[CHNOSZ-commits] r452 - in pkg/CHNOSZ: . R demo inst inst/extdata/Berman inst/extdata/adds man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Apr 20 11:57:37 CEST 2019
Author: jedick
Date: 2019-04-20 11:57:37 +0200 (Sat, 20 Apr 2019)
New Revision: 452
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/NAMESPACE
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/R/nonideal.R
pkg/CHNOSZ/R/retrieve.R
pkg/CHNOSZ/R/util.plot.R
pkg/CHNOSZ/R/zzz.R
pkg/CHNOSZ/demo/aluminum.R
pkg/CHNOSZ/demo/gold.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/Berman/Ber88_1988.csv
pkg/CHNOSZ/inst/extdata/Berman/SHD91_1991.csv
pkg/CHNOSZ/inst/extdata/adds/obigt_check.csv
pkg/CHNOSZ/man/EOSregress.Rd
pkg/CHNOSZ/man/add.obigt.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/man/util.plot.Rd
Log:
submit version 1.3.2 to CRAN
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/DESCRIPTION 2019-04-20 09:57:37 UTC (rev 452)
@@ -1,6 +1,6 @@
-Date: 2019-04-17
+Date: 2019-04-20
Package: CHNOSZ
-Version: 1.3.1-32
+Version: 1.3.2
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/NAMESPACE
===================================================================
--- pkg/CHNOSZ/NAMESPACE 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/NAMESPACE 2019-04-20 09:57:37 UTC (rev 452)
@@ -78,3 +78,5 @@
importFrom("utils", "browseURL", "capture.output", "combn", "demo",
"example", "head", "installed.packages", "read.csv", "tail",
"write.csv", "write.table", "read.table")
+# 20190420 new R functions for HCL color palettes
+if (getRversion() >= "3.6.0") importFrom("grDevices", "hcl.pals", "hcl.colors")
Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/R/diagram.R 2019-04-20 09:57:37 UTC (rev 452)
@@ -554,10 +554,10 @@
# choose an HCL palette 20190411
# matching adapted from hcl.colors()
fx <- function(x) tolower(gsub("[-, _, \\,, (, ), \\ , \\.]", "", x))
- p <- charmatch(fx(fill), fx(grDevices::hcl.pals()))
+ p <- charmatch(fx(fill), fx(hcl.pals()))
if(!is.na(p)) {
if(!p < 1L) {
- fill <- grDevices::hcl.colors(ngroups, fill)
+ fill <- hcl.colors(ngroups, fill)
}
}
}
@@ -740,4 +740,3 @@
# return the indices
return(id[imax, ])
}
-
Modified: pkg/CHNOSZ/R/nonideal.R
===================================================================
--- pkg/CHNOSZ/R/nonideal.R 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/R/nonideal.R 2019-04-20 09:57:37 UTC (rev 452)
@@ -326,9 +326,9 @@
T40 <- c(175, seq(300, 1000, 5)); lines(T40, S40(T40), col=col[11])
T50 <- c(225, seq(300, 1000, 5)); lines(T50, S50(T50), col=col[12])
T60 <- c(250, seq(300, 1000, 5)); lines(T60, S60(T60), col=col[13])
- legend("topleft", pch=c(0, 1, 2, 5, 6),
+ legend("topleft", pch=c(0, 1, 2, 5, 6), bty = "n",
legend=c("Helgeson, 1969", "Helgeson et al., 1981", "Manning et al., 2013", "spline control point", "high-P extrapolation"))
- legend("bottomright", col=c(NA, rev(col)), lty=1,
+ legend("bottomright", col=c(NA, rev(col)), lty=1, bty = "n",
legend=c("kbar", "60", "50", "40", "30", "20", "10", "5", "4", "3", "2", "1", "0.5", "Psat"))
title(main=expression("Deybe-H\u00FCckel extended term ("*italic(b)[gamma]*") parameter"))
} else if(showsplines=="P") {
@@ -370,8 +370,8 @@
P <- seq(10000, 60000, 50); lines(log10(P), bgamma(800, P), col=col[9])
P <- seq(10000, 60000, 50); lines(log10(P), bgamma(900, P), col=col[10])
P <- seq(10000, 60000, 50); lines(log10(P), bgamma(1000, P), col=col[11])
- legend("topleft", col=c(NA, col), lty=1, legend=c("degrees C", 25, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000))
- legend("bottomright", pch=1, legend="points from iso-P splines")
+ legend("topleft", col=c(NA, col), lty=1, bty = "n", legend=c("degrees C", 25, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000))
+ legend("bottomright", pch=1, bty = "n", legend="points from iso-P splines")
title(main=expression("Deybe-H\u00FCckel extended term ("*italic(b)[gamma]*") parameter"))
} else {
# make T and P the same length
Modified: pkg/CHNOSZ/R/retrieve.R
===================================================================
--- pkg/CHNOSZ/R/retrieve.R 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/R/retrieve.R 2019-04-20 09:57:37 UTC (rev 452)
@@ -91,9 +91,11 @@
# for a chemical system, all species are included that do not contain any other elements
ispecies <- unique(unlist(ispecies))
ielements <- colnames(thermo()$stoich) %in% elements
- otherstoich <- thermo()$stoich[, !ielements]
- iother <- rowSums(otherstoich[ispecies, ] != 0) > 0
- ispecies <- ispecies[!iother]
+ if(any(!ielements)) {
+ otherstoich <- thermo()$stoich[, !ielements]
+ iother <- rowSums(otherstoich[ispecies, ] != 0) > 0
+ ispecies <- ispecies[!iother]
+ }
} else {
# get species that have all the elements; the species must be present in each vector
# Reduce() hint from https://stackoverflow.com/questions/27520310/union-of-intersecting-vectors-in-a-list-in-r
Modified: pkg/CHNOSZ/R/util.plot.R
===================================================================
--- pkg/CHNOSZ/R/util.plot.R 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/R/util.plot.R 2019-04-20 09:57:37 UTC (rev 452)
@@ -214,8 +214,10 @@
if(thisside %in% c(1, 3)) pat <- par("usr")[1:2]
if(thisside %in% c(2, 4)) pat <- par("usr")[3:4]
mat <- setdiff(at, pat)
- if(plot.line) axis(thisside, at=mat, labels=do.label, tick=TRUE, lwd=lwd, col.axis=col, col=col)
- else axis(thisside, at=mat, labels=do.label, tick=TRUE, lwd=lwd, col.axis=col, col = NA, col.ticks = col)
+ if(plot.line) axis(thisside, at=mat, labels=FALSE, tick=TRUE, lwd=lwd, col.axis=col, col=col)
+ else axis(thisside, at=mat, labels=FALSE, tick=TRUE, lwd=lwd, col.axis=col, col = NA, col.ticks = col)
+ # plot only the labels at all major tick points (including plot limits) 20190417
+ if(do.label) axis(thisside, at=at, tick=FALSE, col=col)
## plot minor tick marks
# the distance between major tick marks
Modified: pkg/CHNOSZ/R/zzz.R
===================================================================
--- pkg/CHNOSZ/R/zzz.R 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/R/zzz.R 2019-04-20 09:57:37 UTC (rev 452)
@@ -5,7 +5,21 @@
# https://stackoverflow.com/questions/41954302/where-to-create-package-environment-variables
CHNOSZ <- new.env()
+.onLoad <- function(libname, pkgname) {
+
+ # 20190420 add placeholder functions not present in earlier R versions
+ # code inspired by backports::import
+ if(getRversion() < "3.6.0") {
+ pkg = getNamespace(pkgname)
+ no.fun <- function(...) stop("this function is not available in this version of R")
+ assign("hcl.pals", no.fun, envir = pkg)
+ assign("hcl.colors", no.fun, envir = pkg)
+ }
+
+}
+
.onAttach <- function(libname,pkgname) {
+
# version figuring adapted from package mgcv
pkghelp <- library(help=CHNOSZ)$info[[1]]
# things are different for older versions of R
@@ -16,8 +30,11 @@
date <- pkghelp[pmatch("Date:", pkghelp)]
um <- strsplit(date, " ")[[1]]
date <- um[nchar(um)>0][2]
+
# identify the program and version
packageStartupMessage(paste("CHNOSZ version ", version, " (", date, ")", sep=""))
+
# initialize the 'thermo' data object
reset()
+
}
Modified: pkg/CHNOSZ/demo/aluminum.R
===================================================================
--- pkg/CHNOSZ/demo/aluminum.R 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/demo/aluminum.R 2019-04-20 09:57:37 UTC (rev 452)
@@ -80,7 +80,7 @@
## add legend and title
title(main = describe.reaction(Daw1$reaction), cex.main = 0.95)
legend("bottomright", lty = c(0, 0, 0, 1, 2), pch = c(1, 4, NA, NA, NA), col = c("black", "red", NA, "black", "red"), lwd = c(1, 1, 0, 1.5, 1),
- bty = "n", cex = 0.9, legend = c("Ben\u00e9z\u00e9th et al., 2007", "SUPCRTBL with modified", " data for Cp of dawsonite", "CHNOSZ", "Cp(dawsonite) = 0"))
+ bty = "n", cex = 0.9, legend = c("Ben\u00e9z\u00e9th et al., 2007", "SUPCRTBL with Cp", " coefficients for dawsonite", "CHNOSZ", "Cp(dawsonite) = 0"))
legend("topleft", c("Dawsonite solubility", "After Zimmer et al., 2016 Fig. 2"), bty = "n")
reset()
@@ -89,7 +89,7 @@
###########
# After Tutolo et al., 2014, Fig. 2 (doi:10.1016/j.gca.2014.02.036)
dat <- read.csv(system.file("extdata/cpetc/TKSS14_Fig2.csv", package = "CHNOSZ"))
-thermo.plot.new(c(3.5, 1.5), c(-2, 14), quote(1000 / italic(T)*"(K)"), "pK")
+thermo.plot.new(c(3.5, 1.5), c(-2, 14), quote(1000 / italic(T)*"(K)"), quote(p*italic(K)))
points(dat)
# plot line: default database
invTK <- seq(3.5, 1.6, -0.02)
@@ -97,7 +97,7 @@
sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "SiO2"), c(-1, -2, -1, 2, 2), T = T)
pK <- -sres$out$logK
lines(invTK, pK, lwd = 1.5)
-# plot line: default database with AS04 SiO2
+# plot line: SiO2 from Apps and Spycher, 2004
add.obigt("AS04")
sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "SiO2"), c(-1, -2, -1, 2, 2), T = T)
pK <- -sres$out$logK
@@ -117,8 +117,8 @@
title(main = describe.reaction(sres$reaction), cex.main = 1.1)
par(xpd = FALSE)
legend("topright", c("Kaolinite solubility", "After Tutolo et al., 2014 Fig. 2"), bty = "n")
-legend("bottomleft", lty = c(0, 2, 0, 1, 2), pch = c(1, NA, 4, NA, NA), lwd = c(1, 1, 1, 1.5, 1), col = c("black", "blue", "red", "black", "red"),
- legend = c("Tutolo et al., 2014", "SUPCRT92", "SUPCRTBL", "CHNOSZ", 'add.obigt("AS04")'), bty = "n", cex = 0.9)
+legend("bottomleft", lty = c(0, 0, 2, 0, 1, 2), pch = c(1, NA, NA, 4, NA, NA), lwd = c(1, 1, 1, 1, 1.5, 1), col = c("black", "black", "blue", "red", "black", "red"),
+ legend = c("Various sources \u2013", " see Tutolo et al., 2014", "SUPCRT92", "SUPCRTBL", "CHNOSZ", 'add.obigt("AS04")'), bty = "n", cex = 0.9)
reset()
###########
@@ -132,7 +132,7 @@
T <- 100
P <- 150
a <- affinity("K+" = c(4, 7), "Na+" = c(6, 9), T = T, P = P)
-diagram(a, lwd = 1.5, xlab = ratlab("K+"), ylab = ratlab("Na+"))
+diagram(a, lwd = 1.5, xlab = ratlab("K+"), ylab = ratlab("Na+"), names = NULL)
# plot experimental data
dat <- read.csv(system.file("extdata/cpetc/Mer75_Table4.csv", package = "CHNOSZ"))
points(dat$log.aK..aH.., dat$log.aNa..aH..)
@@ -151,7 +151,7 @@
legend("topleft", c("Albite - K-feldspar", "After Tutolo et al., 2014 Fig. 5"), bty = "n", cex = 0.9)
legend("bottomright", lty = c(0, 2, 0, 1), pch = c(1, NA, 4, NA), lwd = c(1, 1, 1, 1.5), col = c("black", "blue", "red", "black"),
legend = c("Merino, 1975", "SUPCRT92", "SUPCRTBL", "CHNOSZ"), bty = "n", cex = 0.9)
-legend("right", describe.property(c("T", "P"), c(T, P)), bty = "n")
+legend("left", describe.property(c("T", "P"), c(T, P)), bty = "n")
reset()
par(opar)
Modified: pkg/CHNOSZ/demo/gold.R
===================================================================
--- pkg/CHNOSZ/demo/gold.R 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/demo/gold.R 2019-04-20 09:57:37 UTC (rev 452)
@@ -105,7 +105,7 @@
NaCl <- NaCl(T = T, P = P, m_tot = m_NaCl + m_KCl)
# calculate logK of K+ + Cl- = KCl, adjusted for ionic strength
logKadj <- subcrt(c("K+", "Cl-", "KCl"), c(-1, -1, 1), T = T, P = P, IS = NaCl$IS)$out$logK
- # what is the molality of K+ from 0.5 mol/kg KCl, assuming total chloride from above
+ # what is the molality of K+ from 0.5 mol KCl in solution with 2 mol total Cl
m_K <- m_KCl / (10^logKadj * NaCl$m_Cl + 1)
list(IS = NaCl$IS, m_Cl = NaCl$m_Cl, m_K = m_K)
}
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/inst/NEWS 2019-04-20 09:57:37 UTC (rev 452)
@@ -1,6 +1,8 @@
-CHANGES IN CHNOSZ 1.3.1-30 (2019-04-16)
----------------------------------------
+CHANGES IN CHNOSZ 1.3.2 (2019-04-20)
+------------------------------------
+NEW FEATURES
+
- Add thermo/stoich.csv.xz (loaded as thermo()$stoich), containing a
precalculated stochiometric matrix for the default database, to speed
up retrieve().
@@ -11,24 +13,9 @@
- Add 'ligands' argument to retrieve(), for getting metal-bearing
species with a range of possible elements in the ligands.
-- In extdata/Berman, rename .csv files to include whole year. berman()
- now uses the years in the filenames to assemble the data in reverse
- chronological order, and keeps only the most recent data for any
- duplicated minerals.
-
-- Add data for sudoite, daphnite, Mg-amesite, and Fe-amesite to
- extdata/Berman (Vidal et al., 1992, 2001, 2005).
-
-- obigt.Rmd: Use Zenodo DOI for citations to slop98.dat, slop07.dat, and
- slop16.dat.
-
- diagram(): Starting with R version 3.6.0, 'fill' can be the name of
any available HCL-based color palette (see hcl.pals() for a list).
-- Move transuranic actinide complexes to optional data (SLOP98), as
- entropies of the elements at 298.15 K are not available to check the
- self-consistency of the GHS values for the complexes.
-
- Add demo/contour.R for gold solubility contours on logfO2-pH diagram.
- In the output of affinity(), the list of 'vals' (the values of the
@@ -43,15 +30,34 @@
- Rename demo/go-IU.R to aluminum.R, and add plots from Tutolo et al.,
2014.
+- Add argument 'plot.box' (default TRUE) to thermo.plot.new() and
+ 'plot.line' (default FALSE) to thermo.axis() to prevent unecessary
+ plotting of axis lines. thermo.axis() also avoids plotting tick
+ marks at the plot limits.
+
+THERMODYNAMIC DATA
+
- OBIGT: use dawsonite Cp coefficients from Tutolo et al., 2014.
- OBIGT: Move H4SiO4 (Stefánsson, 2001) to AS04.csv (optional data).
-- Give thermo.plot.new() argument 'plot.box' (default TRUE) and
- thermo.axis() argument 'plot.line' (default FALSE) to prevent
- unecessary plotting of axis lines on a plot with a box. thermo.axis()
- also avoids plotting tick marks at the plot limits.
+- Berman: rename .csv files to include whole year. berman()
+ now uses the years in the filenames to assemble the data in reverse
+ chronological order, and keeps only the most recent data for any
+ duplicated minerals.
+- Berman: Add data for sudoite, daphnite, Mg-amesite, and Fe-amesite
+ (Vidal et al., 1992, 2001, 2005).
+
+- Berman: make "albite" identical to "albite,low", not "albite,high".
+
+- Move transuranic actinide complexes to optional data (SLOP98), as
+ entropies of the elements at 298.15 K are not available to check the
+ self-consistency of the GHS values for the complexes.
+
+- obigt.Rmd: Use Zenodo DOI for citations of slop98.dat, slop07.dat, and
+ slop16.dat.
+
CHANGES IN CHNOSZ 1.3.1 (2019-03-02)
------------------------------------
Modified: pkg/CHNOSZ/inst/extdata/Berman/Ber88_1988.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/Ber88_1988.csv 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/inst/extdata/Berman/Ber88_1988.csv 2019-04-20 09:57:37 UTC (rev 452)
@@ -1,6 +1,6 @@
name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,k4,k5,k6,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,Vad
akermanite,-3663786,-3860441,212,9.252,387.06,-2938.8,0,-40790000,0,0,0,2.5011,0.00067224,-0.0785,0,358,298,0,0,0,452,,,,,,,,
-albite,-3703293,-3921618,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+albite,-3711715,-3935100,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
"albite,high",-3703293,-3921618,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
"albite,low",-3711715,-3935100,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
almandine,-4941728,-5265502,339.927,11.511,573.96,-1483.1,-29292000,5022080000,0,0,0,1.8613,0.00074539,-0.0558,3.21E-05,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/Berman/SHD91_1991.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/SHD91_1991.csv 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/inst/extdata/Berman/SHD91_1991.csv 2019-04-20 09:57:37 UTC (rev 452)
@@ -5,7 +5,7 @@
"K-feldspar,high",-3745498,-3966398,229.157,10.896,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
"K-feldspar,low",-3752109,-3977485,214.145,10.869,381.37,-1941,-12037300,1836430000,0,0,0,1.5145,0.0005485,-0.1805,0.0005112,,,,,,,,,,,,,,
paragonite,-5570375,-5951011,277.699,13.216,577.57,-1472.8,-32214400,5050080000,0,0,0,3.9424,0.00059701,-0.1973,0.0004933,,,,,,,,,,,,,,
-albite,-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
+albite,-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
"albite,high",-3710096,-3928421,224.412,10.083,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
"albite,low",-3718518,-3941903,207.443,10.043,393.64,-2415.5,-7892800,1070640000,0,0,0,2.6307,0.00032407,-0.1945,0.0004861,,,,,,,,,,,,,,
jadeite,-2853285,-3031921,133.574,6.034,311.29,-2005.1,-5350300,662570000,0,0,0,2.3118,0.00025785,-0.086,0.0002149,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/adds/obigt_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/obigt_check.csv 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/inst/extdata/adds/obigt_check.csv 2019-04-20 09:57:37 UTC (rev 452)
@@ -61,145 +61,145 @@
"OBIGT",705,"Rh(SO4)3-3","aq",,-1.33,
"OBIGT",708,"CF4","aq",5.9,,
"OBIGT",715,"AsH3","aq",-2.67,,
-"OBIGT",801,"AgCl","aq",,-1.88,
-"OBIGT",802,"AgCl2-","aq",1.65,,
-"OBIGT",807,"CuHS","aq",7.35,-16.2,
-"OBIGT",815,"ZnO2-2","aq",,-1.17,
-"OBIGT",841,"methane","aq",-2.61,,
-"OBIGT",846,"hexane","aq",1.43,3.21,
-"OBIGT",849,"ethylene","aq",6.12,-3.82,
-"OBIGT",873,"propanol","aq",-1.89,,
-"OBIGT",1002,"urea","aq",-23.26,23.32,
-"OBIGT",1015,"propanoic acid","aq",1.42,,
-"OBIGT",1038,"formate","aq",1.96,,
-"OBIGT",1040,"propanoate","aq",1.68,,
-"OBIGT",1047,"n-decanoate","aq",-1.93,,
-"OBIGT",1063,"oxalate-2","aq",-3.19,,
-"OBIGT",1330,"Li(Mal)-","aq",,-3.22,
-"OBIGT",1334,"Pb(Mal)","aq",,1.16,
-"OBIGT",1338,"Pb(Succ)","aq",,1.49,
-"OBIGT",1339,"Na(Oxal)-","aq",,-3.14,
-"OBIGT",1340,"K(Oxal)-","aq",,-2.75,
-"OBIGT",1341,"Fe(Oxal)+","aq",,-2.19,
-"OBIGT",1343,"Na(Mal)-","aq",,-3.11,
-"OBIGT",1344,"K(Mal)-","aq",,-2.63,
-"OBIGT",1346,"La(Mal)+","aq",,-1.92,
-"OBIGT",1347,"Gd(Mal)+","aq",,-1.73,
-"OBIGT",1348,"Lu(Mal)+","aq",,-2.25,
-"OBIGT",1349,"Yb(Mal)+","aq",,-2.05,
-"OBIGT",1350,"Th(Mal)+2","aq",-1.29,-4.79,
-"OBIGT",1352,"Ce(Mal)+","aq",,-1.75,
-"OBIGT",1353,"Nd(Mal)+","aq",4.52,,
-"OBIGT",1354,"Sm(Mal)+","aq",,-1.77,
-"OBIGT",1355,"Pr(Mal)+","aq",,-1.75,
-"OBIGT",1356,"Eu(Mal)+","aq",,-1.87,
-"OBIGT",1357,"Tb(Mal)+","aq",,-1.92,
-"OBIGT",1358,"Dy(Mal)+","aq",,-1.89,
-"OBIGT",1359,"Tm(Mal)+","aq",,-2.08,
-"OBIGT",1360,"Ho(Mal)+","aq",,-2.08,
-"OBIGT",1361,"Er(Mal)+","aq",,-2.11,
-"OBIGT",1362,"Sc(Mal)+","aq",,-1.97,
-"OBIGT",1363,"Fe(Mal)+","aq",,-1.97,
-"OBIGT",1364,"Na(Succ)-","aq",,-2.82,
-"OBIGT",1365,"K(Succ)-","aq",,-2.39,
-"OBIGT",1371,"Th(Succ)+2","aq",-1.21,-4.47,
-"OBIGT",1376,"NH4(Oxal)-","aq",,-2.62,
-"OBIGT",1381,"Yb(Oxal)+","aq",,-2.02,
-"OBIGT",1382,"Ce(Oxal)+","aq",,-1.8,
-"OBIGT",1383,"Nd(Oxal)+","aq",,-1.8,
-"OBIGT",1384,"Eu(Oxal)+","aq",,-1.89,
-"OBIGT",1385,"Gd(Oxal)+","aq",,-1.8,
-"OBIGT",1386,"Ru(Oxal)+","aq",,-2.41,
-"OBIGT",1387,"Pa(Oxal)+2","aq",-1.25,-4.63,
-"OBIGT",1388,"Th(Oxal)+2","aq",-1.27,-4.69,
-"OBIGT",1389,"U(Oxal)+2","aq",-1.25,-4.63,
-"OBIGT",1391,"Y(Oxal)+","aq",,-2.11,
-"OBIGT",1396,"La(Oxal)+","aq",,-1.87,
-"OBIGT",1397,"Tb(Oxal)+","aq",,-1.92,
-"OBIGT",1398,"Er(Oxal)+","aq",,-2.05,
-"OBIGT",1399,"Lu(Oxal)+","aq",,-2.19,
-"OBIGT",1400,"Cr(Oxal)+","aq",,-2.58,
-"OBIGT",1401,"Ga(Oxal)+","aq",,-2.66,
-"OBIGT",1402,"Sc(Oxal)+","aq",,-2.13,
-"OBIGT",1403,"In(Oxal)+","aq",,-2.19,
-"OBIGT",1404,"Sm(Oxal)+","aq",,-1.84,
-"OBIGT",1405,"Cs(Mal)-","aq",,-2.39,
-"OBIGT",1406,"NH4(Mal)-","aq",,-2.54,
-"OBIGT",1411,"In(Mal)+","aq",,-2.11,
-"OBIGT",1412,"Y(Mal)+","aq",,-2.02,
-"OBIGT",1420,"La(Succ)+","aq",,-1.52,
-"OBIGT",1421,"NH4(Succ)-","aq",,-2.26,
-"OBIGT",1423,"Fe(Succ)+","aq",,-1.92,
-"OBIGT",1424,"Sc(Succ)+","aq",,-1.77,
-"OBIGT",1426,"Sm(Succ)+","aq",,-1.48,
-"OBIGT",1427,"Er(Succ)+","aq",,-1.68,
-"OBIGT",1428,"U(Succ)+2","aq",-1.15,-4.27,
-"OBIGT",1432,"La(Glut)+","aq",,-1.23,
-"OBIGT",1433,"Y(Glut)+","aq",,-1.46,
-"OBIGT",1434,"Sc(Glut)+","aq",,-1.5,
-"OBIGT",1435,"Th(Glut)+2","aq",-1.09,-4.05,
-"OBIGT",1438,"Fe(Glut)+","aq",,-1.05,
-"OBIGT",1439,"Sm(Glut)+","aq",,-1.2,
-"OBIGT",1441,"Er(Glut)+","aq",,-1.4,
-"OBIGT",1443,"Ba(Adip)","aq",,1.19,
-"OBIGT",1450,"Pb(Adip)","aq",,1.25,
-"OBIGT",1451,"Sc(Adip)+","aq",,-1.22,
-"OBIGT",1453,"Th(Adip)+2","aq",-1.02,-3.76,
-"OBIGT",1454,"U(Adip)+2","aq",-1,-3.71,
-"OBIGT",1456,"Li(Oxal)-","aq",,-3.3,
-"OBIGT",1460,"Li(Succ)-","aq",,-2.94,
-"OBIGT",1462,"Na(Glut)-","aq",,-2.34,
-"OBIGT",1463,"K(Glut)-","aq",,-2.05,
-"OBIGT",1464,"Li(Glut)-","aq",,-2.66,
-"OBIGT",1469,"Na(Adip)-","aq",,-2.05,
-"OBIGT",1470,"K(Adip)-","aq",,-1.76,
-"OBIGT",1471,"Li(Adip)-","aq",,-2.38,
-"OBIGT",1477,"cyclohexane","aq",9.35,6.64,
-"OBIGT",1478,"Ar","aq",-1.24,-8.59,
-"OBIGT",1479,"benzene","aq",,-1.14,
-"OBIGT",1480,"CO2","aq",-4.94,,
-"OBIGT",1481,"Xe","aq",2.8,,
-"OBIGT",1491,"n-butanethiol","aq",2.19,,
-"OBIGT",1513,"methyldiethanolamine","aq",1.61,,
-"OBIGT",1523,"cysteinate","aq",-1,,
-"OBIGT",1549,"glucose","aq",1.11,,
-"OBIGT",1577,"guanine","aq",-4.26,,
-"OBIGT",1621,"dHUMP-","aq",-3.13,,
-"OBIGT",1718,"MgADP-","aq",-1.01,,
-"OBIGT",1729,"HNicMP(ox)","aq",,9.4,
-"OBIGT",1737,"ribose-5-phosphate","aq",,7.48,
-"OBIGT",1739,"ribose-5-phosphate-2","aq",1.53,,
-"OBIGT",1740,"H4NADP(red)","aq",1.73,,
-"OBIGT",1741,"H3NADP(red)-","aq",2.41,,
-"OBIGT",1742,"H2NADP(red)-2","aq",1.28,,
-"OBIGT",1743,"HNADP(red)-3","aq",2.09,,
-"OBIGT",1744,"NADP(red)-4","aq",1.09,,
-"OBIGT",1746,"H3NADP(ox)","aq",1.05,,
-"OBIGT",1817,"diglycine+","aq",-177.69,,
-"OBIGT",1818,"diglycine-","aq",-49.22,,
-"OBIGT",1819,"triglycine+","aq",,1.75,
-"OBIGT",1820,"triglycine-","aq",,1.78,
-"OBIGT",1950,"jarosite","cr",,,20697
-"OBIGT",1951,"natrojarosite","cr",,,17554
-"OBIGT",1970,"dawsonite","cr",,,4653
-"OBIGT",1991,"octadecane","cr",-2.63,,
-"OBIGT",1992,"nonadecane","cr",-13.32,,
-"OBIGT",1993,"eicosane","cr",-2.79,,
-"OBIGT",1994,"heneicosane","cr",-8.61,,
-"OBIGT",1995,"docosane","cr",-2.63,,
-"OBIGT",1996,"tricosane","cr",-5.22,,
-"OBIGT",1997,"tetracosane","cr",-2.02,,
-"OBIGT",1998,"pentacosane","cr",-2.93,,
-"OBIGT",1999,"hexacosane","cr",-1.29,,
-"OBIGT",2000,"heptacosane","cr",-1.23,,
-"OBIGT",2052,"carbazole","cr",-43.39,,
-"OBIGT",2093,"triphenylene","cr",,,541
-"OBIGT",2406,"deoxyadenosine","cr",,,-2977
-"OBIGT",2597,"nonacontane","liq",,,635
-"OBIGT",2604,"2-methyloctane","liq",10,,
-"OBIGT",3017,"5,6-dithiadecane","liq",2,,
-"OBIGT",3097,"ethylene","gas",-4.59,,
-"OBIGT",3107,"3,5-dimethylphenol","gas",,,628
+"OBIGT",800,"AgCl","aq",,-1.88,
+"OBIGT",801,"AgCl2-","aq",1.65,,
+"OBIGT",806,"CuHS","aq",7.35,-16.2,
+"OBIGT",814,"ZnO2-2","aq",,-1.17,
+"OBIGT",840,"methane","aq",-2.61,,
+"OBIGT",845,"hexane","aq",1.43,3.21,
+"OBIGT",848,"ethylene","aq",6.12,-3.82,
+"OBIGT",872,"propanol","aq",-1.89,,
+"OBIGT",1001,"urea","aq",-23.26,23.32,
+"OBIGT",1014,"propanoic acid","aq",1.42,,
+"OBIGT",1037,"formate","aq",1.96,,
+"OBIGT",1039,"propanoate","aq",1.68,,
+"OBIGT",1046,"n-decanoate","aq",-1.93,,
+"OBIGT",1062,"oxalate-2","aq",-3.19,,
+"OBIGT",1329,"Li(Mal)-","aq",,-3.22,
+"OBIGT",1333,"Pb(Mal)","aq",,1.16,
+"OBIGT",1337,"Pb(Succ)","aq",,1.49,
+"OBIGT",1338,"Na(Oxal)-","aq",,-3.14,
+"OBIGT",1339,"K(Oxal)-","aq",,-2.75,
+"OBIGT",1340,"Fe(Oxal)+","aq",,-2.19,
+"OBIGT",1342,"Na(Mal)-","aq",,-3.11,
+"OBIGT",1343,"K(Mal)-","aq",,-2.63,
+"OBIGT",1345,"La(Mal)+","aq",,-1.92,
+"OBIGT",1346,"Gd(Mal)+","aq",,-1.73,
+"OBIGT",1347,"Lu(Mal)+","aq",,-2.25,
+"OBIGT",1348,"Yb(Mal)+","aq",,-2.05,
+"OBIGT",1349,"Th(Mal)+2","aq",-1.29,-4.79,
+"OBIGT",1351,"Ce(Mal)+","aq",,-1.75,
+"OBIGT",1352,"Nd(Mal)+","aq",4.52,,
+"OBIGT",1353,"Sm(Mal)+","aq",,-1.77,
+"OBIGT",1354,"Pr(Mal)+","aq",,-1.75,
+"OBIGT",1355,"Eu(Mal)+","aq",,-1.87,
+"OBIGT",1356,"Tb(Mal)+","aq",,-1.92,
+"OBIGT",1357,"Dy(Mal)+","aq",,-1.89,
+"OBIGT",1358,"Tm(Mal)+","aq",,-2.08,
+"OBIGT",1359,"Ho(Mal)+","aq",,-2.08,
+"OBIGT",1360,"Er(Mal)+","aq",,-2.11,
+"OBIGT",1361,"Sc(Mal)+","aq",,-1.97,
+"OBIGT",1362,"Fe(Mal)+","aq",,-1.97,
+"OBIGT",1363,"Na(Succ)-","aq",,-2.82,
+"OBIGT",1364,"K(Succ)-","aq",,-2.39,
+"OBIGT",1370,"Th(Succ)+2","aq",-1.21,-4.47,
+"OBIGT",1375,"NH4(Oxal)-","aq",,-2.62,
+"OBIGT",1380,"Yb(Oxal)+","aq",,-2.02,
+"OBIGT",1381,"Ce(Oxal)+","aq",,-1.8,
+"OBIGT",1382,"Nd(Oxal)+","aq",,-1.8,
+"OBIGT",1383,"Eu(Oxal)+","aq",,-1.89,
+"OBIGT",1384,"Gd(Oxal)+","aq",,-1.8,
+"OBIGT",1385,"Ru(Oxal)+","aq",,-2.41,
+"OBIGT",1386,"Pa(Oxal)+2","aq",-1.25,-4.63,
+"OBIGT",1387,"Th(Oxal)+2","aq",-1.27,-4.69,
+"OBIGT",1388,"U(Oxal)+2","aq",-1.25,-4.63,
+"OBIGT",1390,"Y(Oxal)+","aq",,-2.11,
+"OBIGT",1395,"La(Oxal)+","aq",,-1.87,
+"OBIGT",1396,"Tb(Oxal)+","aq",,-1.92,
+"OBIGT",1397,"Er(Oxal)+","aq",,-2.05,
+"OBIGT",1398,"Lu(Oxal)+","aq",,-2.19,
+"OBIGT",1399,"Cr(Oxal)+","aq",,-2.58,
+"OBIGT",1400,"Ga(Oxal)+","aq",,-2.66,
+"OBIGT",1401,"Sc(Oxal)+","aq",,-2.13,
+"OBIGT",1402,"In(Oxal)+","aq",,-2.19,
+"OBIGT",1403,"Sm(Oxal)+","aq",,-1.84,
+"OBIGT",1404,"Cs(Mal)-","aq",,-2.39,
+"OBIGT",1405,"NH4(Mal)-","aq",,-2.54,
+"OBIGT",1410,"In(Mal)+","aq",,-2.11,
+"OBIGT",1411,"Y(Mal)+","aq",,-2.02,
+"OBIGT",1419,"La(Succ)+","aq",,-1.52,
+"OBIGT",1420,"NH4(Succ)-","aq",,-2.26,
+"OBIGT",1422,"Fe(Succ)+","aq",,-1.92,
+"OBIGT",1423,"Sc(Succ)+","aq",,-1.77,
+"OBIGT",1425,"Sm(Succ)+","aq",,-1.48,
+"OBIGT",1426,"Er(Succ)+","aq",,-1.68,
+"OBIGT",1427,"U(Succ)+2","aq",-1.15,-4.27,
+"OBIGT",1431,"La(Glut)+","aq",,-1.23,
+"OBIGT",1432,"Y(Glut)+","aq",,-1.46,
+"OBIGT",1433,"Sc(Glut)+","aq",,-1.5,
+"OBIGT",1434,"Th(Glut)+2","aq",-1.09,-4.05,
+"OBIGT",1437,"Fe(Glut)+","aq",,-1.05,
+"OBIGT",1438,"Sm(Glut)+","aq",,-1.2,
+"OBIGT",1440,"Er(Glut)+","aq",,-1.4,
+"OBIGT",1442,"Ba(Adip)","aq",,1.19,
+"OBIGT",1449,"Pb(Adip)","aq",,1.25,
+"OBIGT",1450,"Sc(Adip)+","aq",,-1.22,
+"OBIGT",1452,"Th(Adip)+2","aq",-1.02,-3.76,
+"OBIGT",1453,"U(Adip)+2","aq",-1,-3.71,
+"OBIGT",1455,"Li(Oxal)-","aq",,-3.3,
+"OBIGT",1459,"Li(Succ)-","aq",,-2.94,
+"OBIGT",1461,"Na(Glut)-","aq",,-2.34,
+"OBIGT",1462,"K(Glut)-","aq",,-2.05,
+"OBIGT",1463,"Li(Glut)-","aq",,-2.66,
+"OBIGT",1468,"Na(Adip)-","aq",,-2.05,
+"OBIGT",1469,"K(Adip)-","aq",,-1.76,
+"OBIGT",1470,"Li(Adip)-","aq",,-2.38,
+"OBIGT",1476,"cyclohexane","aq",9.35,6.64,
+"OBIGT",1477,"Ar","aq",-1.24,-8.59,
+"OBIGT",1478,"benzene","aq",,-1.14,
+"OBIGT",1479,"CO2","aq",-4.94,,
+"OBIGT",1480,"Xe","aq",2.8,,
+"OBIGT",1490,"n-butanethiol","aq",2.19,,
+"OBIGT",1512,"methyldiethanolamine","aq",1.61,,
+"OBIGT",1522,"cysteinate","aq",-1,,
+"OBIGT",1548,"glucose","aq",1.11,,
+"OBIGT",1576,"guanine","aq",-4.26,,
+"OBIGT",1620,"dHUMP-","aq",-3.13,,
+"OBIGT",1717,"MgADP-","aq",-1.01,,
+"OBIGT",1728,"HNicMP(ox)","aq",,9.4,
+"OBIGT",1736,"ribose-5-phosphate","aq",,7.48,
+"OBIGT",1738,"ribose-5-phosphate-2","aq",1.53,,
+"OBIGT",1739,"H4NADP(red)","aq",1.73,,
+"OBIGT",1740,"H3NADP(red)-","aq",2.41,,
+"OBIGT",1741,"H2NADP(red)-2","aq",1.28,,
+"OBIGT",1742,"HNADP(red)-3","aq",2.09,,
+"OBIGT",1743,"NADP(red)-4","aq",1.09,,
+"OBIGT",1745,"H3NADP(ox)","aq",1.05,,
+"OBIGT",1816,"diglycine+","aq",-177.69,,
+"OBIGT",1817,"diglycine-","aq",-49.22,,
+"OBIGT",1818,"triglycine+","aq",,1.75,
+"OBIGT",1819,"triglycine-","aq",,1.78,
+"OBIGT",1949,"jarosite","cr",,,20697
+"OBIGT",1950,"natrojarosite","cr",,,17554
+"OBIGT",1969,"dawsonite","cr",,,4653
+"OBIGT",1990,"octadecane","cr",-2.63,,
+"OBIGT",1991,"nonadecane","cr",-13.32,,
+"OBIGT",1992,"eicosane","cr",-2.79,,
+"OBIGT",1993,"heneicosane","cr",-8.61,,
+"OBIGT",1994,"docosane","cr",-2.63,,
+"OBIGT",1995,"tricosane","cr",-5.22,,
+"OBIGT",1996,"tetracosane","cr",-2.02,,
+"OBIGT",1997,"pentacosane","cr",-2.93,,
+"OBIGT",1998,"hexacosane","cr",-1.29,,
+"OBIGT",1999,"heptacosane","cr",-1.23,,
+"OBIGT",2051,"carbazole","cr",-43.39,,
+"OBIGT",2092,"triphenylene","cr",,,541
+"OBIGT",2405,"deoxyadenosine","cr",,,-2977
+"OBIGT",2596,"nonacontane","liq",,,635
+"OBIGT",2603,"2-methyloctane","liq",10,,
+"OBIGT",3016,"5,6-dithiadecane","liq",2,,
+"OBIGT",3096,"ethylene","gas",-4.59,,
+"OBIGT",3106,"3,5-dimethylphenol","gas",,,628
"DEW",15,"BO(OH)","aq",,,-1111
"DEW",19,"CaCl+","aq",,,-593
"DEW",20,"CaCl2","aq",,,-7937
Modified: pkg/CHNOSZ/man/EOSregress.Rd
===================================================================
--- pkg/CHNOSZ/man/EOSregress.Rd 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/man/EOSregress.Rd 2019-04-20 09:57:37 UTC (rev 452)
@@ -121,7 +121,7 @@
\dontshow{reset()}
## fit experimental heat capacities of CH4
## using revised Helgeson-Kirkham-Flowers equations
-# read the data from Hnědkovský and Wood, 1997
+# read the data from Hnedkovsky and Wood, 1997
f <- system.file("extdata/cpetc/Cp.CH4.HW97.csv", package="CHNOSZ")
d <- read.csv(f)
# have to convert J to cal and MPa to bar
Modified: pkg/CHNOSZ/man/add.obigt.Rd
===================================================================
--- pkg/CHNOSZ/man/add.obigt.Rd 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/man/add.obigt.Rd 2019-04-20 09:57:37 UTC (rev 452)
@@ -123,8 +123,8 @@
lines(DLH06$out$T, DLH06$out$G/1000, lty = 2)
legend("topleft", c("Dick et al., 2006", "Kitadai, 2014"), lty = c(2, 1))
title(main = "AABB = UPBB + H2O; after Figure 9 of Kitadai, 2014")
-# reset to default database
-obigt()
+# reset database *and* settings (units)
+reset()
# Another use of add.obigt(): calculate Delta G of
# H4SiO4 = SiO2 + 2H2O using different data for SiO2.
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/man/diagram.Rd 2019-04-20 09:57:37 UTC (rev 452)
@@ -136,7 +136,7 @@
\code{fill} determines the color of the predominance fields, \code{col} that of the boundary lines.
The default of NULL for \code{fill} produces transparent predominance fields.
\code{fill} can be any \code{\link{colors}}, or the word \samp{rainbow}, \samp{heat}, \samp{terrain}, \samp{topo}, or \samp{cm}, indicating a palette from \pkg{grDevices}.
-Starting with \R version 3.6.0, \code{fill} can be the name of any available HCL color palette, matched in the same way as the \code{palette} argument of \code{\link{hcl.colors}}.
+Starting with \R version 3.6.0, \code{fill} can be the name of any available HCL color palette, matched in the same way as the \code{palette} argument of \code{hcl.colors}.
\code{fill.NA} gives the color for empty fields, i.e. points for which NA values are present, possibly by using \code{\link{equilibrate}} at extreme conditions (see \code{test-diagram.Rd}).
\code{fill.NA} is also used to specify the color outside the water stability limits on Eh-pH or pe-pH diagrams, when \code{limit.water} is TRUE.
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/man/extdata.Rd 2019-04-20 09:57:37 UTC (rev 452)
@@ -151,7 +151,7 @@
Hnědkovský, L. and Wood, R. H. (1997) Apparent molar heat capacities of aqueous solutions of \CH4, \CO2, \H2S, and \NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. \emph{J. Chem. Thermodyn.} \bold{29}, 731--747. \url{https://doi.org/10.1006/jcht.1997.0192}
-Joint Genome Institute (2007) Bison Pool Environmental Genome. Protein sequence files downloaded from IMG/M (\url{http://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=FindGenomes&page=findGenomes})
+Joint Genome Institute (2007) Bison Pool Environmental Genome. Protein sequence files downloaded from IMG/M (\url{https://img.jgi.doe.gov/})
Merino, E. (1975) Diagenesis in teriary sandstones from Kettleman North Dome, California. II. Interstitial solutions: distribution of aqueous species at 100°C and chemical relation to diagenetic mineralogy. \emph{Geochim. Cosmochim. Acta} \bold{39}, 1629--1645. \url{https://doi.org/10.1016/0016-7037(75)90085-X}
Modified: pkg/CHNOSZ/man/util.plot.Rd
===================================================================
--- pkg/CHNOSZ/man/util.plot.Rd 2019-04-17 00:48:50 UTC (rev 451)
+++ pkg/CHNOSZ/man/util.plot.Rd 2019-04-20 09:57:37 UTC (rev 452)
@@ -122,7 +122,7 @@
title(main = 'diagram(a, grid = "major")')
diagram(a, grid = "minor")
title(main = 'diagram(a, grid = "minor")')
-diagram(a, fill = "set3")
+diagram(a, fill = "terrain")
thermo.axis(grid = "major", col.grid = "slategray")
title(main = 'thermo.axis(grid = "major")')
par(thermo()$opar)
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