[CHNOSZ-commits] r368 - in pkg/CHNOSZ: . inst vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Fri Jan 25 06:07:31 CET 2019 

Author: jedick
Date: 2019-01-25 06:07:29 +0100 (Fri, 25 Jan 2019)
New Revision: 368

Added:
   pkg/CHNOSZ/vignettes/.install_extras
   pkg/CHNOSZ/vignettes/mklinks.sh
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
anintro.Rmd: add 'mklinks.sh' script to add CHNOSZ and R documentation links


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-01-24 12:36:38 UTC (rev 367)
+++ pkg/CHNOSZ/DESCRIPTION	2019-01-25 05:07:29 UTC (rev 368)
@@ -1,6 +1,6 @@
-Date: 2019-01-24
+Date: 2019-01-25
 Package: CHNOSZ
-Version: 1.1.3-75
+Version: 1.1.3-76
 Title: Thermodynamic Calculations and Diagrams for Geo(bio)chemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2019-01-24 12:36:38 UTC (rev 367)
+++ pkg/CHNOSZ/inst/CHECKLIST	2019-01-25 05:07:29 UTC (rev 368)
@@ -26,6 +26,9 @@
 
 - check reverse dependencies: ecipex and canprot packages
 
+- documentation links: after installation, run doc/mklinks.sh
+  and insert the modified anintro.html in the package
+
 OTHER THINGS TO CHECK:
 
 - remove all "<<-" from sources (leftover from debugging)

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-01-24 12:36:38 UTC (rev 367)
+++ pkg/CHNOSZ/inst/NEWS	2019-01-25 05:07:29 UTC (rev 368)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-75 (2019-01-24)
+CHANGES IN CHNOSZ 1.1.3-76 (2019-01-25)
 ---------------------------------------
 
 BUG FIXES
@@ -77,9 +77,10 @@
   2009). This depends on the revised nonideal() and new NaCl() functions
   described above.
 
-- anintro.Rmd: add section on solubility calculations. Also, add
-  cuprite to mosaic diagram example, and note about implications of
-  changing balance to 1.
+- anintro.Rmd: add section on solubility calculations. Add cuprite to
+  mosaic diagram example, and note about implications of changing
+  balance coefficients to 1. Add 'mklinks.sh' script for adding links
+  to CHNOSZ and R documentation.
 
 - Add demo/bison.R (average oxidation state of carbon of metagenome-
   derived proteins in different microbial phyla at Bison Pool)

Added: pkg/CHNOSZ/vignettes/.install_extras
===================================================================
--- pkg/CHNOSZ/vignettes/.install_extras	                        (rev 0)
+++ pkg/CHNOSZ/vignettes/.install_extras	2019-01-25 05:07:29 UTC (rev 368)
@@ -0,0 +1 @@
+mklinks.sh

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2019-01-24 12:36:38 UTC (rev 367)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2019-01-25 05:07:29 UTC (rev 368)
@@ -1215,7 +1215,7 @@
 ```
 
 Adding the `IS` argument to <span style="color:green">`affinity()`</span>, we can now plot *N*<sub>H<sup>+</sup></sub> at the given ionic strength.
-Here we set `plot.it = FALSE` in `diagram()` because we use the computed α to make our own plot.
+Here we set `plot.it = FALSE` in <span style="color:green">`diagram()`</span> because we use the computed α to make our own plot.
 This is similar to Figure 1.3 of Alberty (2003), but at higher temperature:
 ```{r ATP, eval=FALSE, echo=12:17}
 ```
@@ -1302,7 +1302,7 @@
 Let's compare experimental values of heat capacity of four proteins, from @PM90, with those calculated using group additivity.
 After dividing Privalov and Makhatadze's experimental values by the lengths of the proteins to get per-residue values, we convert those to calories, then plot them.
 
-```{r protein_Cp, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, message=FALSE, fig.cap='The heat capacity calculated by group additivity closely approximates experimental values for aqueous proteins. For a related figure showing the effects of ionization in the calculations, see <span style="color:blue">?ionize.aa</span>.', cache=TRUE, pngquant=pngquant, timeit=timeit}
+```{r protein_Cp, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, message=FALSE, fig.cap='The heat capacity calculated by group additivity closely approximates experimental values for aqueous proteins. For a related figure showing the effects of ionization in the calculations, see <span style="color:blue">`?ionize.aa`</span>.', cache=TRUE, pngquant=pngquant, timeit=timeit}
 PM90 <- read.csv(system.file("extdata/cpetc/PM90.csv", package = "CHNOSZ"))
 plength <- protein.length(colnames(PM90)[2:5])
 Cp_expt <- t(t(PM90[, 2:5]) / plength)
@@ -2190,14 +2190,16 @@
 # Document history
 
 * 2010-09-30 Initial version.
+<!--
 * 2011-08-15 Add <span style="color:green">`browse.refs()`</span>; modifying database hint changed to <span style="color:blue">`help(thermo)`</span>.
 ```{marginfigure}
 <span style="color:green">`browse.refs()`</span> was renamed to <span style="color:green">`thermo.refs()`</span> in 2017.
 ```
-* 2012-06-16 Add "More activity diagrams".
-* 2015-05-14 Add warning about internal consistency of thermodynamic data.
-* 2017-02-15 Completely rewritten; switch from Sweave to knitr (Tufte style).
-* 2019-01-24 Add section on solubility calculations.
+-->
+* 2012-06-16 Add "More activity diagrams" (section no longer exists).
+* 2015-05-14 Add warning about [internal consistency of thermodynamic data](#thermodynamic-database).
+* 2017-02-15 Completely rewritten; switch from Sweave to [knitr](https://yihui.name/knitr/) ([Tufte style](https://rstudio.github.io/tufte/)).
+* 2019-01-24 Add [section on solubility calculations](#complete-equilibrium-solubility).
 
 View the R Markdown source of this document [on R-Forge](https://r-forge.r-project.org/scm/viewvc.php/pkg/CHNOSZ/vignettes/anintro.Rmd?view=markup&root=chnosz) or in R:
 

Added: pkg/CHNOSZ/vignettes/mklinks.sh
===================================================================
--- pkg/CHNOSZ/vignettes/mklinks.sh	                        (rev 0)
+++ pkg/CHNOSZ/vignettes/mklinks.sh	2019-01-25 05:07:29 UTC (rev 368)
@@ -0,0 +1,97 @@
+# CHNOSZ/vignettes/mklinks.sh
+# add documentation links to anintro.html
+# 20190125 jmd
+
+# add links to help topics
+# set background-image:none to remove underlines (from bootstrap theme)
+sed -i 's/<code>?`CHNOSZ-package`<\/code>/<code><a href="..\/html\/CHNOSZ-package.html" style="background-image:none;">?`CHNOSZ-package`<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?basis<\/code>/<code><a href="..\/html\/basis.html" style="background-image:none;">?basis<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?buffer<\/code>/<code><a href="..\/html\/buffer.html" style="background-image:none;">?buffer<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?solubility<\/code>/<code><a href="..\/html\/solubility.html" style="background-image:none;">?solubility<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?ionize.aa<\/code>/<code><a href="..\/html\/ionize.aa.html" style="background-image:none;">?ionize.aa<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?count.aa<\/code>/<code><a href="..\/html\/util.fasta.html" style="background-image:none;">?count.aa<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?objective<\/code>/<code><a href="..\/html\/objective.html" style="background-image:none;">?objective<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?thermo<\/code>/<code><a href="..\/html\/data.html" style="background-image:none;">?thermo<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?hkf<\/code>/<code><a href="..\/html\/eos.html" style="background-image:none;">?hkf<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?cgl<\/code>/<code><a href="..\/html\/eos.html" style="background-image:none;">?cgl<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?water<\/code>/<code><a href="..\/html\/water.html" style="background-image:none;">?water<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?subcrt<\/code>/<code><a href="..\/html\/subcrt.html" style="background-image:none;">?subcrt<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?EOSregress<\/code>/<code><a href="..\/html\/EOSregress.html" style="background-image:none;">?EOSregress<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?wjd<\/code>/<code><a href="..\/html\/wjd.html" style="background-image:none;">?wjd<\/a><\/code>/g' anintro.html
+sed -i 's/<code>?taxonomy<\/code>/<code><a href="..\/html\/taxonomy.html" style="background-image:none;">?taxonomy<\/a><\/code>/g' anintro.html
+
+# add links to function names
+# start at line 120 (below the TOC)
+sed -i '120,$s/<code>info()<\/code>/<code><a href="..\/html\/info.html" style="background-image:none;">info()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>ZC()<\/code>/<code><a href="..\/html\/util.formula.html" style="background-image:none;">ZC()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>affinity()<\/code>/<code><a href="..\/html\/affinity.html" style="background-image:none;">affinity()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>thermo.refs()<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">thermo.refs()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>makeup()<\/code>/<code><a href="..\/html\/makeup.html" style="background-image:none;">makeup()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>as.chemical.formula()<\/code>/<code><a href="..\/html\/util.formula.html" style="background-image:none;">as.chemical.formula()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>subcrt()<\/code>/<code><a href="..\/html\/subcrt.html" style="background-image:none;">subcrt()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>T.units()<\/code>/<code><a href="..\/html\/util.units.html" style="background-image:none;">T.units()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>E.units()<\/code>/<code><a href="..\/html\/util.units.html" style="background-image:none;">E.units()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>P.units()<\/code>/<code><a href="..\/html\/util.units.html" style="background-image:none;">P.units()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>equilibrate()<\/code>/<code><a href="..\/html\/equilibrate.html" style="background-image:none;">equilibrate()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>diagram()<\/code>/<code><a href="..\/html\/diagram.html" style="background-image:none;">diagram()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>basis()<\/code>/<code><a href="..\/html\/basis.html" style="background-image:none;">basis()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>species()<\/code>/<code><a href="..\/html\/species.html" style="background-image:none;">species()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>data(thermo)<\/code>/<code><a href="..\/html\/data.html" style="background-image:none;">data(thermo)<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>describe.reaction()<\/code>/<code><a href="..\/html\/util.expression.html" style="background-image:none;">describe.reaction()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>swap.basis()<\/code>/<code><a href="..\/html\/swap.basis.html" style="background-image:none;">swap.basis()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>water.lines()<\/code>/<code><a href="..\/html\/util.plot.html" style="background-image:none;">water.lines()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>ratlab()<\/code>/<code><a href="..\/html\/util.expression.html" style="background-image:none;">ratlab()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>mosaic()<\/code>/<code><a href="..\/html\/mosaic.html" style="background-image:none;">mosaic()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>convert()<\/code>/<code><a href="..\/html\/util.units.html" style="background-image:none;">convert()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>mod.buffer()<\/code>/<code><a href="..\/html\/buffer.html" style="background-image:none;">mod.buffer()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>thermo\$/<code><a href="..\/html\/data.html" style="background-image:none;">thermo<\/a>\$/g' anintro.html
+sed -i '120,$s/<code>solubility()<\/code>/<code><a href="..\/html\/solubility.html" style="background-image:none;">solubility()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>ZC.col()<\/code>/<code><a href="..\/html\/util.plot.html" style="background-image:none;">ZC.col()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>aminoacids(\"\")<\/code>/<code><a href="..\/html\/util.seq.html" style="background-image:none;">aminoacids(\"\")<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>expr.species()<\/code>/<code><a href="..\/html\/util.expression.html" style="background-image:none;">expr.species()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>nonideal()<\/code>/<code><a href="..\/html\/nonideal.html" style="background-image:none;">nonideal()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>pinfo()<\/code>/<code><a href="..\/html\/protein.info.html" style="background-image:none;">pinfo()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>protein.length()<\/code>/<code><a href="..\/html\/protein.info.html" style="background-image:none;">protein.length()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>protein.formula()<\/code>/<code><a href="..\/html\/protein.info.html" style="background-image:none;">protein.formula()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>ionize.aa()<\/code>/<code><a href="..\/html\/ionize.aa.html" style="background-image:none;">ionize.aa()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>read.fasta()<\/code>/<code><a href="..\/html\/util.fasta.html" style="background-image:none;">read.fasta()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>protein.basis()<\/code>/<code><a href="..\/html\/protein.info.html" style="background-image:none;">protein.basis()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>yeastgfp()<\/code>/<code><a href="..\/html\/yeast.html" style="background-image:none;">yeastgfp()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>unitize()<\/code>/<code><a href="..\/html\/util.misc.html" style="background-image:none;">unitize()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>revisit()<\/code>/<code><a href="..\/html\/revisit.html" style="background-image:none;">revisit()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>axis.label()<\/code>/<code><a href="..\/html\/util.expression.html" style="background-image:none;">axis.label()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>yeast.aa()<\/code>/<code><a href="..\/html\/yeast.html" style="background-image:none;">yeast.aa()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>seq2aa()<\/code>/<code><a href="..\/html\/add.protein.html" style="background-image:none;">seq2aa()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>uniprot.aa()<\/code>/<code><a href="..\/html\/util.fasta.html" style="background-image:none;">uniprot.aa()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>add.protein()<\/code>/<code><a href="..\/html\/add.protein.html" style="background-image:none;">add.protein()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>aminoacids()<\/code>/<code><a href="..\/html\/util.seq.html" style="background-image:none;">aminoacids()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>findit()<\/code>/<code><a href="..\/html\/findit.html" style="background-image:none;">findit()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>add.obigt()<\/code>/<code><a href="..\/html\/add.obigt.html" style="background-image:none;">add.obigt()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>mod.obigt()<\/code>/<code><a href="..\/html\/add.obigt.html" style="background-image:none;">mod.obigt()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>today()<\/code>/<code><a href="..\/html\/add.obigt.html" style="background-image:none;">today()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>checkGHS()<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">checkGHS()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>checkEOS()<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">checkEOS()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>equil.reaction()<\/code>/<code><a href="..\/html\/equilibrate.html" style="background-image:none;">equil.reaction()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>EOSregress()<\/code>/<code><a href="..\/html\/EOSregress.html" style="background-image:none;">EOSregress()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>wjd()<\/code>/<code><a href="..\/html\/wjd.html" style="background-image:none;">wjd()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>RH2obigt()<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">RH2obigt()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/<code>eqdata()<\/code>/<code><a href="..\/html\/eqdata.html" style="background-image:none;">eqdata()<\/a><\/code>/g' anintro.html
+
+# functions from R base packages
+sed -i '120,$s/<code>install.packages/<code><a href="..\/..\/utils\/html\/install.packages.html" style="background-image:none;">install.packages<\/a>/g' anintro.html
+sed -i '120,$s/<code>library/<code><a href="..\/..\/base\/html\/library.html" style="background-image:none;">library<\/a>/g' anintro.html
+sed -i '120,$s/help()/<a href="..\/..\/utils\/html\/help.html" style="background-image:none;">help()<\/a>/g' anintro.html
+sed -i '120,$s/help.start()/<a href="..\/..\/utils\/html\/help.start.html" style="background-image:none;">help.start()<\/a>/g' anintro.html
+sed -i '120,$s/write.table/<a href="..\/..\/utils\/html\/write.table.html" style="background-image:none;">write.table<\/a>/g' anintro.html
+sed -i '120,$s/<code>plot()<\/code>/<code><a href="..\/..\/graphics\/html\/plot.html" style="background-image:none;">plot()<\/a><\/code>/g' anintro.html
+sed -i '120,$s/lapply()/<a href="..\/..\/base\/html\/lapply.html" style="background-image:none;">lapply()<\/a>/g' anintro.html
+sed -i '120,$s/do.call()/<a href="..\/..\/base\/html\/do.call.html" style="background-image:none;">do.call()<\/a>/g' anintro.html
+sed -i '120,$s/rbind()/<a href="..\/..\/base\/html\/cbind.html" style="background-image:none;">rbind()<\/a>/g' anintro.html
+sed -i '120,$s/matplot()/<a href="..\/..\/graphics\/html\/matplot.html" style="background-image:none;">matplot()<\/a>/g' anintro.html
+sed -i '120,$s/unlist()/<a href="..\/..\/base\/html\/unlist.html" style="background-image:none;">unlist()<\/a>/g' anintro.html
+sed -i '120,$s/heat.colors()/<a href="..\/..\/grDevices\/html\/palettes.html" style="background-image:none;">heat.colors()<\/a>/g' anintro.html
+sed -i '120,$s/read.csv()/<a href="..\/..\/utils\/html\/read.table.html" style="background-image:none;">read.csv()<\/a>/g' anintro.html
+sed -i '120,$s/seq()/<a href="..\/..\/base\/html\/seq.html" style="background-image:none;">seq()<\/a>/g' anintro.html
+sed -i '120,$s/substitute()/<a href="..\/..\/base\/html\/substitute.html" style="background-image:none;">substitute()<\/a>/g' anintro.html
+sed -i '120,$s/for()/<a href="..\/..\/base\/html\/Control.html" style="background-image:none;">for()<\/a>/g' anintro.html
+sed -i '120,$s/browseURL()/<a href="..\/..\/utils\/html\/browseURL.html" style="background-image:none;">browseURL()<\/a>/g' anintro.html


Property changes on: pkg/CHNOSZ/vignettes/mklinks.sh
___________________________________________________________________
Added: svn:executable
   + *

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