So to get to the point: I need to use an R package called machuruku. To get familiar with the package I used the dataset provided in the original paper (https://academic.oup.com/sysbio/article/70/5/1033/6171196). While trying to run the code for the simulation I get an error message saying that the command "machu.simulation" doesn't exist. Any of you have any idea why that's happening? Am I missing a package?

CodePudding user response：

I downloaded the dataset zip file, dove into the second nested zip file Guillory_and_Brown_simulation-validation.zip, then into its file code_simulation-validation.R, and noticed that this source file uses machu.simulation several times before defining the function starting in line 519.

Suggestions:

1. Grab lines 519 through the end, save into a different file, source that new file, then try to run the code in the beginning of the file again.

2. Complain (not quietly?) to the authors, the fact that they think this is reproducible means they might have missed something else, too.