[CHNOSZ-commits] r35 - in pkg/CHNOSZ: . R demo inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 31 08:25:08 CET 2012
Author: jedick
Date: 2012-12-31 08:25:08 +0100 (Mon, 31 Dec 2012)
New Revision: 35
Removed:
pkg/CHNOSZ/inst/TODO
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/R/wjd.R
pkg/CHNOSZ/demo/findit.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/wjd.Rd
pkg/CHNOSZ/vignettes/anintro.Rnw
pkg/CHNOSZ/vignettes/anintro.lyx
Log:
add protein example in wjd.Rd
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2012-12-27 12:23:52 UTC (rev 34)
+++ pkg/CHNOSZ/DESCRIPTION 2012-12-31 07:25:08 UTC (rev 35)
@@ -1,6 +1,6 @@
-Date: 2012-12-27
+Date: 2012-12-31
Package: CHNOSZ
-Version: 0.9.8-9
+Version: 0.9.8-10
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey M. Dick
Maintainer: Jeffrey M. Dick <jmdick at asu.edu>
Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R 2012-12-27 12:23:52 UTC (rev 34)
+++ pkg/CHNOSZ/R/diagram.R 2012-12-31 07:25:08 UTC (rev 35)
@@ -376,7 +376,7 @@
# default to heat colors if we're on screen, or to transparent if we're adding to a plot
if(missing(fill)) {
if(add) fill <- "transparent"
- else if(any(grepl(names(dev.cur()), c("X11cairo", "quartz")))) fill <- "heat"
+ else if(any(grepl(names(dev.cur()), c("X11cairo", "quartz", "windows")))) fill <- "heat"
}
if(is.null(fill)) fill <- "transparent"
else if(fill[1]=="rainbow") fill <- rainbow(ngroups)
Modified: pkg/CHNOSZ/R/wjd.R
===================================================================
--- pkg/CHNOSZ/R/wjd.R 2012-12-27 12:23:52 UTC (rev 34)
+++ pkg/CHNOSZ/R/wjd.R 2012-12-31 07:25:08 UTC (rev 35)
@@ -1,6 +1,5 @@
# CHNOSZ/wjd.R
-# Gibbs energy minimization by steepest descent algorithm
-# of White et al., 1958; and supporting functions
+# Gibbs energy minimization and supporting functions
# 20111117 jmd
wjd <- function(
@@ -351,7 +350,8 @@
stop("no method found")
}
-run.wjd <- function(ispecies, B=NULL, method="stoich", Y=run.guess(ispecies, B, method), P=1, T=25, imax=10, Gfrac=1e-7, tol=0.01) {
+run.wjd <- function(ispecies, B=NULL, method="stoich", Y=run.guess(ispecies, B, method),
+ P=1, T=25, nlambda=101, imax=10, Gfrac=1e-7, tol=0.01) {
### set up a Gibbs energy minimization
### using compositions and standard Gibbs energies of species
### from database in CHNOSZ 20120101 jmd
@@ -368,16 +368,16 @@
# the length of Y must be equal to number of species
if(length(Y) != nrow(A)) stop("Y must have same length as number of species")
# a single guess
- w <- wjd(A, G0.RT, Y, P=P, imax=imax, Gfrac=Gfrac)
+ w <- wjd(A, G0.RT, Y, P=P, nlambda=nlambda, imax=imax, Gfrac=Gfrac)
} else {
# if we're using method "central" there is only one guess
if(method=="central") {
- w <- wjd(A, G0.RT, Y, P=P, imax=imax, Gfrac=Gfrac)
+ w <- wjd(A, G0.RT, Y, P=P, nlambda=nlambda, imax=imax, Gfrac=Gfrac)
} else {
# for method "stoich" loop over all the guesses created by run.guess
Y <- Y[!is.na(Y)]
for(i in 1:length(Y)) {
- w <- wjd(A, G0.RT, Y[[i]], P=P, imax=imax, Gfrac=Gfrac)
+ w <- wjd(A, G0.RT, Y[[i]], P=P, nlambda=nlambda, imax=imax, Gfrac=Gfrac)
if(is.near.equil(w, tol=tol)) {
msgout("run.wjd: got within tolerance on initial solution ", i, " of ", length(Y), "\n")
break
@@ -415,8 +415,8 @@
return(Y)
}
-equil.potentials <- function(w) {
+equil.potentials <- function(w, tol=0.01, T=25) {
## return the average of the element.potentials, only if w is.near.equil 20120613
- if(!is.near.equil(w)) return(NULL)
- else return(colMeans(element.potentials(w)))
+ if(!is.near.equil(w, tol=tol)) return(NULL)
+ else return(colMeans(element.potentials(w)) * thermo$opt$R * convert(T, "K"))
}
Modified: pkg/CHNOSZ/demo/findit.R
===================================================================
--- pkg/CHNOSZ/demo/findit.R 2012-12-27 12:23:52 UTC (rev 34)
+++ pkg/CHNOSZ/demo/findit.R 2012-12-31 07:25:08 UTC (rev 35)
@@ -1,50 +1,39 @@
-opar <- par(mfrow=c(2,2))
-# an organic example:
-# find chemical activities where metastable activities of
+opar <- par(mfrow=c(2, 2))
+# find chemical activities where metastable equilibrium activities of
# selected proteins in P. ubique have high correlation
# with a lognormal distribution (i.e., maximize r of q-q plot)
-f <- system.file("extdata/fasta/HTCC1062.faa.xz",package="CHNOSZ")
-# search for three groups of proteins
-myg <- c("ribosomal","nucle","membrane")
-g <- lapply(myg,function(x) grep.file(f,x))
-# note that some proteins match more than one search term
-uug <- unique(unlist(g))
+f <- system.file("extdata/fasta/HTCC1062.faa.xz", package="CHNOSZ")
+# search for ribosomal proteins
+g <- grep.file(f, "ribosomal")
# read their amino acid compositions from the file
-aa <- read.fasta(f,uug)
+aa <- read.fasta(f, g)
# add these proteins to thermo$protein
ip <- add.protein(aa)
# load a predefined set of uncharged basis species
# (speeds things up as we won't model protein ionization)
basis("CHNOS")
-# make colors for the diagram
-rgbargs <- lapply(1:3,function(x) as.numeric(uug %in% g[[x]]))
-col <- do.call(rgb,c(rgbargs,list(alpha=0.5)))
-# get point symbols (use 1,2,4 and their sums)
-pch <- colSums(t(list2array(rgbargs)) * c(1,2,4))
# plot 1: calculated logarithms of chemical activity
# as a function of logfO2 ... a bundle of curves near logfO2 = -77
-a <- affinity(O2=c(-90,-60),iprotein=ip)
+a <- affinity(O2=c(-90, -60), iprotein=ip)
e <- equilibrate(a, loga.balance=0, normalize=TRUE)
-d <- diagram(e, col=col, names=NULL)
-title(as.expression("Selected proteins in"~italic("Pelagibacter ubique")))
-legend("bottomleft", lty=c(1,1,1), col=unique(col), legend=myg, bg="white")
+d <- diagram(e, names=NULL)
+title(as.expression("Ribosomal proteins in"~italic("Pelagibacter ubique")))
db <- describe.basis(ibasis=c(2, 1, 3))
legend("bottomright", legend=db, bg="white")
# plot 2: calculate q-q correlation coefficient
-# the lognormal distribution is favored near logfO2 = -73.6
-r <- revisit(d,"qqr")
+# the lognormal distribution is favored near logfO2 = -77
+r <- revisit(d, "qqr")
title(main="correlation with a normal distribution")
-# plot 3: findit... maximize qqr as a function of O2-H2O-NH3-CO2
-# it shows an optimum at low logaH2O, logaNH3
-f1 <- findit(list(O2=c(-106,-75),H2O=c(-40,-20),CO2=c(-20,10),NH3=c(-15,0)),
- "qqr",iprotein=ip,niter=8,normalize=TRUE)
+text(r$xopt, r$optimum, paste(" qqr", round(r$optimum, 3), sep="="), adj=0)
+# plot 3: findit... maximize qqr as a function of activities of O2-H2O-NH3-CO2
+f1 <- findit(list(O2=c(-106, -75), H2O=c(-40, -20), CO2=c(-20, 10), NH3=c(-15, 0)),
+ "qqr", iprotein=ip, niter=12, normalize=TRUE)
title(main="searching 4-D chemical activity space")
-# plot 5: q-q plot at the final loga O2, H2O, CO2, NH3
+# plot 4: q-q plot at the final loga O2, H2O, CO2, NH3
# higher correlation coefficient than plot 3
a <- affinity(iprotein=ip)
e <- equilibrate(a, loga.balance=0, normalize=TRUE)
-qqr5 <- revisit(e, "qqr",pch=pch)$H
-legend("topleft",pch=c(1,2,4),legend=myg)
+qqr5 <- revisit(e, "qqr")$H
db <- describe.basis(ibasis=c(5, 2, 1, 3))
legend("bottomright", legend=db)
# plot 5: trajectory of O2, H2O, CO2, NH3, and the
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2012-12-27 12:23:52 UTC (rev 34)
+++ pkg/CHNOSZ/inst/NEWS 2012-12-31 07:25:08 UTC (rev 35)
@@ -1,7 +1,7 @@
-CHANGES IN CHNOSZ 0.9.8-9 (2012-12-27)
+CHANGES IN CHNOSZ 0.9.8-10 (2012-12-31)
--------------------------------------
-SIGNIFICANT USER-VISIBLE CHANGES:
+MAJOR CHANGES:
- Split the functionality of diagram() into equilibrate() and diagram().
Old workflow: a <- affinity(); d <- diagram(a) .
@@ -288,7 +288,7 @@
- Add vignette wjd.Rnw to accompany the new function wjd().
-- Add TODO and CHECKLIST to the installation directory of the package.
+- Add a release CHECKLIST to the installation directory of the package.
- Use UTF-8 degree symbol in second argument of \eqn{}{}.
Deleted: pkg/CHNOSZ/inst/TODO
===================================================================
--- pkg/CHNOSZ/inst/TODO 2012-12-27 12:23:52 UTC (rev 34)
+++ pkg/CHNOSZ/inst/TODO 2012-12-31 07:25:08 UTC (rev 35)
@@ -1,103 +0,0 @@
-*********
-for 1.0.0
-*********
-
-- revisit the documentation, make it consistent with code changes!
-
-********
-features
-********
-
-- make is.near.equil() a function of ep (element.potentials), not w (wjd)?
-
-***********
-performance
-***********
-
-- refactor species() ... some simple speed-ups, avoid data frames!
-
-- recheck skarn example against Johnson et al., 1992
-
-- does affinity(iprotein=...) add H2O_RESIDUE to thermo$obigt?
- ... if so stop it from doing so?
-
-- byte-compiling is known to break test-subcrt.R
-
-*****
-style
-*****
-
-- coding style: space after comma; break up long lines
-
-- Rd style: where to use \samp{...} (paths, filenames ??)
-
-- Rd style: what markup to use for TRUE, NULL, etc ??
-
-- Rd style: Use "x" (or z?) in names of objects being plotted to
- indicate unpublished examples (docs, vignettes, longex())
-
-- grepl()! Can use this instead of if(length(grep(...) > 0))
-
-- replace 1:length(x) with seq_along(x)?
-
-- get == and != out of tests (use identical instead)
-
-- get away from determining species indices with rownames(thermo$obigt)
-
-*************
-documentation
-*************
-
-- check docs: does affinity return A/RT or A/2.303RT?
-
-- better documentation on how makeup() handles charge
-
-- does mod.obigt() use order-of-magnitude scaling factors or not?
-
-- under what circumstances does basis() delete the thermo$species?
-
-- find bibstyle for vignettes that still shows doi links
-
-- dd simple example in util.blast.Rd, before the long Bison Pool example
-
-- point to more examples in read.fasta (i.e. the sequence of commands in revisit)
-
-- check Ernst, 1976 example (SiO2 T-P diagram): correct T/P boundaries?
-
-- finish update of source files of vignettes to use LyX's Sweave module;
- R code is contained in the Chunk environment provided by the module.
-
-- add title, author information to vignettes with hyperref
-
-- add PNG files with the first and last frames of animations produced
- by anim.()* functions to 'extdata/anim'
-
-- if formation.Rnw is reinstated, use updated properties of [Met] and
- revise diagrams for EF-Tu proteins
-
-- add a lograt example to revisit.Rd
-
-********
-database
-********
-
-- track down missing sources of data (pers. comm.)
-
-- Add S3- from Pokrovski and Dubrovinsky, 2011 and logfO2-pH diagram.
-
-- add new data(?) from Akinfiev and Zotov, 2010 (doi:10.1134/S0016702910070074)
- Matschei and Glasser, 2010 (doi:10.1016/j.cemconres.2009.11.010)
- Zuccolini et al., 2011 (doi:10.1016/j.cageo.2010.03.024)
-
-- get up-to-date with SLOP07 data set?
-
-***********
-longer term
-***********
-
-- Allow more than one "balanced" component for diagram (see e.g. Richard and Gaona, 2011 for diagrams)
-
-- write a 'buffer' vignette
-
-- reimplement diagram() as an S3 plot() method for the object returned by affinity()
-
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2012-12-27 12:23:52 UTC (rev 34)
+++ pkg/CHNOSZ/man/diagram.Rd 2012-12-31 07:25:08 UTC (rev 35)
@@ -123,7 +123,7 @@
}
\section{Warning}{
-The validity of the maximum affinity method is premised on the calculation of the affinities of formation reactions at equal activities of the species of interest.
+The maximum affinity method is premised on the calculation of the affinities of formation reactions at equal activities of the species of interest.
Then, the species with the highest affinity of formation, after normalization by the balancing coefficients, corresponds to the predominant species in an equilibrium calculation.
The examples below \dQuote{work} because they are relatively simple - the balancing coefficients are unity or all the same value (aqueous aluminum example), or the species are solids with unit activities (the mineral examples).
The examples shown for \code{\link{protein}s} elsewhere also take the balancing coefficients to unity, after normalizing by protein length.
Modified: pkg/CHNOSZ/man/wjd.Rd
===================================================================
--- pkg/CHNOSZ/man/wjd.Rd 2012-12-27 12:23:52 UTC (rev 34)
+++ pkg/CHNOSZ/man/wjd.Rd 2012-12-31 07:25:08 UTC (rev 35)
@@ -39,9 +39,9 @@
B = c(2,1,1), method=c("central", "stoich"), minX = 0.001, iguess = 1, ic = NULL
)
run.wjd(ispecies, B = NULL, method = "stoich", Y = run.guess(ispecies, B, method),
- P=1, T=25, imax = 10, Gfrac = 1e-7, tol = 0.01)
+ P=1, T=25, nlambda=101, imax = 10, Gfrac = 1e-7, tol = 0.01)
run.guess(ispecies, B = NULL, method = "stoich", iguess = NULL)
- equil.potentials(w)
+ equil.potentials(w, tol=0.01, T=25)
}
\arguments{
@@ -110,7 +110,8 @@
\code{run.guess} is a wrapper function to call \code{guess} using the stoichiometric matrix \code{A} built from the \code{ispecies} indices in the thermodynamic database.
- \code{equil.potentials} returns the average (\code{\link{colMeans}}) of \code{element.potentials(w)}, or NULL if not \code{is.near.equil(w)}. The output of this function can be used as the \code{emu} argument for \code{\link{basis.logact}} to calculate the corresponding activities of the basis species.
+\code{equil.potentials} returns the average (\code{\link{colMeans}}) of \code{element.potentials(w)}, or NULL if \code{is.near.equil(w, tol=tol)} is FALSE.
+The output of this function can be used as the \code{emu} argument for \code{\link{basis.logact}} to calculate the corresponding activities of the basis species.
}
@@ -147,13 +148,13 @@
ep <- element.potentials(w, plot.it=TRUE)
# and we're pretty far from equilibrium
is.near.equil(w) # FALSE
+\dontshow{par(thermo$opar)}
\donttest{## test all of the guesses of inititial mole quantities
## provided by guess() using default bulk composition (H2NO)
# 9 of them are not is.near.equil with the tolerance lowered to 0.0001
sapply( 1:32, function(i)
is.near.equil(wjd(Y=guess(method = "stoich", iguess=i)), tol=0.0001) )
-\dontshow{par(opar)}
## using run.wjd(): 20 crystalline amino acids
iaa <- info(aminoacids(""), "cr")
@@ -167,6 +168,38 @@
# because the elements are redistributed among the species,
# the total number of moles of species does not remain constant
sum(w$X) # <20
+
+## run.wjd with proteins: cell periphery of yeast
+# get the proteins in the requested location
+y <- yeastgfp("cell.periphery")
+# get the amino acid compositions of the proteins
+aa <- more.aa(y$protein, "Sce")
+# don't use those with NA abundance or sequence
+ina <- is.na(y$abundance) | is.na(aa$chains)
+aa <- aa[!ina, ]
+# let's try normalizing the proteins to single residues
+# columns 6:25 are the actual amino acid counts
+aa.625 <- aa[, 6:25]
+aa[, 6:25] <- aa.625 / rowSums(aa.625)
+# add proteins to thermo$protein
+add.protein(aa)
+# add proteins to thermo$obigt
+iobigt <- info(paste(aa$protein, aa$organism, sep="_"))
+# use equal initial abundances, with total equal to yeastGFP abundances
+Y <- rep(mean(y$abundance[!ina]), length(y$abundance[!ina]))
+# run the Gibbs energy minimization
+w <- run.wjd(iobigt, Y=Y, imax=100)
+# make a log-log plot
+plot(log10(y$abundance[!ina]), log10(w$X), xlim=c(1.5, 5), ylim=c(1.5, 5))
+# get the element potentials (tolerating "close enough" to equilibrium)
+emu <- equil.potentials(w, tol=1e7)
+# then the logarithms of activities of the basis species
+basis("CHNOS")
+bl <- basis.logact(emu)
+# make a title and legend
+title(main="calculated vs observed abundances: yeast cell periphery")
+basis(names(bl), bl)
+legend("topleft", describe.basis(digits=2))
}
}
Modified: pkg/CHNOSZ/vignettes/anintro.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rnw 2012-12-27 12:23:52 UTC (rev 34)
+++ pkg/CHNOSZ/vignettes/anintro.Rnw 2012-12-31 07:25:08 UTC (rev 35)
@@ -15,7 +15,7 @@
bookmarks=true,bookmarksnumbered=false,bookmarksopen=false,
breaklinks=false,pdfborder={0 0 1},backref=false,colorlinks=true]
{hyperref}
-\hypersetup{pdftitle={An Introduction to CHNOSZ},
+\hypersetup{pdftitle={An introduction to CHNOSZ},
pdfauthor={Jeffrey M. Dick},
citecolor=blue}
\usepackage{breakurl}
@@ -37,7 +37,7 @@
{\end{list}}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands.
-%\VignetteIndexEntry{An Introduction to CHNOSZ}
+%\VignetteIndexEntry{An introduction to CHNOSZ}
% so DOIs in bibliography show up as hyperlinks
\newcommand*{\doi}[1]{\href{http://dx.doi.org/#1}{doi: #1}}
Modified: pkg/CHNOSZ/vignettes/anintro.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.lyx 2012-12-27 12:23:52 UTC (rev 34)
+++ pkg/CHNOSZ/vignettes/anintro.lyx 2012-12-31 07:25:08 UTC (rev 35)
@@ -4,7 +4,7 @@
\begin_header
\textclass article
\begin_preamble
-%\VignetteIndexEntry{An Introduction to CHNOSZ}
+%\VignetteIndexEntry{An introduction to CHNOSZ}
% so DOIs in bibliography show up as hyperlinks
\newcommand*{\doi}[1]{\href{http://dx.doi.org/#1}{doi: #1}}
@@ -37,7 +37,7 @@
\paperfontsize default
\spacing single
\use_hyperref true
-\pdf_title "An Introduction to CHNOSZ"
+\pdf_title "An introduction to CHNOSZ"
\pdf_author "Jeffrey M. Dick"
\pdf_bookmarks true
\pdf_bookmarksnumbered false
@@ -128,7 +128,7 @@
\begin_layout Standard
\begin_inset Branch load
-status collapsed
+status open
\begin_layout Standard
This document will orient you to the basic functionality of CHNOSZ, a package
@@ -179,7 +179,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Standard
CHNOSZ is made up of a set of functions and supporting datasets.
@@ -314,7 +314,7 @@
\begin_layout Standard
\begin_inset Branch load
-status collapsed
+status open
\begin_layout Standard
If you have just installed R, and you are online, installing the CHNOSZ
@@ -334,7 +334,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -363,7 +363,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -400,7 +400,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Subsection
@@ -423,7 +423,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -466,7 +466,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -494,7 +494,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -530,7 +530,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -564,7 +564,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Subsection
@@ -584,7 +584,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -632,7 +632,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -678,7 +678,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Subsection
@@ -694,7 +694,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -762,7 +762,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -800,7 +800,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -833,7 +833,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Subsection
@@ -854,7 +854,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -908,7 +908,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -942,7 +942,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Subsection
@@ -976,7 +976,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1033,7 +1033,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Subsection
A single species
@@ -1072,7 +1072,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1169,7 +1169,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1219,7 +1219,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1331,7 +1331,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1372,7 +1372,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Subsection
What are basis species?
@@ -1409,7 +1409,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1461,7 +1461,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1507,7 +1507,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1553,7 +1553,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1584,7 +1584,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1629,7 +1629,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1694,7 +1694,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1756,7 +1756,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -1879,7 +1879,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Subsection
Carbonate speciation (Bjerrum diagram)
@@ -1943,7 +1943,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -2063,7 +2063,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -2153,7 +2153,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -2197,7 +2197,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -2281,7 +2281,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -2387,7 +2387,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -2431,7 +2431,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -2600,7 +2600,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Standard
You can explore the package documentation through R's help system; just
@@ -2627,7 +2627,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -2663,7 +2663,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -2699,7 +2699,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -2732,7 +2732,7 @@
\begin_layout Standard
\begin_inset Branch stuff
-status collapsed
+status open
\begin_layout Chunk
@@ -2769,7 +2769,7 @@
\begin_layout Standard
\begin_inset Branch more
-status collapsed
+status open
\begin_layout Standard
The following pages contain activity diagrams created with more complex
More information about the CHNOSZ-commits
mailing list