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jedick · Sep 22, 2023 · 8ba8a65 · 8ba8a65
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
-Date: 2023-09-18
+Date: 2023-09-22
 Package: chem16S
-Version: 1.0.0-6
+Version: 1.0.0-7
 Title: Chemical Metrics of Community Reference Proteomes
 Authors@R: c(
     person("Jeffrey", "Dick", , "j3ffdick@gmail.com", role = c("aut", "cre"),

diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
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@@ -19,7 +19,7 @@ Supported reference databases:
 * [Genome Taxonomy Database](https://gtdb.ecogenomic.org/) (GTDB release 207)
 * [NCBI Reference Sequence Database](https://www.ncbi.nlm.nih.gov/refseq/) (RefSeq release 206)
 
-The *chem16S* R package combines taxonomic classifications of high-throughput 16S rRNA gene sequences with precomputed amino acid compositions of reference proteomes for archaea and bacteria to generate the amino acid compositions of **community reference proteomes**.
+The *chem16S* R package combines taxonomic classifications of high-throughput 16S rRNA gene sequences with precomputed amino acid compositions of reference proteomes for archaea and bacteria to obtain the amino acid compositions of **community reference proteomes**.
 Chemical metrics of community reference proteomes such as **carbon oxidation state** (*Z*<sub>C</sub>) and **stoichiometric hydration state** (*n*<sub>H<sub>2</sub>O</sub>) reveal new ways that microbial genomes are adapted to environmental conditions.
 For instance, an association of lower *n*<sub>H<sub>2</sub>O</sub> with higher salinity in the Baltic Sea suggests a genomically encoded dehydration trend:
 
@@ -33,7 +33,7 @@ The sequence data analyzed for this plot was taken from [Herlemann et al. (2016)
 
 ### Methods
 
-* Scripts in the [GTDB](inst/extdata/GTDB) and [RefSeq](inst/extdata/RefSeq) directories were used to generate the reference proteomes for genus- and higher-level archaeal and bacterial taxa (and viruses for RefSeq).
+* Scripts in the [GTDB](inst/extdata/GTDB) and [RefSeq](inst/extdata/RefSeq) 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 a GTDB training set for taxonomic classification (e.g. [*DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea*](https://doi.org/10.5281/zenodo.6655692)) so that taxonomic assignments can be automatically matched to GTDB reference proteomes available in *chem16S*.
 

diff --git a/man/chem16S-package.Rd b/man/chem16S-package.Rd
@@ -168,7 +168,7 @@ Bowen De León K, Gerlach R, Peyton BM, Fields MW. 2013. Archaeal and bacterial
 
 Callahan B. 2020. DADA2 Pipeline Tutorial (1.16). \url{https://benjjneb.github.io/dada2/tutorial.html}, accessed on 2023-06-14.
 
-Dick JM, Meng D. 2023. Community- and genome-based evidence for a shaping influence of redox potential on bacterial protein evolution. \emph{mSystems}. \doi{10.1128/msystems.00014-23}
+Dick JM, Meng D. 2023. Community- and genome-based evidence for a shaping influence of redox potential on bacterial protein evolution. \emph{mSystems} \bold{8}(3): e00014-23. \doi{10.1128/msystems.00014-23}
 
 Dick JM, Tan J. 2023. Chemical links between redox conditions and estimated community proteomes from 16S rRNA and reference protein sequences. \emph{Microbial Ecology} \bold{85}: 1338--1355. \doi{10.1007/s00248-022-01988-9}
 

diff --git a/man/map_taxa.Rd b/man/map_taxa.Rd
@@ -26,7 +26,7 @@ Only exactly matching names are automatically mapped.
 
 For mapping to the NCBI (RefSeq) taxonomy, some group names are manually mapped as follows (see Dick and Tan, 2023):
 \tabular{ll}{
-    \strong{Input (i.e., RDP)} \tab \strong{RefSeq} \cr
+    \strong{RDP training set} \tab \strong{NCBI} \cr
     genus_Escherichia/Shigella \tab genus_Escherichia \cr
     phylum_Cyanobacteria/Chloroplast \tab phylum_Cyanobacteria \cr
     genus_Marinimicrobia_genera_incertae_sedis \tab species_Candidatus Marinimicrobia bacterium \cr