Reprocess datasets using GTDB release 220

Author: jedick

DESCRIPTION

@@ -1,6 +1,6 @@
 Date: 2024-11-19
 Package: chem16S
-Version: 1.1.0-5
+Version: 1.1.0-6
 Title: Chemical Metrics for Microbial Communities
 Authors@R: c(
     person("Jeffrey", "Dick", , "[email protected]", role = c("aut", "cre"),

README.md

@@ -17,7 +17,7 @@ Supported input formats:
 
 Supported reference databases:
 
-* [Genome Taxonomy Database](https://gtdb.ecogenomic.org/) (GTDB release 214)
+* [Genome Taxonomy Database](https://gtdb.ecogenomic.org/) (GTDB release 220)
 * [NCBI Reference Sequence Database](https://www.ncbi.nlm.nih.gov/refseq/) (RefSeq release 206)
 
 ### Description
@@ -36,7 +36,7 @@ The sequence data analyzed for this plot was taken from [Herlemann et al. (2016)
 
 ### Methods
 
-* Scripts in the [GTDB_214](inst/RefDB/GTDB_214) and [RefSeq_206](inst/RefDB/RefSeq_206) directories were used to generate reference proteomes for genus- and higher-level archaeal and bacterial taxa (and viruses for RefSeq).
+* Scripts in the [GTDB_220](inst/RefDB/GTDB_220) and [RefSeq_206](inst/RefDB/RefSeq_206) directories were used to generate reference proteomes for genus- and higher-level archaeal and bacterial taxa (and viruses for RefSeq).
 
 * It is recommended to use *16S rRNA sequences from GTDB* for taxonomic classification (files are available for [DADA2](https://doi.org/10.5281/zenodo.10403693) and the [RDP Classifier](https://doi.org/10.5281/zenodo.12525163)) so that taxonomic assignments can be automatically matched to GTDB reference proteomes available in *chem16S*.
 

data/mouse.GTDB_214.rda

@@ -1,7 +1,7 @@
-CHANGES IN chem16S 1.1.0-4 (2024-11-19)
+CHANGES IN chem16S 1.1.0-6 (2024-11-20)
 ---------------------------------------
 
-- Change default reference database to GTDB version 220.
+- Update reference database to GTDB version 220.
 
 - Add get_metric_byrank() to return chemical metric for all taxa at a given
   rank, calculated by aggregating abundance-weighted amino acid compositions.