fixed bug caused by new taxonomy ranks

[trvinh]

Description

New taxonomy ranks (e.g. biotype, isolate, pathogroup,...) causes issue for class2tree function:

"Error in if (currentIndex <= tmpEnv[[subList[i - 1]]]) { : argument is of length zero"

By including those new ranks, the problem is solved. The list of current ranks is:

c(
      "strain","biotype","isolate","pathogroup","serogroup","serotype",
      "genotype","morph","forma","subspecies","subvariety","varietas",
      "formaspecialis","subspecies","species","speciessubgroup",
      "speciesgroup","series","subgenus","genus","subtribe","tribe",
      "subfamily","family","superfamily",
      "parvorder","infraorder","suborder","order","superorder",
      "subcohort","cohort","infraclass","subclass","class","superclass",
      "subphylum","phylum","superphylum",
      "subkingdom","kingdom","superkingdom"
)

Other ranks (such as clade, section, subsection,...) are treated as same as no rank, since they can appear at different positions in the taxonomy tree.

Related Issue

#838 #835

Example

library(taxize)
spnames <- c("Engraulis mordax", "Mola mola", "Sebastes", "Sardinops sagax",
             "Merluccius productus")
out <- classification(spnames, db = "ncbi", verbose = FALSE)
out <- out[!is.na(out)]
tr <- class2tree(out)
plot(tr)