[CHNOSZ-commits] r156 - in pkg/CHNOSZ: . inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 17 01:31:55 CET 2017
Author: jedick
Date: 2017-02-17 01:31:54 +0100 (Fri, 17 Feb 2017)
New Revision: 156
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
anintro.Rmd: tracking down windows R CMD check warning
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-02-16 16:35:19 UTC (rev 155)
+++ pkg/CHNOSZ/DESCRIPTION 2017-02-17 00:31:54 UTC (rev 156)
@@ -1,6 +1,6 @@
-Date: 2017-02-16
+Date: 2017-02-17
Package: CHNOSZ
-Version: 1.0.8-45
+Version: 1.0.8-46
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-02-16 16:35:19 UTC (rev 155)
+++ pkg/CHNOSZ/inst/NEWS 2017-02-17 00:31:54 UTC (rev 156)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-45 (2017-02-16)
+CHANGES IN CHNOSZ 1.0.8-46 (2017-02-17)
---------------------------------------
DOCUMENTATION:
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2017-02-16 16:35:19 UTC (rev 155)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2017-02-17 00:31:54 UTC (rev 156)
@@ -20,7 +20,7 @@
\usepackage[utf8]{inputenc}
bibliography: vig.bib
link-citations: yes
-# The custom CSL file gives a build error on R-Forge (2017-02-12):
+# The custom CSL file gives a build error on R-Forge (20170212):
# pandoc-citeproc: error while parsing the XML string
#csl: elementa.csl
---
@@ -1137,44 +1137,45 @@
Then, we calculate `r zc` from the formulas of the proteins.
Next, point symbols are assigned according to domain (Archaea, Bacteria, Eukaryota); numbers inside the symbols show the ordering of *T*<sub>opt</sub> in three temperature ranges (0--35 °C, 37.5--60 °C, and 65--100 °C).
+<!--
```{r rubisco_svg, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, out.width="100%", fig.keep='none', fig.ext='svg', custom.plot=TRUE, embed.tag=TRUE, echo=FALSE, results="hide", message=FALSE, fig.cap='Average oxidation state of carbon in Rubisco compared with optimal growth temperature of organisms. **This is an interactive image.** Move the mouse over the points to show the names of the organisms, and click to open a reference in a new window. (Made using [RSVGTipsDevice](https://cran.r-project.org/package=RSVGTipsDevice) with code that can be found in the source of this document.)', cache=TRUE, timeit=timeit}
-if(!identical(class(try(find.package("RSVGTipsDevice"), silent=TRUE)), "try-error")) {
- library(RSVGTipsDevice)
- datfile <- system.file("extdata/cpetc/rubisco.csv", package = "CHNOSZ")
- fastafile <- system.file("extdata/fasta/rubisco.fasta", package = "CHNOSZ")
- dat <- read.csv(datfile)
- aa <- read.fasta(fastafile)
- Topt <- (dat$T1 + dat$T2) / 2
- idat <- match(dat$ID, substr(aa$protein, 4, 9))
- aa <- aa[idat, ]
- ZC <- ZC(protein.formula(aa))
- pch <- match(dat$domain, c("E", "B", "A")) - 1
- col <- match(dat$domain, c("A", "B", "E")) + 1
- # because the tooltip titles in the SVG file are shown by recent browsers,
- # we do not need to draw the tooltips explicitly, so set toolTipMode=0
- devSVGTips(fig_path('.svg'), toolTipMode=0, title="Rubisco")
- par(cex=1.4)
- # unfortunately, plotmath can't be used with devSVGTips,
- # so axis labels here don't contain italics.
- plot(Topt, ZC, type="n", xlab="T, °C", ylab="ZC")
- n <- rep(1:9, 3)
- for(i in seq_along(Topt)) {
- # adjust cex to make the symbols look the same size
- cex <- ifelse(pch[i]==1, 2.5, 3.5)
- points(Topt[i], ZC[i], pch=pch[i], cex=cex, col=col[i])
- URL <- dat$URL[i]
- setSVGShapeURL(URL, target="_blank")
- setSVGShapeContents(paste0("<title>", dat$species[i], "</title>"))
- text(Topt[i], ZC[i], n[i], cex = 1.2)
- }
- abline(v = c(36, 63), lty = 2, col = "grey")
- legend("topright", legend = c("Archaea", "Bacteria", "Eukaryota"),
- pch = c(2, 1, 0), col = 2:4, cex=1.5, pt.cex = c(3, 2.3, 3), bty="n")
- dev.off()
-}
+#if(suppressWarnings(require(RSVGTipsDevice))) {
+# datfile <- system.file("extdata/cpetc/rubisco.csv", package = "CHNOSZ")
+# fastafile <- system.file("extdata/fasta/rubisco.fasta", package = "CHNOSZ")
+# dat <- read.csv(datfile)
+# aa <- read.fasta(fastafile)
+# Topt <- (dat$T1 + dat$T2) / 2
+# idat <- match(dat$ID, substr(aa$protein, 4, 9))
+# aa <- aa[idat, ]
+# ZC <- ZC(protein.formula(aa))
+# pch <- match(dat$domain, c("E", "B", "A")) - 1
+# col <- match(dat$domain, c("A", "B", "E")) + 1
+# # because the tooltip titles in the SVG file are shown by recent browsers,
+# # we do not need to draw the tooltips explicitly, so set toolTipMode=0
+# devSVGTips(fig_path('.svg'), toolTipMode=0, title="Rubisco")
+# par(cex=1.4)
+# # unfortunately, plotmath can't be used with devSVGTips,
+# # so axis labels here don't contain italics.
+# plot(Topt, ZC, type="n", xlab="T, °C", ylab="ZC")
+# n <- rep(1:9, 3)
+# for(i in seq_along(Topt)) {
+# # adjust cex to make the symbols look the same size
+# cex <- ifelse(pch[i]==1, 2.5, 3.5)
+# points(Topt[i], ZC[i], pch=pch[i], cex=cex, col=col[i])
+# URL <- dat$URL[i]
+# setSVGShapeURL(URL, target="_blank")
+# setSVGShapeContents(paste0("<title>", dat$species[i], "</title>"))
+# text(Topt[i], ZC[i], n[i], cex = 1.2)
+# }
+# abline(v = c(36, 63), lty = 2, col = "grey")
+# legend("topright", legend = c("Archaea", "Bacteria", "Eukaryota"),
+# pch = c(2, 1, 0), col = 2:4, cex=1.5, pt.cex = c(3, 2.3, 3), bty="n")
+# dev.off()
+#}
```
+-->
```{r rubisco_ZC, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, message=FALSE, fig.cap="Average oxidation state of carbon in Rubisco compared with optimal growth temperature of organisms.", cache=TRUE, pngquant=pngquant, timeit=timeit}
-if(identical(class(try(find.package("RSVGTipsDevice"), silent=TRUE)), "try-error")) {
+#if(!suppressWarnings(require(RSVGTipsDevice))) {
datfile <- system.file("extdata/cpetc/rubisco.csv", package = "CHNOSZ")
fastafile <- system.file("extdata/fasta/rubisco.fasta", package = "CHNOSZ")
dat <- read.csv(datfile)
@@ -1192,7 +1193,7 @@
abline(v = c(36, 63), lty = 2, col = "grey")
legend("topright", legend = c("Archaea", "Bacteria", "Eukaryota"),
pch = c(2, 1, 0), col = 2:4, pt.cex = 2)
-}
+#}
```
```{r rubisco_ZC, eval=FALSE, echo=2:18}
```
@@ -1496,7 +1497,7 @@
T <- 100
```
-Use the following commands set the basis species, add the variously protonated ATP species, calculate the affinities of the formation reactions, equilibrate the species, and make a degree of formation (α) or mole fraction diagram.
+Use the following commands to set the basis species, add the variously protonated ATP species, calculate the affinities of the formation reactions, equilibrate the system, and make a degree of formation (α) or mole fraction diagram.
This is similar to Figure 1.3 of Alberty (2003), but calculated for *I* = 0 and *T* = 100 °C:
```{marginfigure}
To make the code more readable, commands for plotting titles and legends are not shown.
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