[CHNOSZ-commits] r277 - in pkg/CHNOSZ: . demo man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Nov 5 06:08:13 CET 2017
Author: jedick
Date: 2017-11-05 06:08:12 +0100 (Sun, 05 Nov 2017)
New Revision: 277
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/demo/TCA.R
pkg/CHNOSZ/man/IAPWS95.Rd
pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
demo/TCA.R: change equals signs to reaction arrrows
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-11-02 03:16:38 UTC (rev 276)
+++ pkg/CHNOSZ/DESCRIPTION 2017-11-05 05:08:12 UTC (rev 277)
@@ -1,6 +1,6 @@
-Date: 2017-11-02
+Date: 2017-11-05
Package: CHNOSZ
-Version: 1.1.0-75
+Version: 1.1.0-76
Title: Thermodynamic Calculations for Geobiochemistry
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/demo/TCA.R
===================================================================
--- pkg/CHNOSZ/demo/TCA.R 2017-11-02 03:16:38 UTC (rev 276)
+++ pkg/CHNOSZ/demo/TCA.R 2017-11-05 05:08:12 UTC (rev 277)
@@ -50,20 +50,22 @@
fum <- quote(Fumarate^-2)
h2 <- quote(H[2*(italic(aq))])
mal <- quote(Malate^-2)
+# the reaction double arrow
+eq <- "\u21cc"
sublist <- list(oxal=oxal, pyr=pyr, h2o=h2o, nox=nox, cit=cit, nred=nred,
co2=co2, hplus=hplus, aco=aco, iso=iso, ket=ket, adp=adp,
- hpo4=hpo4, suc=suc, atp=atp, fum=fum, h2=h2, mal=mal)
+ hpo4=hpo4, suc=suc, atp=atp, fum=fum, h2=h2, mal=mal, eq=eq)
# reaction titles
rtitle <- list(
- c(substitute(" "*oxal + pyr + h2o + nox == "", sublist), substitute(cit + nred + co2 + hplus, sublist)),
- substitute(cit == aco + h2o, sublist),
- substitute(aco + h2o == iso*" ", sublist),
- c(substitute(iso + nox == "", sublist), substitute(ket + nred + co2*" ", sublist)),
- c(substitute(ket + adp + hpo4 + nox == "", sublist), substitute(suc + atp + nred + co2, sublist)),
- substitute(suc == fum + h2, sublist),
- substitute(fum + h2o == mal, sublist),
- c(substitute(mal + nox == " ", sublist), substitute(oxal + nred + hplus * " ", sublist)),
- c(substitute(pyr + 4*nox + adp + hpo4 + 2*h2o == " ", sublist),
+ c(substitute(" "*oxal + pyr + h2o + nox ~eq~ "", sublist), substitute(cit + nred + co2 + hplus, sublist)),
+ substitute(cit ~eq~ aco + h2o, sublist),
+ substitute(aco + h2o ~eq~ iso*" ", sublist),
+ c(substitute(iso + nox ~eq~ " ", sublist), substitute(ket + nred + co2*" ", sublist)),
+ c(substitute(ket + adp + hpo4 + nox ~eq~ "", sublist), substitute(" "*suc + atp + nred + co2, sublist)),
+ c(substitute(suc ~eq~ "", sublist), substitute(fum + h2, sublist)),
+ substitute(fum + h2o ~eq~ mal, sublist),
+ c(substitute(mal + nox ~eq~ " ", sublist), substitute(oxal + nred + hplus * " ", sublist)),
+ c(substitute(pyr + 4*nox + adp + hpo4 + 2*h2o ~eq~ " ", sublist),
substitute(3*co2 + 4*nred + 2*hplus + atp + h2 * " ", sublist))
)
# set up plot
Modified: pkg/CHNOSZ/man/IAPWS95.Rd
===================================================================
--- pkg/CHNOSZ/man/IAPWS95.Rd 2017-11-02 03:16:38 UTC (rev 276)
+++ pkg/CHNOSZ/man/IAPWS95.Rd 2017-11-05 05:08:12 UTC (rev 277)
@@ -39,7 +39,7 @@
\examples{
## calculate pressure for given temperature, density
-P <- as.numeric(IAPWS95("P", T=500, rho=838.0235))
+IAPWS95("P", T=500, rho=838.0235)
}
\references{
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2017-11-02 03:16:38 UTC (rev 276)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2017-11-05 05:08:12 UTC (rev 277)
@@ -150,7 +150,8 @@
The major components of the package are shown in the figure below, which is an updated version of the diagram in @Dic08.
Rectangles and ellipses represent functions and datasets; bold text indicates primary functions.
-
+<!-- https://stackoverflow.com/questions/14675913/how-to-change-image-size-markdown -->
+{ width=75% }
Many functions in CHNOSZ have no side effects.
That is, the function only returns a result; to use the result elsewhere, it can be assigned to a variable with `<-`.
@@ -177,12 +178,13 @@
The following pseudocode shows a common sequence of commands.
In actual usage, the `...` are replaced by arguments that define the chemical species and variables:
```{r pseudocode, eval=FALSE}
+data(thermo) ## initialize system settings
basis(...)
species(...)
a <- affinity(...)
e <- equilibrate(a) ## optional
diagram(e) ## or diagram(a)
-data(thermo) ## clear system settings
+data(thermo) ## clear settings for next calculation
```
# The basics
@@ -2031,7 +2033,7 @@
However, the IAPWS-95 equations are useful for other applications, and may be extrapolated to a greater range of *T* and *P* than SUPCRT.
See <span style="color:blue">`?water`</span> for more information, as well as the last example in <span style="color:blue">`?subcrt`</span>, where uncommenting the line for the `IAPWS95` option allows extrapolation to lower temperatures for supercooled water.
-More recently (late 2017), an implementation of the [Deep Earth Water](http://www.dewcommunity.org/) (DEW) model was added; see [optional data](#optional-data) for more information.
+More recently (late 2017), an implementation of the [Deep Earth Water](http://www.dewcommunity.org/) (DEW) model was added; see [Optional data](#optional-data) for more information.
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