Reformat NEWS as NEWS.Rd

DESCRIPTION

@@ -1,6 +1,6 @@
-Date: 2024-03-10
+Date: 2024-03-11
 Package: canprot
-Version: 1.1.2-38
+Version: 1.1.2-39
 Title: Chemical Analysis of Proteins
 Authors@R: c(
     person("Jeffrey", "Dick", email = "[email protected]", role = c("aut", "cre"),

README.md

@@ -47,12 +47,12 @@ demo("thermophiles")
 #demo("redoxins")
 ```
 
-<img src="inst/images/thermophiles.png" alt="Specific entropy and Zc and pI for Nitrososphaeria MAGs" title="Thermophiles demo for canprot" width="600px" />
+<a href="https://chnosz.net/canprot/vignettes/demos.html"><img src="inst/images/thermophiles.png" alt="Specific entropy and Zc and pI for Nitrososphaeria MAGs" title="Thermophiles demo for canprot" width="400px" /></a>
 
 This is a scatter plot of standard specific entropy (*S*<sup>&deg;</sup> per gram) and carbon oxidation state (*Z*<sub>C</sub>) for proteins in *Nitrososphaeria* (syn. *Thaumarchaeota*) MAGs reported by [Luo et al. (2024)](https://doi.org/10.1093/ismejo/wrad031).
 *S*<sup>&deg;</sup> is calculated using amino acid group contributions ([Dick et al, 2006](https://doi.org/10.1111/gbi.12532)) via `canprot::S0g()`.
 This plot reveals that proteins tend to have higher specific entropy in MAGs from thermal habitats compared to those from nonthermal habitats with similar carbon oxidation state.
-This implies that, after correcting for *Z*<sub>C</sub>, proteins in thermophilic genomes have a <ins>more negative derivative</ins> of the standard Gibbs energy per gram of protein with respect to temperature.
+This implies that, after correcting for *Z*<sub>C</sub>, proteins in thermophiles have a <ins>more negative derivative</ins> of the standard Gibbs energy per gram of protein with respect to temperature.
 See the [Demos for canprot](https://chnosz.net/canprot/vignettes/demos.html) vignette for a similar plot for genomes of methanogenic archaea.
 
 <!--

inst/NEWS.Rd

@@ -0,0 +1,60 @@
+\name{NEWS}
+\title{News for Package 'canprot'}
+\encoding{UTF-8}
+
+\section{Changes in canprot version 1.1.2-39 (2024-03-11)}{
+
+    \itemize{
+
+      \item Objects in \code{cplab} are now \code{quote()}-ed instead of
+      \code{expression()}s for easier handling by other functions.
+
+      \item Functions for chemical metrics (\code{ZCAA()}, \code{O2AA()},
+      \code{H2OAA()}, and \code{MWAA()}) have been renamed to \code{Zc()},
+      \code{nO2()}, \code{nH2O()}, and \code{MW()}.
+
+      \item Add \code{terminal_H2O} argument to \code{nH2O()}, used to specify
+      how terminal -H and -OH groups are counted (they are not by default). 
+
+      \item Add \code{...} argument to functions to permit using the same
+      arguments for all metrics in \code{get()} or \code{do.call()}
+      constructions.
+
+      \item Add functions for metrics: \code{plength()} (protein length),
+      \code{V0()} and \code{S0()} (standard molal volume and entropy per
+      residue), \code{pV0()} and \code{pS0()} (volume and entropy per protein),
+      \code{V0g()} and \code{S0g()} (specific volume and entropy),
+      \code{Density()} (mass density), \code{SV()} (entropy density),
+      \code{Cost()} (metabolic cost of amino acids from
+      \href{https://doi.org/10.1073/pnas.062526999}{Akashi and Gojobori,
+        2002}), \code{RespiratoryCost()} and \code{FermentativeCost()}
+      (respiratory and fermentative costs from
+      \href{https://doi.org/10.1093/molbev/msi126}{Wagner, 2005}), and
+      \code{B20Cost()}, \code{Y20Cost()}, and \code{H11Cost()} (biosynthetic
+      costs from \href{https://doi.org/10.1038/s41467-018-06461-1}{Zhang et
+        al., 2018}).
+
+      \item Differential expression datasets (including old to new ID mappings
+      in \file{uniprot_updates.csv}) and chemical analysis vignettes have been
+      moved from \pkg{canprot} to to \pkg{JMDplots}.
+
+      \item \code{read.fasta()}, \code{count.aa()}, and \code{aasum()} have
+      been moved from \pkg{CHNOSZ} to \pkg{canprot}.
+
+      \item \code{calc_metrics()} and \code{add_hull()} have been moved to from
+      \pkg{chem16S} to \code{calc.metrics()} and \code{add.hull()} in
+      \pkg{canprot}.
+
+      \item \code{protcomp()} has been renamed \code{human.aa()}.
+
+      \item Add \code{add.cld()} (add compact letter display to boxplots).
+
+      \item Add demos \file{thermophiles.R}, \file{locations.R}, and
+      \file{redoxins.R}.
+
+      \item Add vignettes \emph{Demos for canprot} and \emph{More about
+        metrics}.
+
+    }
+
+}

inst/NEWS → inst/ONEWS

@@ -1,44 +1,3 @@
-CHANGES IN canprot 1.1.2-38 (2024-03-10)
-----------------------------------------
-
-- Objects in cplab are now `quote()`-ed instead of `expression()`s for easier
-  handling by other functions.
-
-- Functions for chemical metrics (ZCAA(), O2AA(), H2OAA(), and MWAA()) have
-  been renamed to Zc(), nO2(), nH2O(), and MW().
-
-- Add 'terminal_H2O' argument to nH2O(), used to specify how terminal -H and
-  -OH groups are counted (they are not by default). 
-
-- Add '...' argument to chemical metrics to permit using the same arguments for
-  all metrics in get() or do.call() constructions.
-
-- Add functions for metrics: plength() (protein length), V0() and S0()
-  (standard molal volume and entropy per residue), pV0() and pS0 (volume and
-  entropy per protein), V0g() and S0g() (specific volume and entropy), Density()
-  (mass density), SV() (entropy density) Cost() (metabolic cost of amino acids
-  from Akashi and Gojobori, 2002), RespiratoryCost() and FermentativeCost()
-  (respiratory and fermentative costs from Wagner, 2005), and B20Cost(),
-  Y20Cost(), and H11Cost() (biosynthetic costs from Zhang et al., 2018).
-
-- Differential expression datasets (including old to new ID mappings in
-  uniprot_updates.csv) and chemical analysis vignettes have been moved to the
-  JMDplots package.
-
-- read.fasta(), count.aa(), and aasum() have been moved here from the CHNOSZ
-  package.
-
-- Expand vignettes: Introduction to canprot, More about metrics.
-
-- Add add.cld() (add compact letter display to boxplots).
-
-- Move chem16S::calc_metrics() and chem16S::add_hull() to calc.metrics() and
-  add.hull().
-
-- Rename protcomp() to human.aa().
-
-- Add demos \file{thermophiles.R}, \file{locations.R}, and \file{redoxins.R}.
-
 CHANGES IN canprot 1.1.2 (2022-01-17)
 -------------------------------------
 

inst/doc/introduction.html

@@ -344,7 +344,7 @@ <h1 class="title toc-ignore">Introduction to canprot</h1>
 
 
 
-<p>The <strong>canprot</strong> package calculates chemical metrics of proteins from amino acid compositions. This vignette was compiled on 2024-03-10 with <strong>canprot</strong> version 1.1.2-38.</p>
+<p>The <strong>canprot</strong> package calculates chemical metrics of proteins from amino acid compositions. This vignette was compiled on 2024-03-11 with <strong>canprot</strong> version 1.1.2-39.</p>
 <p>Previous vignette: <a href="demos.html">Demos for canprot</a> | Next vignette: <a href="metrics.html">More about metrics</a></p>
 <div id="reading-fasta-files" class="section level2">
 <h2>Reading FASTA files</h2>

inst/doc/metrics.html

@@ -344,7 +344,7 @@ <h1 class="title toc-ignore">More about metrics</h1>
 
 
 
-<p>The <strong>canprot</strong> package calculates chemical metrics of proteins from amino acid compositions. This vignette was compiled on 2024-03-10 with <strong>canprot</strong> version 1.1.2-38.</p>
+<p>The <strong>canprot</strong> package calculates chemical metrics of proteins from amino acid compositions. This vignette was compiled on 2024-03-11 with <strong>canprot</strong> version 1.1.2-39.</p>
 <p>Previous vignette: <a href="introduction.html">Introduction to canprot</a></p>
 <div id="more-details-on-chemical-metrics" class="section level2">
 <h2>More details on chemical metrics</h2>

vignettes/demos.Rmd

@@ -49,7 +49,7 @@ knitr::read_chunk("../demo/thermophiles.R")
 
 The data are from @DBCS23 for methanogen genomes (amino acid composition and optimal growth temperature) and from @LLX+24 for *Nitrososphaeria* MAGs (genome assemblies and habitat and respiration types).
 The plots reveal that proteins tend to have higher specific entropy in thermophilic genomes and MAGs from thermal habitats compared to mesophilic genomes and MAGs from nonthermal habitats, for a given carbon oxidation state.
-This implies that, after correcting for *Z*<sub>C</sub>, proteins in thermophilic genomes have a <ins>more negative derivative</ins> of the standard Gibbs energy per gram of protein with respect to temperature.
+This implies that, after correcting for *Z*<sub>C</sub>, proteins in thermophiles have a <ins>more negative derivative</ins> of the standard Gibbs energy per gram of protein with respect to temperature.
 
 ## canprot demo #2: Subcellular locations