Add new gather_images function

[bschilder]

Description

There are multiple images per species, and not all image UIDs are valid.
This function makes searching for a valid image for each species much easier.
Searches for the best name match per \code{species} and
iteratively tries image UIDs until a viable image is found.

Parallelisation also implemented via parallel::mclapply to help speed up these queries.

Example

species <- c("Mus_musculus","Pan_troglodytes","Homo_sapiens")
res <- rphylopic::gather_images(species=species)

Unit tests added in: tests/testthat/test-gather_images.R

[sckott]

Thanks! this is a good idea. A few requests for change:

• Please use markdown docs, see https://roxygen2.r-lib.org/articles/markdown.html
• I don't use package parallel much. If someone doesn't want to run things in parallel, is that possible with the function as is?
• for the utility functions added, I don't think they each need their own file given their simplicity, please put them in the file zzz.R OR put them both in a file like gather_images_utils.R or similar
• various comments on the code

[sckott]

keep the dev version on please, e.g., 0.3.3.91

[sckott]

I probably don't document this, but I try to push only even number versions to CRAN - change to 0.3.4 please

[bschilder]

This seems to conflict with your previous request. Could you clarify?
#33 (comment)

[sckott]

Makes sense to have the version in the NEWS file be the next to go to cran whereas the version in the DESCRIPTION file i like to use the dev version until the cran push

[bschilder]

• Please use markdown docs, see https://roxygen2.r-lib.org/articles/markdown.html

I'm afraid I don't have time atm to learn this alternative syntax, but feel free to modify to your preference after merging.

• I don't use package parallel much. If someone doesn't want to run things in parallel, is that possible with the function as is?

The default is mc.cores=1, which is equivalent to single-threaded lapply. I always make single-threaded the default because CRAN/Bioc checks require this.

• for the utility functions added, I don't think they each need their own file given their simplicity, please put them in the file zzz.R OR put them both in a file like gather_images_utils.R or similar

I suppose this is a matter of coding preference, I always put separate functions in separate file to make them easy to find.

• various comments on the code

Addressing these now.

[sckott]

Thanks, looks good

[bschilder]

Thanks for all your great work @sckott !

[sckott]

& thx for your contribution