Fix class2tree bug

[gpli]

organisms with unique rank lower than non-unique ranks will give extra wrong rows in 'taxonomy_table_creator' function

Description

Check existence of the lowest non-unique rank (i.e. 'species') before rbind

Related Issue

fix #689

Example

library(taxize)
library(taxizedb)
organisms = c("Haloarcula amylolytica JCM 13557",
              "Haloarcula argentinensis DSM 12282",
              "Haloarcula californiae ATCC 33799",
              "Halarchaeum acidiphilum MH1-52-1")
taxon_IDs = name2taxid(organisms)
taxon_IDs
## [1] "1227452" "1230451" "662475"  "1261545"

classes = taxizedb::classification(taxon_IDs, db = "ncbi")
tr = class2tree(classes)
tr$classification
##                                                     species       genus
## Haloarcula amylolytica JCM 13557     Haloarcula amylolytica  Haloarcula
## Haloarcula argentinensis DSM 12282 Haloarcula argentinensis  Haloarcula
## Haloarcula californiae ATCC 33799    Haloarcula californiae  Haloarcula
## Halarchaeum acidiphilum MH1-52-1    Halarchaeum acidiphilum Halarchaeum
##                                              family           order        class
## Haloarcula amylolytica JCM 13557     Haloarculaceae Halobacteriales Halobacteria
## Haloarcula argentinensis DSM 12282   Haloarculaceae Halobacteriales Halobacteria
## Haloarcula californiae ATCC 33799    Haloarculaceae Halobacteriales Halobacteria
## Halarchaeum acidiphilum MH1-52-1   Halobacteriaceae Halobacteriales Halobacteria
##                                           phylum superkingdom      norank_131567
## Haloarcula amylolytica JCM 13557   Euryarchaeota      Archaea cellular organisms
## Haloarcula argentinensis DSM 12282 Euryarchaeota      Archaea cellular organisms
## Haloarcula californiae ATCC 33799  Euryarchaeota      Archaea cellular organisms
## Halarchaeum acidiphilum MH1-52-1   Euryarchaeota      Archaea cellular organisms

[sckott]

thanks for this PR @gpli

having a look at it now

[sckott]

@gpli can you add a test to https://github.com/ropensci/taxize/blob/master/tests/testthat/test-class2tree.R to address the fixed problem

[gpli]

@sckott the test has been added.

[sckott]

thanks very much @gpli !