improve taxonomy rank indexing

[trvinh]

Description

The previous rank indexing function did not work correctly while sorting the noranks (undefined ranks). This has been fixed now.

Related Issue

Example

[trvinh]

Hi @sckott
sorry, but I don't know how to solve the issue with vcr. I tested the function class2tree using the test file test-class2tree.R, it worked fine by commenting out the vcr::use_cassette function.

[sckott]

Can you please explain the problem in more detail? I'm not sure what problem this is solving.

For the vcr thing, delete the cassette file class2tree_classification_call.yml, from the command line e.g, like rm tests/fixtures/class2tree_classification_call.yml or just in rstudio or however. Then re-run tests again, and it should work. (p.s. we're thinking about how to make this easier for contributors to packages that use vcr in tests - ropensci/vcr#145)

[trvinh]

@sckott removing the cassette files solved the issue, the test for class2tree passed. But the travis-ci has another error: The command "sudo add-apt-repository -y "ppa:marutter/rrutter3.5"" failed and exited with 1 during . . I think it has nothing to do with the taxize package, right?

[sckott]

thanks for fixing cassettes

for the travis failure, i restarted it, its a server system dependency problem - probably intermittent

please answer the above too: Can you please explain the problem in more detail? I'm not sure what problem this is solving.

[trvinh]

I will use this small example to reproduce the issue

library("data.table")
library("ape")
library("taxize")
library("zoo")

spnames <- c("Streptomyces coelicolor", "Mus musculus", "Rattus norvegicus")
input <- classification(spnames, db='ncbi')

# prepare rank list
rankList <- dt2df(lapply(input, get_rank), idcol = FALSE)
# index all ranks of input species
rank_indexing(rankList)

This is the result:

# using the OLD function
> rank_indexing(rankList)
   index           rank
1      5        species
2      6  species group
3      8       subgenus
4      9          genus
5     12      subfamily
6     13         family
8     14  norank_337687
10    17       suborder
7     18          order
13    19  norank_314147
15    20     superorder
17    21 norank_1437010
18    22    norank_9347
19    23   norank_32525
9     24          class
20    25   norank_32524
12    26 norank_1783272
21    26   norank_32523
22    27 norank_1338369
23    28     superclass
24    29  norank_117571
25    30  norank_117570
26    31    norank_7776
27    32    norank_7742
28    33      subphylum
11    34         phylum
29    35   norank_33511
30    36   norank_33213
31    37    norank_6072
32    38        kingdom
33    39   norank_33154
14    40   superkingdom
16    41  norank_131567

# using the NEW function
> rank_indexing(rankList)
   index           rank
1      5        species
2      6  species group
3      8       subgenus
4      9          genus
5     12      subfamily
6     13         family
8     14  norank_337687
10    17       suborder
7     18          order
13    19  norank_314147
15    20     superorder
17    21 norank_1437010
18    22    norank_9347
19    23   norank_32525
9     24          class
20    25   norank_32524
21    26   norank_32523
22    27 norank_1338369
23    28     superclass
24    29  norank_117571
25    30  norank_117570
26    31    norank_7776
27    32    norank_7742
28    33      subphylum
11    34         phylum
12    35 norank_1783272
29    35   norank_33511
30    36   norank_33213
31    37    norank_6072
32    38        kingdom
33    39   norank_33154
14    40   superkingdom
16    41  norank_131567

So, please notice the position of the norank_1783272. According to the order of the NCBI taxonomy ranks for the first species, this rank must be placed between phylum and superkingdom:

> input[1]
$`Streptomyces coelicolor`
                              name          rank      id
1               cellular organisms       no rank  131567
2                         Bacteria  superkingdom       2
3              Terrabacteria group       no rank 1783272
4                   Actinobacteria        phylum  201174
5                   Actinobacteria         class    1760
6                 Streptomycetales         order   85011
7                Streptomycetaceae        family    2062
8                     Streptomyces         genus    1883
9  Streptomyces albidoflavus group species group 1477431
10         Streptomyces coelicolor       species    1902

However, the old rank_indexing places it way before phylum (pos 26 vs 34). With the new function, norank_1783272 (pos 35) can be placed correctly between phylum and superkingdom (pos 34 and 40).

P.S.: the changes in other functions (get_rank, get_name and taxonomy_table_creator) are just code formatting :)

P.P.S.: the travis-ci still failed because of other cassettes, should I also removed them and run the test agains for the whole package?

[sckott]

• okay, thanks for the explanation of the issue. makes sense now.
• okay on formatting changes
• don't worry about tests for other fxns

Looks good to me, thanks for the fix!