[CHNOSZ-commits] r445 - in pkg/CHNOSZ: . R demo inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 16 06:25:41 CEST 2019
Author: jedick
Date: 2019-04-16 06:25:40 +0200 (Tue, 16 Apr 2019)
New Revision: 445
Added:
pkg/CHNOSZ/demo/aluminum.R
Removed:
pkg/CHNOSZ/demo/go-IU.R
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/man/extdata.Rd
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/obigt.Rmd
Log:
rename demo/go-IU.R to aluminum.R
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2019-04-15 14:00:52 UTC (rev 444)
+++ pkg/CHNOSZ/DESCRIPTION 2019-04-16 04:25:40 UTC (rev 445)
@@ -1,6 +1,6 @@
-Date: 2019-04-15
+Date: 2019-04-16
Package: CHNOSZ
-Version: 1.3.1-25
+Version: 1.3.1-26
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/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2019-04-15 14:00:52 UTC (rev 444)
+++ pkg/CHNOSZ/R/examples.R 2019-04-16 04:25:40 UTC (rev 445)
@@ -30,7 +30,7 @@
demos <- function(which=c("sources", "protein.equil", "affinity", "NaCl", "density",
"ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "yeastgfp", "glycinate",
"mosaic", "copper", "arsenic", "solubility", "gold", "contour", "wjd", "bugstab", "Shh", "saturation",
- "adenine", "DEW", "lambda", "TCA", "go-IU", "bison", "AkDi"), save.png=FALSE) {
+ "adenine", "DEW", "lambda", "TCA", "aluminum", "bison", "AkDi"), 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 2019-04-15 14:00:52 UTC (rev 444)
+++ pkg/CHNOSZ/demo/00Index 2019-04-16 04:25:40 UTC (rev 445)
@@ -26,7 +26,7 @@
DEW Deep Earth Water (DEW) model for high pressures
lambda Thermodynamic properties of lambda transition in quartz
TCA Standard Gibbs energies of steps of the citric acid cycle
-go-IU Reactions involving Al-bearing minerals
+aluminum Reactions involving Al-bearing minerals
carboxylase Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase
bison Average oxidation state of carbon in proteins for phyla at Bison Pool
AkDi Henry's constant of dissolved gases
Copied: pkg/CHNOSZ/demo/aluminum.R (from rev 444, pkg/CHNOSZ/demo/go-IU.R)
===================================================================
--- pkg/CHNOSZ/demo/aluminum.R (rev 0)
+++ pkg/CHNOSZ/demo/aluminum.R 2019-04-16 04:25:40 UTC (rev 445)
@@ -0,0 +1,137 @@
+# CHNOSZ/demo/aluminum.R
+# 20171018 comparisons with calculations of SUPCRTBL
+# 20190415 add diagrams from Tutolo et al., 2014
+
+## set up plotting area
+opar <- par(mfrow = c(2, 2))
+
+###########
+### plot 1: boehmite - kaolinite equilibrium
+###########
+# After Zhu and Lu, 2009 (doi:10.1016/j.gca.2009.03.015)
+# experimental data from Table 1 of Hemley et al., 1980 (doi:10.2113/gsecongeo.75.2.210)
+xT <- c(200, 200, 200, 200, 250, 250, 265, 300, 300, 300, 300)
+xlogaSiO2 <- -c(2.54, 2.59, 2.65, 2.77, 2.21, 2.32, 2.12, 1.90, 1.95, 1.94, 1.90)
+## set up basis species so that axis.label shows activity of SiO2
+basis(c("Al2O3","SiO2", "H2O", "O2"))
+T <- 125:350
+thermo.plot.new(xlim = range(T), ylim = c(-3.5, -1.5), xlab = axis.label("T"), ylab = axis.label("SiO2"))
+points(xT, xlogaSiO2)
+basis(delete = TRUE)
+## first calculation: as in SUPCRT92
+add.obigt("SUPCRT92") # gets kaolinite and boehmite from HDNB78
+r1 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE)
+# we need exceed.Ttr = TRUE because the T limit for boehmite is 500 K (Helgeson et al., 1978)
+## second calculation: CHNOSZ default
+# kaolinite from Berman, 1988
+# boehmite from Hemingway et al., 1991
+# SiO2 from Apps and Spycher, 2004
+reset()
+r2 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE)
+## third calculation: get SiO2(aq) from SHS89
+add.obigt("AS04")
+r3 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE)
+## log activity of SiO2 is -ve logK
+lines(T, -r1$out$logK, col = "blue1", lty = 2)
+lines(T, -r2$out$logK, lwd = 1.5)
+lines(T, -r3$out$logK, col = "red", lty = 2)
+## add points calculated using the SUPCRTBL package
+points(seq(125, 350, 25), -c(3.489, 3.217, 2.967, 2.734, 2.517, 2.314, 2.124, 1.946, 1.781, 1.628), pch = 4, col = "red")
+## add legend and title
+title(main = describe.reaction(r1$reaction), cex.main = 1.1)
+legend("bottomright", lty = c(0, 0, 2, 1, 2), pch = c(1, 4, NA, NA, NA), lwd = c(1, 1, 1, 1.5, 1),
+ col = c("black", "red", "black", "black", "red"), bty = "n", cex = 0.9,
+ legend = c("Hemley et al., 1980", "SUPCRTBL", "SUPCRT92", "CHNOSZ", 'add.obigt("AS04")'))
+legend("topleft", c("Boehmite - Kaolinite", "After Zhu and Lu, 2009 Fig. A1"), bty = "n")
+reset()
+# Helgeson et al., 1978 (HDNB78): http://www.worldcat.org/oclc/13594862
+# Shock et al., 1989 (SHS89): doi:10.1016/0016-7037(89)90341-4
+# Berman, 1988 (Ber88): doi:10.1093/petrology/29.2.445
+# Holland and Powell, 2011 (HP11): 10.1111/j.1525-1314.2010.00923.x
+# Hemingway et al., 1991 (HRA91): http://pubs.er.usgs.gov/publication/70016664
+# Apps and Spycher, 2004 (AS04): Bechtel SAIC Company, LLC ANL-NBS-HS-000043 REV 00 (DOC.20041118.0004)
+
+###########
+### plot 2: dawsonite solubility
+###########
+# After Zimmer et al., 2016 (doi:10.1016/j.cageo.2016.02.013)
+# experimental data from Benezeth et al., 2007 Table 5 (doi:10.1016/j.gca.2007.07.003)
+# (averages for each temperature in a single run)
+T <- c(100.1, 100.1, 150.1, 100.1, 150.1, 99.8, 99.8, 200.7, 99.8, 50.1, 75.1, 100.3, 150.1)
+logK <- -c(14.825, 14.735, 13.625, 14.79, 13.665, 14.725, 14.1775, 12.74, 14.4925, 16.8625, 15.61, 14.51, 13.455)
+plot(T, logK, xlim = c(25, 250), ylim = c(-18, -10), xlab = axis.label("T"), ylab = axis.label("logK"))
+T <- 0:250
+# calculation 1: CHNOSZ default
+species <- c("dawsonite", "H2O", "Al(OH)4-", "HCO3-", "Na+", "H+")
+coeffs <- c(-1, -2, 1, 1, 1, 1)
+Daw1 <- subcrt(species, coeffs, T = T)
+# calculation 2: dawsonite with Cp = 0
+mod.obigt("dawsonite", Cp = 0)
+Daw2 <- subcrt(species, coeffs, T = T)
+## plot the calculated logKs
+lines(T, Daw1$out$logK, lwd = 1.5)
+lines(T, Daw2$out$logK, col = "red", lty = 2)
+## add points calculated using the SUPCRTBL package
+points(seq(25, 250, 25), c(-17.829, -16.523, -15.402, -14.425, -13.568, -12.815, -12.154, -11.581, -11.094, -10.699), pch=4, col="red")
+## add legend and title
+title(main = describe.reaction(Daw1$reaction), cex.main = 0.95)
+legend("bottomright", lty = c(0, 0, 1, 2), pch = c(1, 4, NA, NA), col = c("black", "red", "black", "red"), lwd = c(1, 1, 1.5, 1),
+ bty = "n", cex = 0.9, legend = c("Ben\u00e9z\u00e9th et al., 2007", "SUPCRTBL", "CHNOSZ", 'mod.obigt("dawsonite", Cp = 0)'))
+legend("topleft", c("Dawsonite solubility", "After Zimmer et al., 2016 Fig. 2"), bty = "n")
+reset()
+
+###########
+### plot 3: kaolinite solubility
+###########
+# 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"))
+plot(dat, type = "p", xlim = c(3.5, 1.5), ylim = c(-2, 14), xlab = "1000/T(K)", ylab = "pK")
+# plot line: default database
+invTK <- seq(3.5, 1.6, -0.02)
+T <- 1000/invTK - 273.15
+sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "H4SiO4"), c(-1, -2, -5, 2, 2), T = T)
+pK <- -sres$out$logK
+lines(invTK, pK, lwd = 1.5)
+# plot line: SUPCRT92
+add.obigt("SUPCRT92")
+sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "H4SiO4"), c(-1, -2, -5, 2, 2), T = T)
+pK <- -sres$out$logK
+lines(invTK, pK, col = "blue", lty = 2)
+# add title and legend
+par(xpd = NA)
+title(main = describe.reaction(sres$reaction), cex.main = 1.1)
+par(xpd = FALSE)
+legend("topright", c("Kaolinite solubility", "After Tutolo et al., 2014 Fig. 2"), bty = "n")
+legend("bottomleft", lty = c(0, 2, 1), pch = c(1, NA, NA), lwd = c(1, 1, 1.5), col = c("black", "blue", "black"),
+ legend = c("Tutolo et al., 2014", "SUPCRT92", "CHNOSZ"), bty = "n", cex = 0.9)
+reset()
+
+###########
+### plot 4: albite - K-feldspar exchange
+###########
+# After Tutolo et al., 2014, Fig. 5 (doi:10.1016/j.gca.2014.02.036)
+# experimental data from Merino, 1975, Table 4 (doi:10.1016/0016-7037(75)90085-X)
+# plot line calculated using default database
+basis(c("Al2O3", "SiO2", "K+", "Na+", "O2", "H2O", "H+"))
+species(c("albite", "K-feldspar"))
+T <- 100
+P <- 150
+a <- affinity("K+" = c(4, 7), "Na+" = c(6, 9), T = T, P = P)
+diagram(a, lwd = 1.5, xlab = ratlab("K+"), ylab = ratlab("Na+"))
+# plot experimental data
+dat <- read.csv(system.file("extdata/cpetc/Mer75_Table4.csv", package = "CHNOSZ"))
+points(dat$log.aK..aH.., dat$log.aNa..aH..)
+# plot line calculated using SUPCRT92 data
+add.obigt("SUPCRT92")
+a <- affinity("K+" = c(4, 7), "Na+" = c(6, 9), T = 100, P = 150)
+diagram(a, col = "blue", lty = 2, add = TRUE, names = NULL)
+# add title and legend
+sres <- subcrt(c("albite", "K+", "K-feldspar", "Na+"), c(-1, -1, 1, 1))
+title(main = describe.reaction(sres$reaction), cex.main = 1.1)
+legend("topleft", c("Albite - K-feldspar", "After Tutolo et al., 2014 Fig. 5"), bty = "n", cex = 0.9)
+legend("bottomright", lty = c(0, 2, 1), pch = c(1, NA, NA), lwd = c(1, 1, 1.5), col = c("black", "blue", "black"),
+ legend = c("Merino, 1975", "SUPCRT92", "CHNOSZ"), bty = "n", cex = 0.9)
+legend("right", describe.property(c("T", "P"), c(T, P)), bty = "n")
+reset()
+
+par(opar)
Deleted: pkg/CHNOSZ/demo/go-IU.R
===================================================================
--- pkg/CHNOSZ/demo/go-IU.R 2019-04-15 14:00:52 UTC (rev 444)
+++ pkg/CHNOSZ/demo/go-IU.R 2019-04-16 04:25:40 UTC (rev 445)
@@ -1,138 +0,0 @@
-# CHNOSZ/demo/go-IU.R
-# 20171018 comparisons with calculations of SUPCRTBL
-# (BL = Bloomington campus of Indiana University)
-# 20190415 add diagrams from Tutolo et al., 2014
-
-## set up plotting area
-opar <- par(mfrow = c(2, 2))
-
-###########
-### plot 1: boehmite - kaolinite equilibrium
-###########
-# After Zhu and Lu, 2009 (doi:10.1016/j.gca.2009.03.015)
-# experimental data from Table 1 of Hemley et al., 1980 (doi:10.2113/gsecongeo.75.2.210)
-xT <- c(200, 200, 200, 200, 250, 250, 265, 300, 300, 300, 300)
-xlogaSiO2 <- -c(2.54, 2.59, 2.65, 2.77, 2.21, 2.32, 2.12, 1.90, 1.95, 1.94, 1.90)
-## set up basis species so that axis.label shows activity of SiO2
-basis(c("Al2O3","SiO2", "H2O", "O2"))
-T <- 125:350
-thermo.plot.new(xlim = range(T), ylim = c(-3.5, -1.5), xlab = axis.label("T"), ylab = axis.label("SiO2"))
-points(xT, xlogaSiO2)
-basis(delete = TRUE)
-## first calculation: as in SUPCRT92
-add.obigt("SUPCRT92") # gets kaolinite and boehmite from HDNB78
-r1 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE)
-# we need exceed.Ttr = TRUE because the T limit for boehmite is 500 K (Helgeson et al., 1978)
-## second calculation: CHNOSZ default
-# kaolinite from Berman, 1988
-# boehmite from Hemingway et al., 1991
-# SiO2 from Apps and Spycher, 2004
-reset()
-r2 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE)
-## third calculation: get SiO2(aq) from SHS89
-add.obigt("AS04")
-r3 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE)
-## log activity of SiO2 is -ve logK
-lines(T, -r1$out$logK, col = "blue1", lty = 2)
-lines(T, -r2$out$logK, lwd = 1.5)
-lines(T, -r3$out$logK, col = "red", lty = 2)
-## add points calculated using the SUPCRTBL package
-points(seq(125, 350, 25), -c(3.489, 3.217, 2.967, 2.734, 2.517, 2.314, 2.124, 1.946, 1.781, 1.628), pch = 4, col = "red")
-## add legend and title
-title(main = describe.reaction(r1$reaction), cex.main = 1.1)
-legend("bottomright", lty = c(0, 0, 2, 1, 2), pch = c(1, 4, NA, NA, NA), lwd = c(1, 1, 1, 1.5, 1),
- col = c("black", "red", "black", "black", "red"), bty = "n", cex = 0.9,
- legend = c("Hemley et al., 1980", "SUPCRTBL", "SUPCRT92", "CHNOSZ", 'add.obigt("AS04")'))
-legend("topleft", c("Boehmite - Kaolinite", "After Zhu and Lu, 2009 Fig. A1"), bty = "n")
-reset()
-# Helgeson et al., 1978 (HDNB78): http://www.worldcat.org/oclc/13594862
-# Shock et al., 1989 (SHS89): doi:10.1016/0016-7037(89)90341-4
-# Berman, 1988 (Ber88): doi:10.1093/petrology/29.2.445
-# Holland and Powell, 2011 (HP11): 10.1111/j.1525-1314.2010.00923.x
-# Hemingway et al., 1991 (HRA91): http://pubs.er.usgs.gov/publication/70016664
-# Apps and Spycher, 2004 (AS04): Bechtel SAIC Company, LLC ANL-NBS-HS-000043 REV 00 (DOC.20041118.0004)
-
-###########
-### plot 2: dawsonite solubility
-###########
-# After Zimmer et al., 2016 (doi:10.1016/j.cageo.2016.02.013)
-# experimental data from Benezeth et al., 2007 Table 5 (doi:10.1016/j.gca.2007.07.003)
-# (averages for each temperature in a single run)
-T <- c(100.1, 100.1, 150.1, 100.1, 150.1, 99.8, 99.8, 200.7, 99.8, 50.1, 75.1, 100.3, 150.1)
-logK <- -c(14.825, 14.735, 13.625, 14.79, 13.665, 14.725, 14.1775, 12.74, 14.4925, 16.8625, 15.61, 14.51, 13.455)
-plot(T, logK, xlim = c(25, 250), ylim = c(-18, -10), xlab = axis.label("T"), ylab = axis.label("logK"))
-T <- 0:250
-# calculation 1: CHNOSZ default
-species <- c("dawsonite", "H2O", "Al(OH)4-", "HCO3-", "Na+", "H+")
-coeffs <- c(-1, -2, 1, 1, 1, 1)
-Daw1 <- subcrt(species, coeffs, T = T)
-# calculation 2: dawsonite with Cp = 0
-mod.obigt("dawsonite", Cp = 0)
-Daw2 <- subcrt(species, coeffs, T = T)
-## plot the calculated logKs
-lines(T, Daw1$out$logK, lwd = 1.5)
-lines(T, Daw2$out$logK, col = "red", lty = 2)
-## add points calculated using the SUPCRTBL package
-points(seq(25, 250, 25), c(-17.829, -16.523, -15.402, -14.425, -13.568, -12.815, -12.154, -11.581, -11.094, -10.699), pch=4, col="red")
-## add legend and title
-title(main = describe.reaction(Daw1$reaction), cex.main = 0.95)
-legend("bottomright", lty = c(0, 0, 1, 2), pch = c(1, 4, NA, NA), col = c("black", "red", "black", "red"), lwd = c(1, 1, 1.5, 1),
- bty = "n", cex = 0.9, legend = c("Ben\u00e9z\u00e9th et al., 2007", "SUPCRTBL", "CHNOSZ", 'mod.obigt("dawsonite", Cp = 0)'))
-legend("topleft", c("Dawsonite solubility", "After Zimmer et al., 2016 Fig. 2"), bty = "n")
-reset()
-
-###########
-### plot 3: kaolinite solubility
-###########
-# 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"))
-plot(dat, type = "p", xlim = c(3.5, 1.5), ylim = c(-2, 14), xlab = "1000/T(K)", ylab = "pK")
-# plot line: default database
-invTK <- seq(3.5, 1.6, -0.02)
-T <- 1000/invTK - 273.15
-sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "H4SiO4"), c(-1, -2, -5, 2, 2), T = T)
-pK <- -sres$out$logK
-lines(invTK, pK, lwd = 1.5)
-# plot line: SUPCRT92
-add.obigt("SUPCRT92")
-sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "H4SiO4"), c(-1, -2, -5, 2, 2), T = T)
-pK <- -sres$out$logK
-lines(invTK, pK, col = "blue", lty = 2)
-# add title and legend
-par(xpd = NA)
-title(main = describe.reaction(sres$reaction), cex.main = 1.1)
-par(xpd = FALSE)
-legend("topright", c("Kaolinite solubility", "After Tutolo et al., 2014 Fig. 2"), bty = "n")
-legend("bottomleft", lty = c(0, 2, 1), pch = c(1, NA, NA), lwd = c(1, 1, 1.5), col = c("black", "blue", "black"),
- legend = c("Tutolo et al., 2014", "SUPCRT92", "CHNOSZ"), bty = "n", cex = 0.9)
-reset()
-
-###########
-### plot 4: albite - K-feldspar exchange
-###########
-# After Tutolo et al., 2014, Fig. 5 (doi:10.1016/j.gca.2014.02.036)
-# experimental data from Merino, 1975, Table 4 (doi:10.1016/0016-7037(75)90085-X)
-# plot line calculated using default database
-basis(c("Al2O3", "SiO2", "K+", "Na+", "O2", "H2O", "H+"))
-species(c("albite", "K-feldspar"))
-T <- 100
-P <- 150
-a <- affinity("K+" = c(4, 7), "Na+" = c(6, 9), T = T, P = P)
-diagram(a, lwd = 1.5, xlab = ratlab("K+"), ylab = ratlab("Na+"))
-# plot experimental data
-dat <- read.csv(system.file("extdata/cpetc/Mer75_Table4.csv", package = "CHNOSZ"))
-points(dat$log.aK..aH.., dat$log.aNa..aH..)
-# plot line calculated using SUPCRT92 data
-add.obigt("SUPCRT92")
-a <- affinity("K+" = c(4, 7), "Na+" = c(6, 9), T = 100, P = 150)
-diagram(a, col = "blue", lty = 2, add = TRUE, names = NULL)
-# add title and legend
-sres <- subcrt(c("albite", "K+", "K-feldspar", "Na+"), c(-1, -1, 1, 1))
-title(main = describe.reaction(sres$reaction), cex.main = 1.1)
-legend("topleft", c("Albite - K-feldspar", "After Tutolo et al., 2014 Fig. 5"), bty = "n", cex = 0.9)
-legend("bottomright", lty = c(0, 2, 1), pch = c(1, NA, NA), lwd = c(1, 1, 1.5), col = c("black", "blue", "black"),
- legend = c("Merino, 1975", "SUPCRT92", "CHNOSZ"), bty = "n", cex = 0.9)
-legend("right", describe.property(c("T", "P"), c(T, P)), bty = "n")
-reset()
-
-par(opar)
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2019-04-15 14:00:52 UTC (rev 444)
+++ pkg/CHNOSZ/inst/NEWS 2019-04-16 04:25:40 UTC (rev 445)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.3.1-25 (2019-04-15)
+CHANGES IN CHNOSZ 1.3.1-26 (2019-04-16)
---------------------------------------
- Add thermo/stoich.csv.xz (loaded as thermo()$stoich), containing a
@@ -40,7 +40,8 @@
- Add demo/arsenic.R (Eh-pH diagram after Lu and Zhu, 2011).
-- demo/go-IU.R: add plots from Tutolo et al., 2014.
+- Rename demo/go-IU.R to aluminum.R, and add plots from Tutolo et al.,
+ 2014.
CHANGES IN CHNOSZ 1.3.1 (2019-03-02)
------------------------------------
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2019-04-15 14:00:52 UTC (rev 444)
+++ pkg/CHNOSZ/man/diagram.Rd 2019-04-16 04:25:40 UTC (rev 445)
@@ -274,7 +274,7 @@
species(c(AlOH, Al, AlF, AlOHF), "aq")
res <- 300
a <- affinity(pH = c(0.5, 6.5, res), `F-` = c(-2, -9, res), T = 200)
-diagram(a, fill = "pastel")
+diagram(a, fill = "terrain")
dprop <- describe.property(c("T", "P"), c(200, "Psat"))
legend("topright", legend = dprop, bty = "n")
mtitle(c("Aqueous aluminum species",
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2019-04-15 14:00:52 UTC (rev 444)
+++ pkg/CHNOSZ/man/examples.Rd 2019-04-16 04:25:40 UTC (rev 445)
@@ -17,7 +17,7 @@
"density", "ORP", "revisit", "findit", "ionize", "buffer",
"protbuff", "yeastgfp", "glycinate", "mosaic", "copper",
"arsenic", "solubility", "gold", "contour", "wjd", "bugstab",
- "Shh", "saturation", "adenine", "DEW", "lambda", "TCA", "go-IU",
+ "Shh", "saturation", "adenine", "DEW", "lambda", "TCA", "aluminum",
"bison", "AkDi"),
save.png=FALSE)
}
@@ -59,7 +59,7 @@
\code{DEW} \tab Deep Earth Water (DEW) model for high pressures (Sverjensky et al., 2014a and 2014b) \cr
\code{lambda} \tab Effects of lambda transition on thermodynamic properties of quartz (Berman, 1988) \cr
\code{TCA} \tab Standard Gibbs energies of the tricarboxylic (citric) acid cycle (Canovas and Shock, 2016) \cr
- \code{go-IU} \tab Reactions involving Al-bearing minerals (Zimmer et al., 2016; Tutolo et al., 2014) \cr
+ \code{aluminum} \tab Reactions involving Al-bearing minerals (Zimmer et al., 2016; Tutolo et al., 2014) \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
\code{AkDi} \tab Henry's constant of dissolved gases (Akinfiev and Diamond, 2003) \cr
Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd 2019-04-15 14:00:52 UTC (rev 444)
+++ pkg/CHNOSZ/man/extdata.Rd 2019-04-16 04:25:40 UTC (rev 445)
@@ -48,8 +48,8 @@
\item \code{rubisco.csv} UniProt IDs for Rubisco, ranges of optimal growth temperature of organisms, domain and name of organisms, and URL of reference for growth temperature, from Dick, 2014. See the vignette \code{anintro.Rmd} for an example that uses this file.
\item \code{bluered.txt} Blue - light grey - red color palette, computed using \CRANpkg{colorspace}\code{::diverge_hcl(1000,} \code{c = 100, l = c(50, 90), power = 1)}. This is used by \code{\link{ZC.col}}.
\item \code{AD03_Fig1?.csv} Experimental data points digitized from Figure 1 of Akinfiev and Diamond, 2003, used in \code{\link{demos}("AkDi")}.
- \item \code{TKSS14_Fig2.csv} Experimental data points digitized from Figure 2 of Tutolo et al., 2014, used in \code{\link{demos}("go-IU")}.
- \item \code{Mer75_Table4.csv} Values of log(aK+/aH+) and log(aNa+/aH+) from Table 4 of Merino, 1975, used in \code{\link{demos}("go-IU")}.
+ \item \code{TKSS14_Fig2.csv} Experimental data points digitized from Figure 2 of Tutolo et al., 2014, used in \code{\link{demos}("aluminum")}.
+ \item \code{Mer75_Table4.csv} Values of log(aK+/aH+) and log(aNa+/aH+) from Table 4 of Merino, 1975, used in \code{\link{demos}("aluminum")}.
}
Files in \code{fasta} contain protein sequences:
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2019-04-15 14:00:52 UTC (rev 444)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2019-04-16 04:25:40 UTC (rev 445)
@@ -1975,7 +1975,7 @@
<span style="color:red">`add.obigt("AS04")`</span> -- This file has data for aqueous `r sio2` from @AS04 and modified HSiO<sub>3</sub><sup>-</sup>.
These data are included to help transition to the "higher solubility of quartz paradigm" [@WJ17], but are not included in the default database in order to maintain compatibility with existing data for minerals that are linked to the older aqueous `r sio2` data.
-See [<span style="color:blue">`demo(go-IU)`</span>](../demo) for an example.
+See [<span style="color:blue">`demo(aluminum)`</span>](../demo) for an example.
<span style="color:red">`add.obigt("DEW")`</span> -- These are aqueous species, with modified parameters, that are intended for use with the [Deep Earth Water](http://www.dewcommunity.org/) (DEW) model [@SHA14].
You should also run <span style="color:red">`water("DEW")`</span> to activate the equations in the model; then, they will be used by <span style="color:green">`subcrt()`</span> and <span style="color:green">`affinity()`</span>.
Modified: pkg/CHNOSZ/vignettes/obigt.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.Rmd 2019-04-15 14:00:52 UTC (rev 444)
+++ pkg/CHNOSZ/vignettes/obigt.Rmd 2019-04-16 04:25:40 UTC (rev 445)
@@ -250,7 +250,7 @@
### `r setfile("AS04.csv")`
```{r AS04, results="asis", echo=FALSE}
-cat('This file has data for aqueous SiO<sub>2</sub> from @AS04 and modified HSiO<sub>3</sub><sup>-</sup>. Use <span style="color:red">`add.obigt("AS04")`</span> to load the data; see [<span style="color:blue">`demo(go-IU)`</span>](../demo) for an example.\n\n')
+cat('This file has data for aqueous SiO<sub>2</sub> from @AS04 and modified HSiO<sub>3</sub><sup>-</sup>. Use <span style="color:red">`add.obigt("AS04")`</span> to load the data; see [<span style="color:blue">`demo(aluminum)`</span>](../demo) for an example.\n\n')
```
```{r optreflist, results="asis", echo=FALSE}
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