From noreply at r-forge.r-project.org Sun May 6 08:41:32 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sun, 6 May 2018 08:41:32 +0200 (CEST) Subject: [CHNOSZ-commits] r318 - in pkg/CHNOSZ: . R demo inst man Message-ID: <20180506064132.4413D1806C2@r-forge.r-project.org> Author: jedick Date: 2018-05-06 08:41:29 +0200 (Sun, 06 May 2018) New Revision: 318 Added: pkg/CHNOSZ/demo/bison.R Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/examples.R pkg/CHNOSZ/demo/00Index pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/man/examples.Rd Log: add demo/bison.R Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2018-04-29 08:08:08 UTC (rev 317) +++ pkg/CHNOSZ/DESCRIPTION 2018-05-06 06:41:29 UTC (rev 318) @@ -1,6 +1,6 @@ -Date: 2018-04-29 +Date: 2018-05-06 Package: CHNOSZ -Version: 1.1.3-25 +Version: 1.1.3-26 Title: Thermodynamic Calculations and Diagrams for Geochemistry Authors at R: c( person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"), @@ -27,7 +27,7 @@ (Sverjensky et al., 2014 ) and estimates of parameters in the extended Debye-H?ckel equation (Manning et al., 2013 ) to calculate standard-state properties and activity coefficients for given ionic strength at high - pressure (to 60 kb). Functions are provided to calculate standard-state properties of species and + pressure (to 6 GPa). Functions are provided to calculate standard-state properties of species and reactions, define the basis species of a chemical system, automatically balance reactions, calculate the chemical affinities of formation reactions for selected species, calculate the equilibrium activities of those species, and plot the results on chemical activity diagrams. Modified: pkg/CHNOSZ/R/examples.R =================================================================== --- pkg/CHNOSZ/R/examples.R 2018-04-29 08:08:08 UTC (rev 317) +++ pkg/CHNOSZ/R/examples.R 2018-05-06 06:41:29 UTC (rev 318) @@ -29,7 +29,7 @@ demos <- function(which=c("sources", "protein.equil", "affinity", "NaCl", "density", "ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "yeastgfp", "mosaic", "copper", "solubility", "wjd", "bugstab", "Shh", "activity_ratios", - "adenine", "DEW", "lambda", "TCA", "go-IU"), save.png=FALSE) { + "adenine", "DEW", "lambda", "TCA", "go-IU", "bison"), save.png=FALSE) { # run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one for(i in 1:length(which)) { # say something so the user sees where we are Modified: pkg/CHNOSZ/demo/00Index =================================================================== --- pkg/CHNOSZ/demo/00Index 2018-04-29 08:08:08 UTC (rev 317) +++ pkg/CHNOSZ/demo/00Index 2018-05-06 06:41:29 UTC (rev 318) @@ -24,3 +24,4 @@ TCA Standard Gibbs energies of steps of the citric acid cycle go-IU Diagrams using thermodynamic data in the SUPCRTBL compilation carboxylase Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase +bison Average oxidation state of carbon in proteins for phyla at Bison Pool Added: pkg/CHNOSZ/demo/bison.R =================================================================== --- pkg/CHNOSZ/demo/bison.R (rev 0) +++ pkg/CHNOSZ/demo/bison.R 2018-05-06 06:41:29 UTC (rev 318) @@ -0,0 +1,44 @@ +# CHNOSZ/demo/bison.R +# average oxidation state of carbon (ZC) of metagenome-derived +# proteins in different microbial phyla at Bison Pool 20171217 + +par(mar=c(3.5, 4, 2.5, 2), las=1, mgp=c(2.2, 0.8, 0)) +# read the amino acid compositions +aa.annot <- read.csv(system.file("extdata/protein/DS11.csv", package="CHNOSZ"), as.is=TRUE) +aa.phyla <- read.csv(system.file("extdata/protein/DS13.csv", package="CHNOSZ"), as.is=TRUE) +sites <- c("N", "S", "R", "Q", "P") +sitenames <- paste("bison", sites, sep="") +# the names of the phyla in alphabetical order (except Deinococcus-Thermus at end) +phyla.abc <- sort(unique(aa.phyla$organism))[c(1:7,9:11,8)] +# an abbreviation for Dein.-Thermus +phyla.abbrv <- phyla.abc +phyla.abbrv[[11]] <- "Dein.-Thermus" +phyla.cols <- c("#f48ba5", "#f2692f", "#cfdd2a", + "#962272", "#87c540", "#66c3a2", "#12a64a", "#f58656", + "#ee3237", "#25b7d5", "#3953a4") +# set Chlorobi color to NA because no line is needed (it's identifed only at one location) +phyla.cols[4] <- NA +# chemical formula and ZC of proteins +pf.phyla <- protein.formula(aa.phyla) +ZC.phyla <- ZC(pf.phyla) +# set up plot +plot(0, 0, xlim=c(1, 5), ylim=c(-0.23, -0.14), xlab="distance from source, m", ylab=NA, xaxt="n") +distance <- c(0, 6, 11, 14, 22) +axis(1, at=1:5, labels=distance) +mtext(axis.label("ZC"), side=2, line=3, las=0) +for(i in 1:length(phyla.abc)) { + # skip Euryarchaeota because it occurs at one location, on top of Dein.-Thermus and Firmicutes + if(phyla.abc[i]=="Euryarchaeota") next + # which of the model proteins correspond to this phylum + iphy <- which(aa.phyla$organism==phyla.abc[i]) + # the locations (of 1, 2, 3, 4, 5) where this phylum is found + ilocs <- match(aa.phyla$protein[iphy], sitenames) + # the plotting symbol: determined by alphabetical position of the phylum + points(ilocs, ZC.phyla[iphy], pch=i-1, cex=1.2) + # lines to connect the phyla + lines(ilocs, ZC.phyla[iphy], type="c", col=phyla.cols[i], lwd=2) +} +text(c(4.75, 2.0, 4.0, 4.0, 4.0, 2.0, 3.0, NA, 2.9, 1.3, 3.0), + c(-0.146, -0.224, -0.161, -0.184, -0.145, -0.201, -0.144, NA, -0.176, -0.158, -0.192), + phyla.abbrv, cex=0.9) +title(main="Bison Pool hot spring, Yellowstone National Park") Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2018-04-29 08:08:08 UTC (rev 317) +++ pkg/CHNOSZ/inst/NEWS 2018-05-06 06:41:29 UTC (rev 318) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.1.3-25 (2018-04-29) +CHANGES IN CHNOSZ 1.1.3-26 (2018-05-06) --------------------------------------- THERMODYNAMIC DATA @@ -81,6 +81,8 @@ plot saturation lines for minerals (where their affinity equals zero). +- Add demo/bison.R (average oxidation state of carbon of metagenome- + derived proteins in different microbial phyla at Bison Pool) CHANGES IN CHNOSZ 1.1.3 (2017-11-13) ------------------------------------ Modified: pkg/CHNOSZ/man/examples.Rd =================================================================== --- pkg/CHNOSZ/man/examples.Rd 2018-04-29 08:08:08 UTC (rev 317) +++ pkg/CHNOSZ/man/examples.Rd 2018-05-06 06:41:29 UTC (rev 318) @@ -17,7 +17,7 @@ "density", "ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "yeastgfp", "mosaic", "copper", "solubility", "wjd", "bugstab", "Shh", "activity_ratios", "adenine", - "DEW", "lambda", "TCA", "go-IU"), + "DEW", "lambda", "TCA", "go-IU", "bison"), save.png=FALSE) } @@ -57,6 +57,7 @@ \code{TCA} \tab * Standard Gibbs energies of the tricarboxylic (citric) acid cycle (Canovas and Shock, 2016) \cr \code{go-IU} \tab * Diagrams using thermodynamic data in the SUPCRTBL compilation (Zimmer et al., 2016) \cr \code{carboxylase} \tab * Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase \cr + \code{bison} \tab Average oxidation state of carbon in proteins for phyla at Bison Pool (Dick and Shock, 2013) \cr } For either function, if \code{save.png} is TRUE, the plots are saved in \code{\link{png}} files whose names begin with the names of the help topics or demos. @@ -94,6 +95,8 @@ Dick, J. M. and Shock, E. L. (2011) Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. \emph{PLoS ONE} \bold{6}, e22782. \url{https://doi.org/10.1371/journal.pone.0022782} +Dick, J. M. and Shock, E. L. (2013) A metastable equilibrium model for the relative abundance of microbial phyla in a hot spring. \emph{PLoS ONE} \bold{8}, e72395. \url{https://doi.org/10.1371/journal.pone.0072395} + Dick, J. M. (2015) Chemical integration of proteins in signaling and development. \emph{bioRxiv}. \url{https://doi.org/10.1101/015826} Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. \emph{PeerJ} \bold{4}:e2238. \url{https://doi.org/10.7717/peerj.2238} From noreply at r-forge.r-project.org Mon May 14 07:08:15 2018 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 14 May 2018 07:08:15 +0200 (CEST) Subject: [CHNOSZ-commits] r319 - in pkg/CHNOSZ: . R data inst man Message-ID: <20180514050815.A7349187B8A@r-forge.r-project.org> Author: jedick Date: 2018-05-14 07:08:15 +0200 (Mon, 14 May 2018) New Revision: 319 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/palply.R pkg/CHNOSZ/data/opt.csv pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/man/data.Rd Log: add thermo$opt$maxcores Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2018-05-06 06:41:29 UTC (rev 318) +++ pkg/CHNOSZ/DESCRIPTION 2018-05-14 05:08:15 UTC (rev 319) @@ -1,6 +1,6 @@ -Date: 2018-05-06 +Date: 2018-05-14 Package: CHNOSZ -Version: 1.1.3-26 +Version: 1.1.3-27 Title: Thermodynamic Calculations and Diagrams for Geochemistry Authors at R: c( person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"), Modified: pkg/CHNOSZ/R/palply.R =================================================================== --- pkg/CHNOSZ/R/palply.R 2018-05-06 06:41:29 UTC (rev 318) +++ pkg/CHNOSZ/R/palply.R 2018-05-14 05:08:15 UTC (rev 319) @@ -6,7 +6,7 @@ if(length(X) >= get("thermo")$opt$paramin) { # Use option mc.cores to choose an appropriate cluster size. # and set max at 2 for now (per CRAN policies) - nCores <- min(getOption("mc.cores"), 2) + nCores <- min(getOption("mc.cores"), get("thermo")$opt$maxcores) # don't load methods package, to save startup time - ?makeCluster cl <- parallel::makeCluster(nCores, methods=FALSE) # export the variables and notify the user Modified: pkg/CHNOSZ/data/opt.csv =================================================================== --- pkg/CHNOSZ/data/opt.csv 2018-05-06 06:41:29 UTC (rev 318) +++ pkg/CHNOSZ/data/opt.csv 2018-05-14 05:08:15 UTC (rev 319) @@ -1,2 +1,2 @@ -cutoff,E.units,T.units,P.units,state,water,G.tol,Cp.tol,V.tol,varP,IAPWS.sat,paramin,ideal.H,ideal.e,nonideal,Berman -1E-10,cal,C,bar,aq,SUPCRT92,100,1,1,FALSE,liquid,1000,TRUE,TRUE,Helgeson,NA +cutoff,E.units,T.units,P.units,state,water,G.tol,Cp.tol,V.tol,varP,IAPWS.sat,paramin,ideal.H,ideal.e,nonideal,Berman,maxcores +1E-10,cal,C,bar,aq,SUPCRT92,100,1,1,FALSE,liquid,1000,TRUE,TRUE,Helgeson,NA,2 Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2018-05-06 06:41:29 UTC (rev 318) +++ pkg/CHNOSZ/inst/NEWS 2018-05-14 05:08:15 UTC (rev 319) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.1.3-26 (2018-05-06) +CHANGES IN CHNOSZ 1.1.3-27 (2018-05-14) --------------------------------------- THERMODYNAMIC DATA @@ -84,6 +84,9 @@ - Add demo/bison.R (average oxidation state of carbon of metagenome- derived proteins in different microbial phyla at Bison Pool) +- Add thermo$opt$maxcores (default 2) to specify maximum number of + cores for parallel calculations with palply(). + CHANGES IN CHNOSZ 1.1.3 (2017-11-13) ------------------------------------ Modified: pkg/CHNOSZ/man/data.Rd =================================================================== --- pkg/CHNOSZ/man/data.Rd 2018-05-06 06:41:29 UTC (rev 318) +++ pkg/CHNOSZ/man/data.Rd 2018-05-14 05:08:15 UTC (rev 319) @@ -59,7 +59,8 @@ \code{ideal.H} \tab logical \tab Should \code{\link{nonideal}} ignore the proton? [\code{TRUE}] \cr \code{ideal.e} \tab logical \tab Should \code{\link{nonideal}} ignore the electron? [\code{TRUE}] \cr \code{nonideal} \tab character \tab Method for \code{\link{nonideal}} [\code{Helgeson}] \cr - \code{Berman} \tab character \tab User data file for mineral parameters in the Berman equations [\code{NA}] + \code{Berman} \tab character \tab User data file for mineral parameters in the Berman equations [\code{NA}] \cr + \code{maxcores} \tab numeric \tab Maximum number of cores for parallel calculations with \code{\link{palply}} [\code{2}] } \item \code{thermo$element}