code rev

[smwindecker]

Hi Jorge et al,

As part of a BES hackathon to review data and code provided with published papers I downloaded this repo and ran the code to review whether I could reproduce the analyses. I wanted to reach out because I was almost entirely successful (huge congrats on that!) but there were two issues that I thought you may be interested in knowing/addressing, which I've addressed in this very small pull request.

1. The only code I couldn't run was in Code.Rmd at line 2046 using the vif_func(). It errored at line 14 form_in <- formula(paste(val, '~', form)) because the column names had spaces which formula() doesn't like. I added one line to remove the spaces from the column names and it works fine.

2. The only other change I needed to make to run the code was related to file paths. In your Code.Rmd file they were hardcoded as follows:

seeds_trees <- read.csv("~/Documents/GitHub/MS_JuniperusProgeny/Data/seeds_trees.csv", sep=";")

The PR fixes these paths so they are generically usable for anyone opening the code in an rstudio project (ie seeds_trees <- read.csv("../Data/seeds_trees.csv", sep=";"). Alternatively, you could use the here package or provide the user an option at the top of the script to point to the directory location.

Hope these small changes are of interest, I've submitted them in good faith simply because I'd gone to the effort of rerunning the code anyway. Of course, feel free to ignore!