted here

mm_iowa2024's Issues

pak::pkg_install is much faster

I've recently been exploring the pak package for package management.
In your setup script, try this:
pak::pkg_install(all_pkgs)
Because of parallel downloads, it is much faster than built-in install.packages.

prediction package needs github install

When installing github_pkgs, I got an error with the prediction package

> github_pkgs <- c("leeper/margins", "fsolt/dotwhisker")
> for (p in github_pkgs) remotes::install_github(p)
Downloading GitHub repo leeper/margins@HEAD
Installing 1 packages: prediction
trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.4/prediction_0.3.14.tgz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.4/prediction_0.3.14.tgz'

Adding it to the list of github_pkgs succeeds

github_pkgs <- c("leeper/prediction", "leeper/margins", "fsolt/dotwhisker")

INLA might need Bioconductor packages?

When installing INLA, it warns that it can't find Rgraphviz or graph; these seem to be on Bioconductor.

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install(c("Rgraphviz", "graph"))

The BiocManager install process also warns about two old packages, prediction and survival; when I tried updating them survival was able to be updated but prediction was not; apparently update.packages() thinks a newer version is available on CRAN but can't actually find it. See more below.

In any case, if you want people to install these packages, perhaps best to recommend either "some" or "none" in the interactive prompt
Update all/some/none? [a/s/n]:
or simply to use the update=FALSE option

BiocManager::install(c("Rgraphviz", "graph"), update=FALSE)

About updating prediction, there's something odd, though, where 0.3.15 is installed (that's what's on github), it thinks 0.3.17 is on CRAN, but it tries to download 0.3.14.

prediction :
 Version 0.3.15 installed in /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library 
 Version 0.3.17 available at https://cran.rstudio.com
Update? (Yes/no/cancel) Yes
trying URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.4/prediction_0.3.14.tgz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'https://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.4/prediction_0.3.14.tgz'