functions in inputObjects should produce a single object only

[achubaty]

@ianmseddy @CeresBarros @eliotmcintire

loadkNNSpeciesLayers produces a list that contains 2 input objects: speciesLayers and speciesList.

When providing a custom speciesLayers, the speciesList object wasn't being created and/or was being created from the default by running loadkNNSpeciesLayers and overwriting the custom speciesLayers object.

I am splitting the function in twain and reworking .inputObjects of the 3 modules that use loadkNNSpeciesLayers accordingly.

Please ensure to avoid this in the future.

[eliotmcintire]

Seems unnecessary, at this point. Just extract the two objects in the code:

a <- loadkNNSpeciesLayers(...)
if (!suppliedElsewhere("speciesLayers", sim) && (!suppliedElsewhere("speciesList", sim))) {
  sim$speciesLayers <- a$speciesLayers
  sim$speciesList <- a$speciesList
} else if (!(exists("speciesList", envir = sim) && exists("speciesLayers", envir = sim))) {
  stop("You must provide both speciesList and speciesLayers")
}

[CeresBarros]

@achubaty loadKnnSpeciesLayers should no longer be in Boreal_LBMRDataPrep, but only in pemisc. Are you putting it back then?
Also, the behoviour of loadKnnSpeciesLayers has changed. Please use BiomassSpeciesData as a basis too replicate the use of loadKnnSpeciesLayers in Boreal_LBMRDataPrep

Finally, due to the use of equivalentNames the object speciesList had to be replaced in BiomassSpeciesData with a vector of species names sppNameVector. I didn't have time to do this in Boreal_LBMRDataPrep, but I can do it today if you prefer that I do this. Please let me know @achubaty.

[achubaty]

To clarify, I'm fixing the version in pemisc (master branch) which is used in 3 modules. I cannot use the development version as it breaks to many things at this point. Likewise BiomassSpeciesData.

[achubaty]

This issue was moved to PredictiveEcology/pemisc#7