Uncaught errors when important fields are missing (using drop)

[Lobz]

I created a small test script for the workflow, which can be used to test:

library(plantR) # used foi reading and cleaning occurrence data
occs_gbif <- rgbif2(species = "Rosaceae",
    country = "BR",
    n.records = 10)
occs <- formatDwc(gbif_data = occs_gbif, drop.empty = TRUE)
occs
occs <- formatOcc(occs)
occs <- formatLoc(occs)
occs <- formatCoord(occs)
occs <- formatTax(occs)

When using small sample datasets like this, it's not unusual that some essential fields will be empty. The problem is that the format functions do not detect this, and instead of failing gracefully they crash with uncaught errors. In this case, the errors are as follows:

> occs <- formatOcc(occs)
Error in `$<-.data.frame`(`*tmp*`, "recordNumber.new", value = character(0)) : 
  replacement has 0 rows, data has 10
> occs <- formatLoc(occs)
Error in `[.data.frame`(x, , match(loc.levels, colnames(x)), drop = FALSE) : 
  undefined columns selected
> occs <- formatCoord(occs)
Error in getCoord(x = coords1, lat.orig, lon.orig, lat.gazet, lon.gazet,  : 
  One or more column names were not found: please check or specify column names
> occs <- formatTax(occs)
> 

[LimaRAF]

Thanks for this issue. I have not used the package for running such small datasets. But you it should deal with smaller ones with missing fields. I added some patches along formatLoc() to make sure it does not fail any more. Not sure now if any other function may need the same patches. But at least I could not reproduce the error using your small test script after the changes I did in commit ac17995. Please let me know if you find any other issue related to this in other functions.