Don't subscript elemental formulas in labels

Author: jedick

DESCRIPTION

@@ -1,6 +1,6 @@
-Date: 2024-12-01
+Date: 2024-12-02
 Package: chem16S
-Version: 1.1.0-10
+Version: 1.1.0-11
 Title: Chemical Metrics for Microbial Communities
 Authors@R: c(
     person("Jeffrey", "Dick", , "[email protected]", role = c("aut", "cre"),

README.md

@@ -16,7 +16,7 @@ Potential applications range from human microbiomes to Earth-life coevolution.
 
 The user provides taxonomic classifications of high-throughput 16S rRNA gene sequences.
 These are combined with reference proteomes for archaea and bacteria to obtain the amino acid compositions of **community reference proteomes**.
-Amino acid compositions used to calculate chemical metrics including **carbon oxidation state** (*Z*<sub>C</sub>) and **stoichiometric hydration state** (*n*<sub>H<sub>2</sub>O</sub>).
+Amino acid compositions used to calculate chemical metrics including **carbon oxidation state** (*Z*<sub>C</sub>) and **stoichiometric hydration state** (*n*<sub>2</sub>O).
 
 Supported input formats:
 * `phyloseq-class` objects created using [*phyloseq*](https://doi.org/doi:10.18129/B9.bioc.phyloseq)
@@ -37,7 +37,7 @@ Training files are available for [DADA2](https://doi.org/10.5281/zenodo.13984843
 ### Example
 
 The Baltic Sea has a salinity gradient from freshwater to marine conditions.
-Progressively lower *n*<sub>H<sub>2</sub>O</sub> of community reference proteomes along this gradient represent a genomically coded dehydration trend.
+Progressively lower *n*H<sub>2</sub>O of community reference proteomes along this gradient represent a genomically coded dehydration trend.
 
 <!-- Default image is too big
 ![chem16S::plot_metrics example: Baltic Sea nH2O-Zc plot](inst/images/plot_metrics.png)

inst/NEWS

@@ -1,4 +1,4 @@
-CHANGES IN chem16S 1.1.0-10 (2024-12-01)
+CHANGES IN chem16S 1.1.0-11 (2024-12-02)
 ---------------------------------------
 
 - Update reference database to GTDB release 220.
@@ -18,6 +18,8 @@ CHANGES IN chem16S 1.1.0-10 (2024-12-01)
 - Add 'rootrank' (Root) taxon to RefDB/GTDB_220/taxon_AA.csv.xz to permit
   complete mapping of RDP output with GTDB reference database.
 
+- Elemental formulas (O2 and H2O) are no longer subscripted in documentation.
+
 CHANGES IN chem16S 1.1.0 (2024-07-01)
 -------------------------------------
 

man/macros/macros.Rd

@@ -1,10 +1,10 @@
 % extracted from CHNOSZ's macros.Rd 20190929
 \newcommand{\Zc}{\ifelse{latex}{\eqn{Z_\mathrm{C}}}{\ifelse{html}{\out{<I>Z</I><sub>C</sub>}}{Zc}}}
 % 20190930
-\newcommand{\nH2O}{\ifelse{latex}{\eqn{n_{\mathrm{H_{2}O}}}}{\ifelse{html}{\out{<i>n</i><sub>H<sub>2</sub>O</sub>}}{nH2O}}}
+\newcommand{\nH2O}{\ifelse{latex}{\eqn{n{\mathrm{H_{2}O}}}}{\ifelse{html}{\out{<i>n</i>H<sub>2</sub>O}}{nH2O}}}
 
 % 20230602
-\newcommand{\nO2}{\ifelse{latex}{\eqn{n_{\mathrm{O_{2}}}}}{\ifelse{html}{\out{<i>n</i><sub>O<sub>2</sub></sub>}}{nO2}}}
+\newcommand{\nO2}{\ifelse{latex}{\eqn{n{\mathrm{O_{2}}}}}{\ifelse{html}{\out{<i>n</i>O<sub>2</sub>}}{nO2}}}
 
 % 20230704 copied from canprot
 \newcommand{\H2O}{\ifelse{latex}{\eqn{\mathrm{H_{2}O}}}{\ifelse{html}{\out{H<sub>2</sub>O}}{H2O}}}

vignettes/metrics.Rmd

@@ -41,7 +41,7 @@ if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL
 
 ```{r HTML, include = FALSE}
 Zc <- "<i>Z</i><sub>C</sub>"
-nH2O <- "<i>n</i><sub>H<sub>2</sub>O</sub>"
+nH2O <- "<i>n</i>H<sub>2</sub>O"
 ```
 
 Here we visualize chemical metrics for archaeal and bacterial taxa and viruses using precomputed reference proteomes in the **chem16S** package.

vignettes/phyloseq.Rmd

@@ -17,8 +17,8 @@ link-citations: true
 
 ```{r HTML, include = FALSE}
 Zc <- "<i>Z</i><sub>C</sub>"
-nH2O <- "<i>n</i><sub>H<sub>2</sub>O</sub>"
-nO2 <- "<i>n</i><sub>O<sub>2</sub></sub>"
+nH2O <- "<i>n</i>H<sub>2</sub>O"
+nO2 <- "<i>n</i>O<sub>2</sub>"
 H2O <- "H<sub>2</sub>O"
 O2 <- "O<sub>2</sub>"
 ```

vignettes/plotting.Rmd

@@ -34,7 +34,7 @@ function ToggleDiv(ID) {
 
 ```{r HTML, include = FALSE}
 Zc <- "<i>Z</i><sub>C</sub>"
-nH2O <- "<i>n</i><sub>H<sub>2</sub>O</sub>"
+nH2O <- "<i>n</i>H<sub>2</sub>O"
 ```
 
 ```{r setup, include = FALSE}