[CHNOSZ-commits] r806 - in pkg/CHNOSZ: . inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Sep 19 08:32:43 CEST 2023
Author: jedick
Date: 2023-09-19 08:32:42 +0200 (Tue, 19 Sep 2023)
New Revision: 806
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/vignettes/FAQ.Rmd
pkg/CHNOSZ/vignettes/mklinks.sh
Log:
Minor documentation updates
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2023-09-14 11:53:54 UTC (rev 805)
+++ pkg/CHNOSZ/DESCRIPTION 2023-09-19 06:32:42 UTC (rev 806)
@@ -1,6 +1,6 @@
-Date: 2023-09-14
+Date: 2023-09-19
Package: CHNOSZ
-Version: 2.0.0-25
+Version: 2.0.0-26
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2023-09-14 11:53:54 UTC (rev 805)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2023-09-19 06:32:42 UTC (rev 806)
@@ -12,11 +12,11 @@
% links to vignettes 20220723
\newcommand{\viglink}{\ifelse{html}{\out{<a href="../CHNOSZ/doc/#1.html"><strong>#1.Rmd</strong></a>}}{\bold{#1.Rmd}}}
-\section{Changes in CHNOSZ version 2.0.0-24 (2023-09-11)}{
+\section{Changes in CHNOSZ version 2.0.0-26 (2023-09-19)}{
\itemize{
- \item Add FAQ vignette with the following questions:
+ \item Add \viglink{FAQ} vignette with the following questions:
\itemize{
@@ -34,17 +34,20 @@
in the FAQ (\dQuote{How can minerals with phase transitions be added to
the database?}).
- \item Restore \file{EOSregress.R}, \file{eos-regress.Rmd}, and
- \file{demo/adenine.R}.
+ \item Restore \file{EOSregress.R} and its reverse dependencies
+ \file{eos-regress.Rmd} and \file{demo/adenine.R}. Thanks to Kris Fecteau
+ and Kirt Robinson for the suggestion.
\item Rename \code{checkGHS()} and \code{checkEOS()} to
\code{check.GHS()} and \code{check.EOS()} and make
\code{return.difference} TRUE by default.
- \item Where the alternate basis species include one of the axis variables
- on a diagram, \code{mosaic()} now calls \code{affinity()} with the
- appropriate argument names and adjusts the labels for the diagram
- (\dQuote{total C}, \dQuote{total S}, etc.).
+ \item \code{mosaic()} now handles the situation where the alternate basis
+ species include one of the axis variables on a diagram (by changing the
+ argument names in its internal calls to \code{affinity()}) and
+ adjusts the labels for the diagram accordingly (e.g. \dQuote{total C},
+ \dQuote{total S}, etc.). Thanks to Evgeniy Bastrakov for the feature
+ request.
\item Fix bug in \code{subcrt()} for \code{exceed.Ttr} not applied to
automatically balanced reactions (it was stuck on FALSE regardless of the
Modified: pkg/CHNOSZ/vignettes/FAQ.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/FAQ.Rmd 2023-09-14 11:53:54 UTC (rev 805)
+++ pkg/CHNOSZ/vignettes/FAQ.Rmd 2023-09-19 06:32:42 UTC (rev 806)
@@ -168,9 +168,9 @@
## How should CHNOSZ be cited?
-* Cite this paper as the general reference for CHNOSZ: @Dic19.
-* Cite this paper for diagrams with multiple metals: @Dic21b.
-* Cite this paper for metastable equilibrium calculations for proteins: @Dic08.
+* This paper is the general reference for CHNOSZ: @Dic19.
+* This paper describes diagrams with multiple metals: @Dic21b.
+* This paper describes metastable equilibrium calculations for proteins: @Dic08.
* The [<span style="color:blue">*OBIGT thermodynamic database*</span>](OBIGT.html) represents the work of many researchers.
**If you publish results that depend on any of these data, please cite the primary sources.**
Use `r info_` to show the reference keys for particular species and `r thermo.refs_` to list the bibliographic details:
Modified: pkg/CHNOSZ/vignettes/mklinks.sh
===================================================================
--- pkg/CHNOSZ/vignettes/mklinks.sh 2023-09-14 11:53:54 UTC (rev 805)
+++ pkg/CHNOSZ/vignettes/mklinks.sh 2023-09-19 06:32:42 UTC (rev 806)
@@ -21,74 +21,74 @@
sed -i 's/<code>?check.GHS<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">?check.GHS<\/a><\/code>/g' anintro.html
# anintro.html: add links to function names
-# Start at line 312 (below the TOC)
-sed -i '312,$s/<code>info()<\/code>/<code><a href="..\/html\/info.html" style="background-image:none;">info()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>ZC()<\/code>/<code><a href="..\/html\/util.formula.html" style="background-image:none;">ZC()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>affinity()<\/code>/<code><a href="..\/html\/affinity.html" style="background-image:none;">affinity()<\/a><\/code>/g' anintro.html
-sed -i '312,$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 '312,$s/<code>makeup()<\/code>/<code><a href="..\/html\/makeup.html" style="background-image:none;">makeup()<\/a><\/code>/g' anintro.html
-sed -i '312,$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 '312,$s/<code>subcrt()<\/code>/<code><a href="..\/html\/subcrt.html" style="background-image:none;">subcrt()<\/a><\/code>/g' anintro.html
-sed -i '312,$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 '312,$s/<code>E.units()<\/code>/<code><a href="..\/html\/util.units.html" style="background-image:none;">E.units()<\/a><\/code>/g' anintro.html
-sed -i '312,$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 '312,$s/<code>equilibrate()<\/code>/<code><a href="..\/html\/equilibrate.html" style="background-image:none;">equilibrate()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>diagram()<\/code>/<code><a href="..\/html\/diagram.html" style="background-image:none;">diagram()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>basis()<\/code>/<code><a href="..\/html\/basis.html" style="background-image:none;">basis()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>species()<\/code>/<code><a href="..\/html\/species.html" style="background-image:none;">species()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>reset()<\/code>/<code><a href="..\/html\/thermo.html" style="background-image:none;">reset()<\/a><\/code>/g' anintro.html
-sed -i '312,$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 '312,$s/<code>swap.basis()<\/code>/<code><a href="..\/html\/swap.basis.html" style="background-image:none;">swap.basis()<\/a><\/code>/g' anintro.html
-sed -i '312,$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 '312,$s/<code>ratlab()<\/code>/<code><a href="..\/html\/util.expression.html" style="background-image:none;">ratlab()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>mosaic()<\/code>/<code><a href="..\/html\/mosaic.html" style="background-image:none;">mosaic()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>convert()<\/code>/<code><a href="..\/html\/util.units.html" style="background-image:none;">convert()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>mod.buffer()<\/code>/<code><a href="..\/html\/buffer.html" style="background-image:none;">mod.buffer()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>reset\$/<code><a href="..\/html\/thermo.html" style="background-image:none;">reset<\/a>\$/g' anintro.html
-sed -i '312,$s/<code>solubility()<\/code>/<code><a href="..\/html\/solubility.html" style="background-image:none;">solubility()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>ZC.col()<\/code>/<code><a href="..\/html\/util.plot.html" style="background-image:none;">ZC.col()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>aminoacids(\"\")<\/code>/<code><a href="..\/html\/util.seq.html" style="background-image:none;">aminoacids(\"\")<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>expr.species()<\/code>/<code><a href="..\/html\/util.expression.html" style="background-image:none;">expr.species()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>nonideal()<\/code>/<code><a href="..\/html\/nonideal.html" style="background-image:none;">nonideal()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>pinfo()<\/code>/<code><a href="..\/html\/protein.info.html" style="background-image:none;">pinfo()<\/a><\/code>/g' anintro.html
-sed -i '312,$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 '312,$s/<code>protein.formula()<\/code>/<code><a href="..\/html\/protein.info.html" style="background-image:none;">protein.formula()<\/a><\/code>/g' anintro.html
-sed -i '312,$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 '312,$s/<code>read.fasta()<\/code>/<code><a href="..\/html\/util.fasta.html" style="background-image:none;">read.fasta()<\/a><\/code>/g' anintro.html
-sed -i '312,$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 '312,$s/<code>unitize()<\/code>/<code><a href="..\/html\/util.misc.html" style="background-image:none;">unitize()<\/a><\/code>/g' anintro.html
-sed -i '312,$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 '312,$s/<code>seq2aa()<\/code>/<code><a href="..\/html\/add.protein.html" style="background-image:none;">seq2aa()<\/a><\/code>/g' anintro.html
-sed -i '312,$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 '312,$s/<code>aminoacids()<\/code>/<code><a href="..\/html\/util.seq.html" style="background-image:none;">aminoacids()<\/a><\/code>/g' anintro.html
-sed -i '312,$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 '312,$s/<code>mod.OBIGT()<\/code>/<code><a href="..\/html\/add.OBIGT.html" style="background-image:none;">mod.OBIGT()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>check.GHS()<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">check.GHS()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>check.EOS()<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">check.EOS()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>equil.reaction()<\/code>/<code><a href="..\/html\/equilibrate.html" style="background-image:none;">equil.reaction()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>EOSregress()<\/code>/<code><a href="..\/html\/EOSregress.html" style="background-image:none;">EOSregress()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>RH2OBIGT()<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">RH2OBIGT()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/<code>retrieve()<\/code>/<code><a href="..\/html\/retrieve.html" style="background-image:none;">retrieve()<\/a><\/code>/g' anintro.html
+# Start at line 152 (below the TOC)
+sed -i '152,$s/<code>info()<\/code>/<code><a href="..\/html\/info.html" style="background-image:none;">info()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>ZC()<\/code>/<code><a href="..\/html\/util.formula.html" style="background-image:none;">ZC()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>affinity()<\/code>/<code><a href="..\/html\/affinity.html" style="background-image:none;">affinity()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>thermo.refs()<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">thermo.refs()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>makeup()<\/code>/<code><a href="..\/html\/makeup.html" style="background-image:none;">makeup()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>as.chemical.formula()<\/code>/<code><a href="..\/html\/util.formula.html" style="background-image:none;">as.chemical.formula()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>subcrt()<\/code>/<code><a href="..\/html\/subcrt.html" style="background-image:none;">subcrt()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>T.units()<\/code>/<code><a href="..\/html\/util.units.html" style="background-image:none;">T.units()<\/a><\/code>/g' anintro.html
+sed -i '152,$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 '152,$s/<code>P.units()<\/code>/<code><a href="..\/html\/util.units.html" style="background-image:none;">P.units()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>equilibrate()<\/code>/<code><a href="..\/html\/equilibrate.html" style="background-image:none;">equilibrate()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>diagram()<\/code>/<code><a href="..\/html\/diagram.html" style="background-image:none;">diagram()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>basis()<\/code>/<code><a href="..\/html\/basis.html" style="background-image:none;">basis()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>species()<\/code>/<code><a href="..\/html\/species.html" style="background-image:none;">species()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>reset()<\/code>/<code><a href="..\/html\/thermo.html" style="background-image:none;">reset()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>describe.reaction()<\/code>/<code><a href="..\/html\/util.expression.html" style="background-image:none;">describe.reaction()<\/a><\/code>/g' anintro.html
+sed -i '152,$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 '152,$s/<code>water.lines()<\/code>/<code><a href="..\/html\/util.plot.html" style="background-image:none;">water.lines()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>ratlab()<\/code>/<code><a href="..\/html\/util.expression.html" style="background-image:none;">ratlab()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>mosaic()<\/code>/<code><a href="..\/html\/mosaic.html" style="background-image:none;">mosaic()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>convert()<\/code>/<code><a href="..\/html\/util.units.html" style="background-image:none;">convert()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>mod.buffer()<\/code>/<code><a href="..\/html\/buffer.html" style="background-image:none;">mod.buffer()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>reset\$/<code><a href="..\/html\/thermo.html" style="background-image:none;">reset<\/a>\$/g' anintro.html
+sed -i '152,$s/<code>solubility()<\/code>/<code><a href="..\/html\/solubility.html" style="background-image:none;">solubility()<\/a><\/code>/g' anintro.html
+sed -i '152,$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 '152,$s/<code>aminoacids(\"\")<\/code>/<code><a href="..\/html\/util.seq.html" style="background-image:none;">aminoacids(\"\")<\/a><\/code>/g' anintro.html
+sed -i '152,$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 '152,$s/<code>nonideal()<\/code>/<code><a href="..\/html\/nonideal.html" style="background-image:none;">nonideal()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>pinfo()<\/code>/<code><a href="..\/html\/protein.info.html" style="background-image:none;">pinfo()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>protein.length()<\/code>/<code><a href="..\/html\/protein.info.html" style="background-image:none;">protein.length()<\/a><\/code>/g' anintro.html
+sed -i '152,$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 '152,$s/<code>ionize.aa()<\/code>/<code><a href="..\/html\/ionize.aa.html" style="background-image:none;">ionize.aa()<\/a><\/code>/g' anintro.html
+sed -i '152,$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 '152,$s/<code>protein.basis()<\/code>/<code><a href="..\/html\/protein.info.html" style="background-image:none;">protein.basis()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>unitize()<\/code>/<code><a href="..\/html\/util.misc.html" style="background-image:none;">unitize()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>axis.label()<\/code>/<code><a href="..\/html\/util.expression.html" style="background-image:none;">axis.label()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>seq2aa()<\/code>/<code><a href="..\/html\/add.protein.html" style="background-image:none;">seq2aa()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>add.protein()<\/code>/<code><a href="..\/html\/add.protein.html" style="background-image:none;">add.protein()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>aminoacids()<\/code>/<code><a href="..\/html\/util.seq.html" style="background-image:none;">aminoacids()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>add.OBIGT()<\/code>/<code><a href="..\/html\/add.OBIGT.html" style="background-image:none;">add.OBIGT()<\/a><\/code>/g' anintro.html
+sed -i '152,$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 '152,$s/<code>check.GHS()<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">check.GHS()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>check.EOS()<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">check.EOS()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>equil.reaction()<\/code>/<code><a href="..\/html\/equilibrate.html" style="background-image:none;">equil.reaction()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>EOSregress()<\/code>/<code><a href="..\/html\/EOSregress.html" style="background-image:none;">EOSregress()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>RH2OBIGT()<\/code>/<code><a href="..\/html\/util.data.html" style="background-image:none;">RH2OBIGT()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/<code>retrieve()<\/code>/<code><a href="..\/html\/retrieve.html" style="background-image:none;">retrieve()<\/a><\/code>/g' anintro.html
# anintro.html: functions from R base packages
-sed -i '312,$s/<code>install.packages/<code><a href="..\/..\/utils\/html\/install.packages.html" style="background-image:none;">install.packages<\/a>/g' anintro.html
-sed -i '312,$s/<code>library/<code><a href="..\/..\/base\/html\/library.html" style="background-image:none;">library<\/a>/g' anintro.html
-sed -i '312,$s/help()/<a href="..\/..\/utils\/html\/help.html" style="background-image:none;">help()<\/a>/g' anintro.html
-sed -i '312,$s/help.start()/<a href="..\/..\/utils\/html\/help.start.html" style="background-image:none;">help.start()<\/a>/g' anintro.html
-sed -i '312,$s/write.table/<a href="..\/..\/utils\/html\/write.table.html" style="background-image:none;">write.table<\/a>/g' anintro.html
-sed -i '312,$s/<code>plot()<\/code>/<code><a href="..\/..\/graphics\/html\/plot.html" style="background-image:none;">plot()<\/a><\/code>/g' anintro.html
-sed -i '312,$s/lapply()/<a href="..\/..\/base\/html\/lapply.html" style="background-image:none;">lapply()<\/a>/g' anintro.html
-sed -i '312,$s/do.call()/<a href="..\/..\/base\/html\/do.call.html" style="background-image:none;">do.call()<\/a>/g' anintro.html
-sed -i '312,$s/rbind()/<a href="..\/..\/base\/html\/cbind.html" style="background-image:none;">rbind()<\/a>/g' anintro.html
-sed -i '312,$s/matplot()/<a href="..\/..\/graphics\/html\/matplot.html" style="background-image:none;">matplot()<\/a>/g' anintro.html
-sed -i '312,$s/unlist()/<a href="..\/..\/base\/html\/unlist.html" style="background-image:none;">unlist()<\/a>/g' anintro.html
-sed -i '312,$s/heat.colors()/<a href="..\/..\/grDevices\/html\/palettes.html" style="background-image:none;">heat.colors()<\/a>/g' anintro.html
-sed -i '312,$s/read.csv()/<a href="..\/..\/utils\/html\/read.table.html" style="background-image:none;">read.csv()<\/a>/g' anintro.html
-sed -i '312,$s/seq()/<a href="..\/..\/base\/html\/seq.html" style="background-image:none;">seq()<\/a>/g' anintro.html
-sed -i '312,$s/substitute()/<a href="..\/..\/base\/html\/substitute.html" style="background-image:none;">substitute()<\/a>/g' anintro.html
-sed -i '312,$s/for()/<a href="..\/..\/base\/html\/Control.html" style="background-image:none;">for()<\/a>/g' anintro.html
-sed -i '312,$s/browseURL()/<a href="..\/..\/utils\/html\/browseURL.html" style="background-image:none;">browseURL()<\/a>/g' anintro.html
-sed -i '312,$s/Sys.Date()/<a href="..\/..\/base\/html\/Sys.time.html" style="background-image:none;">Sys.Date()<\/a>/g' anintro.html
+sed -i '152,$s/<code>install.packages/<code><a href="..\/..\/utils\/html\/install.packages.html" style="background-image:none;">install.packages<\/a>/g' anintro.html
+sed -i '152,$s/<code>library/<code><a href="..\/..\/base\/html\/library.html" style="background-image:none;">library<\/a>/g' anintro.html
+sed -i '152,$s/help()/<a href="..\/..\/utils\/html\/help.html" style="background-image:none;">help()<\/a>/g' anintro.html
+sed -i '152,$s/help.start()/<a href="..\/..\/utils\/html\/help.start.html" style="background-image:none;">help.start()<\/a>/g' anintro.html
+sed -i '152,$s/write.table/<a href="..\/..\/utils\/html\/write.table.html" style="background-image:none;">write.table<\/a>/g' anintro.html
+sed -i '152,$s/<code>plot()<\/code>/<code><a href="..\/..\/graphics\/html\/plot.html" style="background-image:none;">plot()<\/a><\/code>/g' anintro.html
+sed -i '152,$s/lapply()/<a href="..\/..\/base\/html\/lapply.html" style="background-image:none;">lapply()<\/a>/g' anintro.html
+sed -i '152,$s/do.call()/<a href="..\/..\/base\/html\/do.call.html" style="background-image:none;">do.call()<\/a>/g' anintro.html
+sed -i '152,$s/rbind()/<a href="..\/..\/base\/html\/cbind.html" style="background-image:none;">rbind()<\/a>/g' anintro.html
+sed -i '152,$s/matplot()/<a href="..\/..\/graphics\/html\/matplot.html" style="background-image:none;">matplot()<\/a>/g' anintro.html
+sed -i '152,$s/unlist()/<a href="..\/..\/base\/html\/unlist.html" style="background-image:none;">unlist()<\/a>/g' anintro.html
+sed -i '152,$s/heat.colors()/<a href="..\/..\/grDevices\/html\/palettes.html" style="background-image:none;">heat.colors()<\/a>/g' anintro.html
+sed -i '152,$s/read.csv()/<a href="..\/..\/utils\/html\/read.table.html" style="background-image:none;">read.csv()<\/a>/g' anintro.html
+sed -i '152,$s/seq()/<a href="..\/..\/base\/html\/seq.html" style="background-image:none;">seq()<\/a>/g' anintro.html
+sed -i '152,$s/substitute()/<a href="..\/..\/base\/html\/substitute.html" style="background-image:none;">substitute()<\/a>/g' anintro.html
+sed -i '152,$s/for()/<a href="..\/..\/base\/html\/Control.html" style="background-image:none;">for()<\/a>/g' anintro.html
+sed -i '152,$s/browseURL()/<a href="..\/..\/utils\/html\/browseURL.html" style="background-image:none;">browseURL()<\/a>/g' anintro.html
+sed -i '152,$s/Sys.Date()/<a href="..\/..\/base\/html\/Sys.time.html" style="background-image:none;">Sys.Date()<\/a>/g' anintro.html
# Add links to OBIGT.html
sed -i 's/reset()/<a href="..\/html\/thermo.html" style="color:\ red;">reset()<\/a>/g' OBIGT.html
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