Problem with converting a phyloseq object to a taxmap object

[lara.c...@gmail.com]

Hi Zach, 

I've been trying the new example for converting a phyloseq object to a taxmap object and appear to be running into a few problems. 

Here are a few of the errors that are popping up: 

> library("metacoder")

> library("phyloseq")

Attaching package: ‘phyloseq’

The following object is masked from ‘package:taxa’:

    filter_taxa

and then when I run the example:

> data(GlobalPatterns)

> x <- parse_phyloseq(GlobalPatterns)

Error in taxa::parse_tax_data(tax_data = tax_data, datasets = datasets,  : 

  unused argument (named_by_rank = TRUE)

Many thanks for your help! 

Lara

[Zachary Foster]

Hello Lara,

Looks like a bug in the version I just released to CRAN. Sorry about that. I was using the development version of "taxa" when I was testing it instead of the CRAN version. It should work with the development version of "taxa". Try the following and let me know if you have problems.

best,

Zach

```
> devtools::install_github("ropensci/taxa")
Skipping install of 'taxa' from a github remote, the SHA1 (7d939b01) has not changed since last install.
  Use `force = TRUE` to force installation
> library(metacoder)
Loading required package: taxa
> library(phyloseq)

Attaching package: ‘phyloseq’

The following object is masked from ‘package:taxa’:

    filter_taxa

> data(GlobalPatterns)
> x <- parse_phyloseq(GlobalPatterns)
>
> x
<Taxmap>
  2692 taxa: aab. Archaea, aac. Bacteria ... hkg. Thermanaerovibrioacidaminovorans, hkk. Jonquetellaanthropi
  2692 edges: NA->aab, NA->aac, aab->aad, aab->aae, aac->aaf ... dzb->hju, dzc->hjv, dzf->hjy, dzn->hkg, dzr->hkk
  4 data sets:
    otu_table:
      # A tibble: 19,216 x 28
        taxon… otu_…   CL3   CC1   SV1 M31F… M11F… M31P… M11P… F21P… M31T… M11T… LMEp… SLEp… AQC1… AQC4cm AQC7cm   NP2   NP3   NP5
        <chr>  <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>  <dbl>  <dbl> <dbl> <dbl> <dbl>
      1 acs    5493…     0     0     0     0     0     0  0        0     0     0     0  1.00  27.0 100    130     1.00     0     0
      2 acs    5224…     0     0     0     0     0     0  0        0     0     0     0  0      0     2.00   6.00  0        0     0
      3 dzw    951       0     0     0     0     0     0  1.00     0     0     0     0  0      0     0      0     0        0     0
      # ... with 1.921e+04 more rows, and 8 more variables: TRRsed1 <dbl>, TRRsed2 <dbl>, TRRsed3 <dbl>, TS28 <dbl>, TS29 <dbl>,
      #   Even1 <dbl>, Even2 <dbl>, Even3 <dbl>
    tax_data:
      # A tibble: 19,216 x 8
        taxon_id Kingdom Phylum        Class        Order        Family        Genus      Species                
        <chr>    <chr>   <chr>         <chr>        <chr>        <chr>         <chr>      <chr>                  
      1 acs      Archaea Crenarchaeota Thermoprotei <NA>         <NA>          <NA>       <NA>                   
      2 acs      Archaea Crenarchaeota Thermoprotei <NA>         <NA>          <NA>       <NA>                   
      3 dzw      Archaea Crenarchaeota Thermoprotei Sulfolobales Sulfolobaceae Sulfolobus Sulfolobusacidocaldarius
      # ... with 1.921e+04 more rows
    sam_data:
      # A tibble: 26 x 8
        sample_ids X.SampleID Primer  Final_Barcode Barcode_truncated_plus_T Barcode_full_length SampleType Description          
        <chr>      <chr>      <chr>   <chr>         <chr>                    <chr>               <chr>      <chr>                
      1 CL3        CL3        ILBC_01 AACGCA        TGCGTT                   CTAGCGTGCGT         Soil       Calhoun South Carolin…
      2 CC1        CC1        ILBC_02 AACTCG        CGAGTT                   CATCGACGAGT         Soil       Cedar Creek Minnesota…
      3 SV1        SV1        ILBC_03 AACTGT        ACAGTT                   GTACGCACAGT         Soil       Sevilleta new Mexico,…
      # ... with 23 more rows
    list()
  0 functions:
```

[Lara Puetz]

Success!!! 

Many thanks for you help and fast response!

Lara

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