[CHNOSZ-commits] r280 - in pkg/CHNOSZ: . R man
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noreply at r-forge.r-project.org
Tue Nov 7 17:08:39 CET 2017
Author: jedick
Date: 2017-11-07 17:08:39 +0100 (Tue, 07 Nov 2017)
New Revision: 280
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/nonideal.R
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/nonideal.Rd
pkg/CHNOSZ/man/objective.Rd
pkg/CHNOSZ/man/protein.Rd
pkg/CHNOSZ/man/revisit.Rd
pkg/CHNOSZ/man/util.expression.Rd
Log:
complete/capitalize example plot titles
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-11-06 09:45:36 UTC (rev 279)
+++ pkg/CHNOSZ/DESCRIPTION 2017-11-07 16:08:39 UTC (rev 280)
@@ -1,6 +1,6 @@
-Date: 2017-11-06
+Date: 2017-11-07
Package: CHNOSZ
-Version: 1.1.0-78
+Version: 1.1.0-79
Title: Thermodynamic Calculations for Geobiochemistry
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/nonideal.R
===================================================================
--- pkg/CHNOSZ/R/nonideal.R 2017-11-06 09:45:36 UTC (rev 279)
+++ pkg/CHNOSZ/R/nonideal.R 2017-11-07 16:08:39 UTC (rev 280)
@@ -224,7 +224,7 @@
}
# show points and spline(T) curves
if(showsplines == "T") {
- thermo.plot.new(c(0, 1000), c(-.2, .7), xlab=axis.label("T"), ylab=expression(b[gamma]))
+ thermo.plot.new(c(0, 1000), c(-.2, .7), xlab=axis.label("T"), ylab=expression(italic(b)[gamma]))
points(T0, B0, pch=0)
points(T0.5, B0.5, pch=1)
points(T1, B1, pch=1)
@@ -261,8 +261,9 @@
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=c("kbar", "60", "50", "40", "30", "20", "10", "5", "4", "3", "2", "1", "0.5", "Psat"))
+ title(main=expression("Deybe-H\u00FCckel "*italic(b)[gamma]*" ('B-dot') parameter"))
} else if(showsplines=="P") {
- thermo.plot.new(c(0, 5), c(-.2, .7), xlab="log P(bar)", ylab=expression(b[gamma]))
+ thermo.plot.new(c(0, 5), c(-.2, .7), xlab=expression(log~italic(P)*"(bar)"), ylab=expression(italic(b)[gamma]))
# pressures that are used to make the isothermal splines (see below)
P25 <- c(1, 500, 1000, 2000, 3000, 4000, 5000)
P100 <- c(1, 500, 1000, 2000, 3000, 4000, 5000, 10000, 20000)
@@ -302,6 +303,7 @@
P <- seq(10000, 60000, 50); lines(log10(P), Bdot(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")
+ title(main=expression("Deybe-H\u00FCckel "*italic(b)[gamma]*" ('B-dot') parameter"))
} else {
# make T and P the same length
ncond <- max(length(T), length(P))
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2017-11-06 09:45:36 UTC (rev 279)
+++ pkg/CHNOSZ/man/diagram.Rd 2017-11-07 16:08:39 UTC (rev 280)
@@ -172,7 +172,7 @@
species(c("ethanol", "lactic acid", "deoxyribose", "ribose"))
a <- affinity(T=c(0, 150))
diagram(a, what="O2", legend.x="topleft", col=rev(rainbow(4)), lwd=2)
-title(main="equilibrium logfO2 for 1e-3 mol/kg of CO2 and ... ")
+title(main="Equilibrium logfO2 for 1e-3 mol/kg of CO2 and ... ")
### 1-D diagrams: logarithms of activities
Modified: pkg/CHNOSZ/man/nonideal.Rd
===================================================================
--- pkg/CHNOSZ/man/nonideal.Rd 2017-11-06 09:45:36 UTC (rev 279)
+++ pkg/CHNOSZ/man/nonideal.Rd 2017-11-07 16:08:39 UTC (rev 280)
@@ -82,7 +82,7 @@
nonidealprops <- nonideal(species, speciesprops, IS = IS, T = convert(T[j], "K"))
for(i in 1:4) lines(IS, 10^(nonidealprops[[i]]$loggam), lty=lty[j], col=col[i])
}
-t1 <- "activity coefficient (gamma) of -1,-2,-3,-4 charged species"
+t1 <- "Activity coefficient (gamma) of -1,-2,-3,-4 charged species"
t2 <- quote("at 0, 25, and 40 "*degree*"C, after Alberty, 2003")
mtitle(as.expression(c(t1, t2)))
legend("topright", lty=c(NA, 1:3), bty="n",
Modified: pkg/CHNOSZ/man/objective.Rd
===================================================================
--- pkg/CHNOSZ/man/objective.Rd 2017-11-06 09:45:36 UTC (rev 279)
+++ pkg/CHNOSZ/man/objective.Rd 2017-11-07 16:08:39 UTC (rev 280)
@@ -121,7 +121,7 @@
lines(a$vals[[1]], DGtr.out)
text(-6, 5.5, expr.property("DDGmix/2.303RT"))
text(-6, 2.3, expr.property("DGtr/2.303RT"))
-title(main=paste("transformation between metastable equilibrium\n",
+title(main=paste("Transformation between metastable equilibrium\n",
"assemblages of n-alkanes"))
# take-home message: use DGtr to measure distance from equilibrium in
# open-system transformations (constant T, P, chemical potentials of basis species)
Modified: pkg/CHNOSZ/man/protein.Rd
===================================================================
--- pkg/CHNOSZ/man/protein.Rd 2017-11-06 09:45:36 UTC (rev 279)
+++ pkg/CHNOSZ/man/protein.Rd 2017-11-07 16:08:39 UTC (rev 280)
@@ -25,6 +25,7 @@
ip <- add.protein(aa)
a <- affinity(pH=c(0, 14), O2=c(-64, -61), T=75, iprotein=ip)
diagram(a)
+title(main="Sequences for transferase at Bison Pool")
## surface-layer proteins from Methanococcus and others
## as a function of oxygen fugacity, after Dick, 2008, Fig. 5b
Modified: pkg/CHNOSZ/man/revisit.Rd
===================================================================
--- pkg/CHNOSZ/man/revisit.Rd 2017-11-06 09:45:36 UTC (rev 279)
+++ pkg/CHNOSZ/man/revisit.Rd 2017-11-07 16:08:39 UTC (rev 280)
@@ -99,13 +99,13 @@
e <- equilibrate(a)
# make a plot
r <- revisit(e, "count", -5)
-title(main="amino acids with metastable log activities > -5")
+title(main="Amino acids with metastable log activities > -5")
# can also make a 2-D plot
a <- affinity(O2=c(-74, -60, 25), H2O=c(-3, 3, 25))
e <- equilibrate(a)
r <- revisit(e, "count", -5, style.2D="image", plot.optval=FALSE)
-title(main="amino acids with metastable log activities > -5")
+title(main="Amino acids with metastable log activities > -5")
## 'revisit' calculations for amino acids
opar <- par(mfrow=c(2, 2))
Modified: pkg/CHNOSZ/man/util.expression.Rd
===================================================================
--- pkg/CHNOSZ/man/util.expression.Rd 2017-11-06 09:45:36 UTC (rev 279)
+++ pkg/CHNOSZ/man/util.expression.Rd 2017-11-07 16:08:39 UTC (rev 280)
@@ -162,6 +162,7 @@
text(3, 4.25, describe.reaction(reaction))
text(3, 4.5, describe.reaction(reaction, states="all"))
text(3, 4.75, describe.reaction(reaction, iname=1:4))
+title(main="Plot labels for chemical species and thermodynamic properties")
}
\concept{Utility functions}
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