Potential clarification for accessionToTaxa and getAccessions documentation

[mooreryan]

I was thinking that the function docs for accessionToTaxa and getAccessions could mention that "version" is the default value for the version argument. Something like this maybe:

#' @param version either 'version' indicating that taxaids are versioned e.g. Z17427.1 or 'base' indicating that taxaids do not have version numbers e.g. Z17427 (default: 'version')

The function docs do state the two available options, but I wasn't sure what the default would be until I read the code and saw those functions calling match.arg. I guess a user might reasonably assume that the first element of that vector would be the default, but I wasn't sure until I read the code.

taxonomizr/R/taxa.R

Line 805 in 915f4d2

accessionToTaxa<-function(accessions,sqlFile,version=c('version','base')){

taxonomizr/R/taxa.R

Line 1194 in 915f4d2

getAccessions<-function(taxaId,sqlFile,version=c('version','base'),limit=NULL){

What do you think?

---

Alternatively, the function signatures could change to something like this, which would make the default value clear.

accessionToTaxa <- function(accessions, sqlFile, version = 'version') { 
    version <- match.arg(version, choices = c('version', 'base'))

[sherrillmix]

I see where you're coming from but the arg=c('default','option2','option3') convention is sort of standard for R e.g.:

• cor's function (..., method = c("pearson", "kendall", "spearman"))
• binom.test's function (...,alternative = c("two.sided", "less", "greater"))
• tidyverse

But I do see how it could be confusing (similarly the tidyverse link adds the caveat "The main downside of this technique is that many users aren’t aware of this convention and that the first value of the vector will be used as a default") so I added the "default:" text to argument definition in the github version of the package. I'll probably wait until a more major issue comes up to hassle the CRAN volunteers with an update.

[sherrillmix]

And thanks for the suggestion! Good luck in your research.