cran-comments.md

In brpetrucci/paleobuddy: Simulating Diversification Dynamics

Test environments

• local macOS Big Sur 11.6, R 4.1.1
• devtools::check_win (devel, release, oldrelease)
• rhub::check (all available platforms)
• GitHub actions (macOS latest, windows latest release; ubuntu latest release, devel and oldrel-1)

R CMD check results

There were no ERRORs, WARNINGs, or NOTEs

This is the first submission of this package, so there may be a first submission NOTE.

Downstream dependencies

There are currently no downstream dependencies for this package

Resubmission

This is a resubmission. In this version I have resolved comments by a CRAN member---great thanks on the feedback. The following have been changed:

• "Please always write package names, software names and API (application programming interface) names in single quotes in title and description. e.g: --> 'paleotree', 'APE', 'RPANDA', 'paleobuddy'" ** Changed all cases of package names in description to be wrapped in single quotes. No instances in title.

• "Please write references in the description of the DESCRIPTION file in the form authors (year) authors (year) authors (year, ISBN:...) or if those are not available: authors (year) with no space after 'doi:', 'arXiv:', 'https:' and angle brackets for auto-linking. (If you want to add a title as well please put it in quotes: "Title")" ** Changed reference of RPANDA to the first mentioned format. No other instances of references in DESCRIPTION

• "Please make sure that you do not change the user's options, par or working directory. If you really have to do so within functions, please ensure with an immediate call of on.exit() that the settings are reset when the function is exited. e.g.: ... oldpar <- par(no.readonly = TRUE) # code line i on.exit(par(oldpar)) # code line i + 1 ... par(mfrow=c(2,2)) # somewhere after ... e.g.: R/draw.sim.R, R/sim.R If you're not familiar with the function, please check ?on.exit. This function makes it possible to restore options before exiting a function even if the function breaks. Therefore it needs to be called immediately after the option change within a function." ** Included first two lines mentioned before any change in par within functions, i.e. draw.sim.R (par(yaxt = "n")); sim.R (par(mfrow = c(1, 3))). No other instances of par or options changes within functions.

• "In examples and vignettes and demos: Please always make sure to reset to user's options(), working directory or par() after you changed it: e.g.: oldpar <- par(mfrow = c(1,2)) ... par(oldpar)" ** Included the first line mentioned before any changes to par in examples, and the second before the end of any plotting, in examples for make.phylo.R and find.lineages.R

• "\dontrun{} should only be used if the example really cannot be executed (e.g. because of missing additional software, missing API keys, ...) by the user. That's why wrapping examples in \dontrun{} adds the comment ('# Not run:') as a warning for the user. Does not seem necessary.

Please unwrap the examples if they are executable in < 5 sec, or replace \dontrun{} with \donttest{}." ** Excluded \dontrun{} from any examples that took less than 5 sec in my local machine. Changed \dontrun{} to \donttest{} in other cases. Kept \dontrun{} in case of examples that will error on run, just used for illustration of wrong usage.

brpetrucci/paleobuddy documentation built on July 26, 2023, 8:15 p.m.