diff --git a/DESCRIPTION b/DESCRIPTION
index 1f31989..75f658e 100644
--- 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
index 0e28937..15790dc 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
-[![CRAN](https://www.r-pkg.org/badges/version/chem16S)](https://cran.r-project.org/package=chem16S)
+[![CRAN](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2Fchem16S%2FDESCRIPTION&query=%24.Version&logo=r&label=CRAN&color=4bc51e)](https://cran.r-project.org/package=chem16S)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6793059.svg)](https://doi.org/10.5281/zenodo.6793059)
[![R-CMD-check](https://github.com/jedick/chem16S/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jedick/chem16S/actions/workflows/R-CMD-check.yaml)
@@ -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*C) and **stoichiometric hydration state** (*n*H2O) reveal new ways that microbial genomes are adapted to environmental conditions.
For instance, an association of lower *n*H2O 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
index 5b7e5c4..c746810 100644
--- 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
index 04c7360..0b8a1ba 100644
--- 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