[CHNOSZ-commits] r125 - in pkg/CHNOSZ: . R inst tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Feb 2 18:17:23 CET 2017
Author: jedick
Date: 2017-02-02 18:17:22 +0100 (Thu, 02 Feb 2017)
New Revision: 125
Added:
pkg/CHNOSZ/vignettes/CHNOSZ.png
pkg/CHNOSZ/vignettes/newintro.Rmd
Removed:
pkg/CHNOSZ/vignettes/EOSregress.bib
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/info.R
pkg/CHNOSZ/R/util.units.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/tests/testthat/test-info.R
pkg/CHNOSZ/vignettes/EOSregress.Rmd
pkg/CHNOSZ/vignettes/vig.bib
pkg/CHNOSZ/vignettes/vig.css
Log:
begin writing newintro.Rmd
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-01-31 15:07:36 UTC (rev 124)
+++ pkg/CHNOSZ/DESCRIPTION 2017-02-02 17:17:22 UTC (rev 125)
@@ -1,6 +1,6 @@
-Date: 2017-01-29
+Date: 2017-02-02
Package: CHNOSZ
-Version: 1.0.8-14
+Version: 1.0.8-15
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/info.R
===================================================================
--- pkg/CHNOSZ/R/info.R 2017-01-31 15:07:36 UTC (rev 124)
+++ pkg/CHNOSZ/R/info.R 2017-02-02 17:17:22 UTC (rev 125)
@@ -160,7 +160,7 @@
if(length(approx.species)==1) {
message("info.approx: '", species, "' is similar to ", info.text(approx.species))
} else {
- napprox.max <- 25
+ napprox.max <- 100
exttext <- ":"
if(length(approx.species) > napprox.max) exttext <- paste(" (showing first ", napprox.max, ")", sep="")
message("info.approx: '", species, "' is ambiguous; has approximate matches to ",
Modified: pkg/CHNOSZ/R/util.units.R
===================================================================
--- pkg/CHNOSZ/R/util.units.R 2017-01-31 15:07:36 UTC (rev 124)
+++ pkg/CHNOSZ/R/util.units.R 2017-02-02 17:17:22 UTC (rev 125)
@@ -11,7 +11,7 @@
# set the units and return them
if(units=="bar") with(as.environment("CHNOSZ"), thermo$opt$P.units <- "bar")
if(units=="mpa") with(as.environment("CHNOSZ"), thermo$opt$P.units <- "MPa")
- return(get("thermo")$opt$P.units)
+ message("changed pressure units to ", get("thermo")$opt$P.units)
}
T.units <- function(units=NULL) {
@@ -24,7 +24,7 @@
# set the units and return them
if(units=="c") with(as.environment("CHNOSZ"), thermo$opt$T.units <- "C")
if(units=="k") with(as.environment("CHNOSZ"), thermo$opt$T.units <- "K")
- return(get("thermo")$opt$T.units)
+ message("changed temperature units to ", get("thermo")$opt$T.units)
}
E.units <- function(units=NULL) {
@@ -37,7 +37,7 @@
# set the units and return them
if(units=="cal") with(as.environment("CHNOSZ"), thermo$opt$E.units <- "cal")
if(units=="j") with(as.environment("CHNOSZ"), thermo$opt$E.units <- "J")
- return(get("thermo")$opt$E.units)
+ message("changed energy units to ", get("thermo")$opt$E.units)
}
outvert <- function(value,units) {
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-01-31 15:07:36 UTC (rev 124)
+++ pkg/CHNOSZ/inst/NEWS 2017-02-02 17:17:22 UTC (rev 125)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-14 (2017-01-29)
+CHANGES IN CHNOSZ 1.0.8-15 (2017-02-02)
---------------------------------------
- Add "AA" as a keyword for preset species in basis() (cysteine,
@@ -39,6 +39,8 @@
message() from base R. As a result, the messages don't appear in Sweave
vignettes, but can now be turned on or off easily in knitr vignettes.
+- Add vignette newintro.Rmd.
+
CHANGES IN CHNOSZ 1.0.8 (2016-05-28)
------------------------------------
Modified: pkg/CHNOSZ/tests/testthat/test-info.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-info.R 2017-01-31 15:07:36 UTC (rev 124)
+++ pkg/CHNOSZ/tests/testthat/test-info.R 2017-02-02 17:17:22 UTC (rev 125)
@@ -19,7 +19,6 @@
})
test_that("info.approx() produces expected messages", {
- expect_message(info.approx("lact"), "showing first 25")
expect_message(info.approx("lactic"), "is similar to lactic acid")
expect_message(info.approx("lactic acid"), "is ambiguous")
# note though that info("lactic acid") finds a match b/c info.character is used first...
Added: pkg/CHNOSZ/vignettes/CHNOSZ.png
===================================================================
(Binary files differ)
Property changes on: pkg/CHNOSZ/vignettes/CHNOSZ.png
___________________________________________________________________
Added: svn:mime-type
+ image/png
Modified: pkg/CHNOSZ/vignettes/EOSregress.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/EOSregress.Rmd 2017-01-31 15:07:36 UTC (rev 124)
+++ pkg/CHNOSZ/vignettes/EOSregress.Rmd 2017-02-02 17:17:22 UTC (rev 125)
@@ -5,7 +5,7 @@
date: "`r Sys.Date()`"
output:
tufte::tufte_html:
- tufte_features: ["background", "italics"]
+ tufte_features: ["background"]
css: "vig.css"
tufte::tufte_handout:
citation_package: natbib
@@ -17,7 +17,7 @@
%\VignetteIndexEntry{Regressing thermodynamic data}
%\VignetteEngine{knitr::rmarkdown}
\usepackage[utf8]{inputenc}
-bibliography: EOSregress.bib
+bibliography: vig.bib
link-citations: yes
---
Deleted: pkg/CHNOSZ/vignettes/EOSregress.bib
===================================================================
--- pkg/CHNOSZ/vignettes/EOSregress.bib 2017-01-31 15:07:36 UTC (rev 124)
+++ pkg/CHNOSZ/vignettes/EOSregress.bib 2017-02-02 17:17:22 UTC (rev 125)
@@ -1,108 +0,0 @@
-% Encoding: UTF-8
-
- at Article{HKF81,
- author = {Helgeson, Harold C. and Kirkham, David H. and Flowers, George C.},
- journal = {American Journal of Science},
- title = {{T}heoretical prediction of the thermodynamic behavior of aqueous electrolytes at high pressures and temperatures: {IV}. {C}alculation of activity coefficients, osmotic coefficients, and apparent molal and standard and relative partial molal properties to 600°{C} and 5 {K}b},
- year = {1981},
- volume = {281},
- number = {10},
- pages = {1249--1516},
- doi = {10.2475/ajs.281.10.1249},
- size = {268 p.},
-}
-
- at Article{SSW01,
- author = {Schulte, Mitchell D. and Shock, Everett L. and Wood, Robert H.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{T}he temperature dependence of the standard-state thermodynamic properties of aqueous nonelectrolytes},
- year = {2001},
- volume = {65},
- number = {21},
- pages = {3919--3930},
- doi = {10.1016/S0016-7037(01)00717-7},
-}
-
- at Article{SH90,
- author = {Shock, Everett L. and Helgeson, Harold C.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {S}tandard partial molal properties of organic species},
- year = {1990},
- volume = {54},
- number = {4},
- pages = {915 -- 945},
- doi = {10.1016/0016-7037(90)90429-O},
-}
-
- at Article{SOJSH92,
- author = {Shock, Everett L. and Oelkers, Eric H. and Johnson, James W. and Sverjensky, Dimitri A. and Helgeson, Harold C.},
- journal = {Journal of the Chemical Society, Faraday Transactions},
- title = {{C}alculation of the thermodynamic properties of aqueous species at high pressures and temperatures: {E}ffective electrostatic radii, dissociation constants, and standard partial molal properties to 1000 °{C} and 5 kbar},
- year = {1992},
- volume = {88},
- number = {6},
- pages = {803 -- 826},
- doi = {10.1039/FT9928800803},
-}
-
- at Article{TH88,
- author = {Tanger, IV, John C. and Helgeson, Harold C.},
- journal = {American Journal of Science},
- title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {R}evised equations of state for the standard partial molal properties of ions and electrolytes},
- year = {1988},
- volume = {288},
- number = {1},
- pages = {19--98},
- doi = {10.2475/ajs.288.1.19},
-}
-
- at Article{HW97,
- author = {Hn\v{e}dkovsk\'y, Lubom\'ir and Wood, Robert H.},
- journal = {Journal of Chemical Thermodynamics},
- title = {{A}pparent molar heat capacities of aqueous solutions of {CH}4, {CO}2, {H}2{S}, and {NH}3 at temperatures from 304 {K} to 704 {K} at a pressure of 28 {MP}a},
- year = {1997},
- volume = {29},
- number = {7},
- pages = {731--747},
- doi = {10.1006/jcht.1997.0192},
- issn = {0021-9614},
-}
-
- at Article{MKDW15,
- author = {Miron, George D. and Kulik, Dmitrii A. and Dmytrieva, Svitlana V. and Wagner, Thomas},
- journal = {Applied Geochemistry},
- title = {{GEMSFITS}: {C}ode package for optimization of geochemical model parameters and inverse modeling},
- year = {2015},
- volume = {55},
- number = {0},
- pages = {28 - 45},
- note = {Geochemical Speciation Codes and Databases},
- doi = {10.1016/j.apgeochem.2014.10.013},
- issn = {0883-2927},
-}
-
- at Article{Shv15,
- author = {Shvarov, Yuri},
- journal = {Applied Geochemistry},
- title = {{A} suite of programs, {O}ptim{A}, {O}ptim{B}, {O}ptim{C}, and {O}ptim{S} compatible with the {U}nitherm database, for deriving the thermodynamic properties of aqueous species from solubility, potentiometry and spectroscopy measurements},
- year = {2015},
- volume = {55},
- number = {0},
- pages = {17 - 27},
- note = {Geochemical Speciation Codes and Databases},
- doi = {10.1016/j.apgeochem.2014.11.021},
- issn = {0883-2927},
-}
-
- at Article{HWM96,
- author = {Hn\v{e}dkovsk\'y, Lubom\'ir and Wood, Robert H. and Majer, Vladimir},
- journal = {Journal of Chemical Thermodynamics},
- title = {{V}olumes of aqueous solutions of {CH}4, {CO}2, {H}2{S}, and {NH}3 at temperatures from 298.15 {K} to 705 {K} and pressures to 35 {MP}a},
- year = {1996},
- volume = {28},
- number = {2},
- pages = {125 -- 142},
- doi = {10.1006/jcht.1996.0011},
- issn = {0021-9614},
-}
-
Added: pkg/CHNOSZ/vignettes/newintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/newintro.Rmd (rev 0)
+++ pkg/CHNOSZ/vignettes/newintro.Rmd 2017-02-02 17:17:22 UTC (rev 125)
@@ -0,0 +1,309 @@
+---
+title: "An Introduction to [CHNOSZ](http://www.chnosz.net)"
+author: "Jeffrey M. Dick"
+date: "`r Sys.Date()`"
+output:
+ tufte::tufte_html:
+ tufte_features: ["background"]
+ css: "vig.css"
+ toc: true
+ tufte::tufte_handout:
+ citation_package: natbib
+ latex_engine: xelatex
+ tufte::tufte_book:
+ citation_package: natbib
+ latex_engine: xelatex
+vignette: >
+ %\VignetteIndexEntry{An Introduction to CHNOSZ}
+ %\VignetteEngine{knitr::rmarkdown}
+ \usepackage[utf8]{inputenc}
+bibliography: vig.bib
+link-citations: yes
+---
+
+```{r options, include=FALSE}
+options(width = 80)
+options(digits = 6)
+```
+
+```{r setup, include=FALSE}
+# invalidate cache when the tufte version changes
+knitr::opts_chunk$set(tidy = FALSE, cache.extra = packageVersion('tufte'))
+options(htmltools.dir.version = FALSE)
+knitr::knit_hooks$set(small.mar = function(before, options, envir) {
+ if (before) par(mar = c(4, 4, .1, .1)) # smaller margin on top and right
+})
+```
+
+# About
+
+This document introduces the basic functionality of CHNOSZ, a package for the [R software environment](http://r-project.org).
+For more information on R, see "An Introduction to R" and other documents in [The R Manuals](http://cran.r-project.org/manuals.html).
+
+Since 2006, CHNOSZ has been developed to support a research project on the thermodynamic properties of proteins.
+Over time, the package has grown to calculate thermodynamic properties of reactions and to construct equilibrium chemical activity diagrams for both inorganic and organic systems.
+Development since 2009 has focused on the calculation of chemical affinities and metastable equilibrium for large numbers of proteins with applications to -omic (metagenomic and proteomic) data in various environments.
+Nevertheless, the database and functions are flexible, allowing one to model the relative stabilities of proteins, minerals or aqueous species using similar commands.
+
+## Installing and loading CHNOSZ
+
+If you have just installed R for the first time, and you have an internet connection, installing CHNOSZ should be as simple as selecting the "Install packages from CRAN" or similar menu item in the R GUI or using the following command to start the package installation process:^[Or, install the package from a local package file, which you can download from [CRAN](http://cran.r-project.org) or from the [CHNOSZ website](http://chnosz.net).
+][]()
+```{r install_CHNOSZ, eval=FALSE}
+install.packages("CHNOSZ")
+```
+
+Then load the CHNOSZ package to make its functions available in your working session.
+```{r library_CHNOSZ}
+library(CHNOSZ)
+```
+
+Then load the thermo object, which contains the thermodynamic database and is also where your system settings will be stored.
+```{r data_thermo}
+data(thermo)
+```
+
+## Organization of major functions
+
+CHNOSZ is made up of a set of functions and supporting datasets.
+The major components of the package are shown in the figure below, which is an updated version of the flowchart from @Dic08 (boxes – functions; ellipses – datasets; bold text – major user functions).
+
+
+Many functions in CHNOSZ have no side effects.
+That is, the function only returns a result; to use the result in other functions, it can be assigned to a variable with `<-`.
+Major functions without side effects in CHNOSZ are:
+
+* `info()`: search for species in the thermodynamic database
+* `subcrt()`: calculate the thermodynamic properties of species and reactions
+* `affinity()`: calculate the affinities of formation reactions using given chemical activities
+* `equilibrate()`: calculate the equilibrium chemical activities of the species of interest
+* `diagram()`: plot the results
+
+Some functions in CHNOSZ do have side effects: they modify the `thermo` data object in the current R session.
+In the text (not code) of this document, the names of these functions are shown in <span style="color:red">red</span>.
+The major functions with side effects are:
+
+* <span style="color:red">`basis()`</span>: set the basis species and their chemical activities
+* <span style="color:red">`species()`</span>: set the species of interest and their (non-equilibrium) chemical activities
+* <span style="color:red">`data(thermo)`</span>: reset the database, restoring all settings to their default values.
+
+The following pseudocode shows a common sequence of commands.
+In actual usage, the ... are replaced by arguments that define the chemical makeup and range of conditions of the system:
+```{r, eval=FALSE}
+basis(...)
+species(...)
+a <- affinity(...)
+e <- equilibrate(a) ## optional
+diagram(e) ## or diagram(a)
+data(thermo) ## clear system settings
+```
+
+Some experimental functions are available:
+
+* (**experimental**) using `revisit()` to calculate/plot summary statistics of the chemical activities of the species of interest and `findit()` to search for combinations of activities of basis species, temperature and/or pressure that optimize those statistics.
+
+# Thermodynamic database and chemical formulas
+
+While an attempt has been made to provide a primary database (`OBIGT.csv`) that is generally internally consistent, all thermodynamic data, calculations, and examples are provided *as is*.^[
+For crucial problems, check not only the accuracy of the database, but also the *suitability of the data* for your problem.
+If there is any doubt about the suitability of data, please consult the primary sources (which can be located using `browse.refs()`; see Section XXX).
+As with the data, please check the *suitability and accuracy of the available computational techniques*, at least by comparing the construction and output of the examples to the primary sources cited in each help page.
+Some examples without references demonstrate the more experimental features of CHNOSZ.
+]
+Where possible, data with known or suspected inconsistencies have been placed into a secondary database (`OBIGT-2.csv`) that should be regarded as experimental.
+
+## The `info()` function
+
+The `info()` function provides an interface to the thermodynamic database packaged with CHNOSZ.
+Suppose you are interested in the thermodynamic properties aqueous ethylene.
+You can search for the species by name:
+```{r info_ethylene}
+info("ethylene")
+```
+
+Multiple entries exist for ethylene; the index of the `aq` (aqueous) species is returned by default.
+A second argument can be used to specify a different physical state:
+```{r info_ethylene_gas}
+info("ethylene", "gas")
+```
+
+Knowing that aqueous ethylene is species number 88 in the database, you can again use `info()` to retrieve the set of standard molal thermodynamic properties and equations of state parameters:
+```{r info_88}
+info(88)
+```
+
+This number can be used as an argument (`ispecies`) for other functions in CHNOSZ to uniquely identify any species; some commonly used functions also accept the species names.
+Liquid water is species number 1; it has NA entries in the database because specialized functions are used to compute its properties:
+```{r info_info_water}
+info(info("water"))
+```
+
+## Fuzzy searches
+
+Calling `info()` with a string that does not exactly match the name of any species invokes a fuzzy search of the database:
+```{r width180, include=FALSE}
+options(width = 180)
+```
+```{r info_acid}
+info("acid")
+```
+```{r width80, include=FALSE}
+options(width = 80)
+```
+
+The message includes e.g. "uracil" and "metacinnabar" because their names have some similarity to the search term.
+
+As "ribose" is the name of a species in the database, to find species with similar names, add an extra character to the search:
+```{r info_ribose}
+info(" ribose")
+```
+
+The messages may be useful for browsing the database, but owing to their ambiguous results, these fuzzy searches return an `NA` value for the species index.
+
+## Counting elements, chemical formulas, `ZC()`
+
+Continuing with the example of ethylene, let's look at its chemical formula:
+```{r info_88_formula}
+info(88)$formula
+```
+
+We can use the `makeup()` function to count the elements in the formula, followed by `as.chemical.formula()` to return to the formula:
+```{r makeup_88}
+makeup(88)
+as.chemical.formula(makeup(88))
+```
+
+For organic species, a simple calculation of the average oxidation state of carbon ($Z_C$) is possible given the species index, chemical formula, or elemental count:
+```{r ZC_88}
+ZC(88)
+ZC(info(88)$formula)
+ZC(makeup(88))
+```
+
+# Calculating thermodynamic properties
+
+To calculate the standard molal properties of species and reactions, use `subcrt()`.^[
+The inspiration for this function (as well as its name), and the source of the FORTRAN subroutine used to calculate the thermodynamic properties of H<sub>2</sub>O, is SUPCRT (Johnson et al. 1992).]<sup> [- at JOH92]</sup>
+If no reaction coefficients are given, `subcrt()` calculates the standard molal properties of invididual species:
+```{r subcrt_water}
+subcrt("water")
+```
+
+That uses the default temperature and pressure settings: equally-spaced temperature grid from 0 to 350 °C at _P_<sub>sat</sub>.^[_P_<sub>sat</sub> is 1 bar below 100 °C, or the pressure of liquid-vapor coexistence at higher temperatures.]
+The columns in the output are^[The corresponding units are °C (`T`), bar (`P`), g cm<sup>-3</sup> (`rho`), cal mol<sup>-1</sup> (`G` and `H`), cal K<sup>-1</sup> mol<sup>-1</sup> (`S`), cm<sup>3</sup> mol<sup>-1</sup> (`V`), and cal K<sup>-1</sup> mol<sup>-1</sup> (`Cp`).] temperature, pressure, density of water, logarithm of the equilibrium constant (only meaningful for reactions; see below), standard molal Gibbs energy and enthalpy of formation from the elements, standard molal entropy, volume, and heat capacity.
+
+A custom temperature-pressure grid can be specified.
+Here, we calculate the properties of H<sub>2</sub>O on a _T_,_P_ grid in the supercritical region, with conditions grouped by pressure:
+```{r subcrt_water_grid}
+subcrt("water", T=c(400, 500, 600), P=c(200, 400, 600), grid="P")$out$water
+```
+
+```{r subcrt_water_plot, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=50, out.width="100%", echo=FALSE, message=FALSE, fig.cap="Isothermal contours of density (g cm<sup>-3</sup>) and pressure (bar) of H<sub>2</sub>O.", cache=TRUE}
+H2O <- subcrt("water", T=seq(0, 1000, 100), P=c(NA, seq(1, 500, 1)), grid="T")
+H2O <- H2O$out$water
+plot(H2O$P, H2O$rho, type="l")
+```
+The additional operations (`$out$water`) are used to extract a specific part of the results; this can be used with e.g. `write.table()` or `plot()` for further processing:
+```{r subcrt_water_plot, eval=FALSE}
+```
+
+## Changing units
+
+The default units of temperature, pressure, and energy are °C, bar, and calories.
+The functions <span style="color:red">`T.units()`</span>, <span style="color:red">`P.units()`</span>, and <span style="color:red">`E.units()`</span> can be used to change the units used by various functions in CHNOSZ.
+What is the Gibbs energy (J/mol) of aqueous methane at 298.15 K and 0.1 MPa?
+```{r methane_units, message=FALSE}
+T.units("K")
+P.units("MPa")
+E.units("J")
+subcrt("methane", T=298.15, P=0.1)$out$methane$G
+data(thermo) ## restore default settings
+```
+
+A related function, `convert()`, can be used to convert given values between units.
+Let's convert the standard Gibbs energy of aqueous methane listed in the database from cal/mol to J/mol:
+```{r methane_G, message=FALSE}
+convert(info(info("methane"))$G, "J")
+```
+
+As expected, we get the same result from both operations.
+
+# Properties of reactions
+
+## Reaction definitions
+
+To calculate the thermodynamic properties of reactions, give the names of species, the physical states (optional), and reaction coefficients as the arguments to `subcrt()`.
+Here we calculate properties for the dissolution of CO<sub>2</sub>:
+```{r CO2_dissolution}
+subcrt(c("CO2", "CO2"), c("gas", "aq"), c(-1, 1))
+```
+
+<p> <!--- needed to make the citation appear correction 20170202 -->
+In order to make a plot like that shown by Manning et al. [- at MSS13, Figure 18], let's run more calculations and store the results.
+In addition to the reaction definition, we specify a greater number of temperature points than the default:
+```{r dissolution, echo=FALSE, message=FALSE}
+T <- seq(0, 350, 10)
+CO2 <- subcrt(c("CO2", "CO2"), c("gas", "aq"), c(-1, 1), T=T)$out$logK
+CO <- subcrt(c("CO", "CO"), c("gas", "aq"), c(-1, 1), T=T)$out$logK
+CH4 <- subcrt(c("CH4", "CH4"), c("gas", "aq"), c(-1, 1), T=T)$out$logK
+logK <- data.frame(T, CO2, CO, CH4)
+```
+```{r dissolution_plot, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=50, out.width="100%", echo=FALSE, message=FALSE, fig.cap="Equilibrium constants calculated for dissolution of CO<sub>2</sub>, CO, and CH<sub>4</sub>.", cache=TRUE}
+matplot(logK[, 1], logK[, -1], type="l",
+ xlab=axis.label("T"), ylab=axis.label("logK"))
+```
+```{r dissolution, eval=FALSE}
+```
+
+Now we can make the plot.
+Here, the `axis.label()` function of CHNOSZ is used to create formatted axis labels:
+```{r dissolution_plot, eval=FALSE}
+```
+
+## Unbalanced reactions
+
+## Setting the basis species
+
+## Auto-balancing reactions
+
+# Basic diagrams
+
+## Setting the species of interest
+
+## Thermodynamic potential: `affinity()`
+
+## Predominance: the `diagram()` function
+
+## Labels, colors, etc.
+
+# Equilibration
+
+## Getting from affinity to equilibrium
+
+## Setting the constraints
+
+# Other things you can do with affinity
+
+## Buffers
+
+## T-, P-, activity-transect
+
+# Other things you can do with equilibrate
+
+## Choosing different balancing constraints
+
+# Other things you can do with diagrams
+
+## Mosaic diagrams
+
+## Groups of species
+
+# Proteins
+
+## Group additivity
+
+## Sources of amino acid data
+
+## Ionization
+
+## Normalizing for different lengths
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2017-01-31 15:07:36 UTC (rev 124)
+++ pkg/CHNOSZ/vignettes/vig.bib 2017-02-02 17:17:22 UTC (rev 125)
@@ -299,6 +299,18 @@
url = {http://www.worldcat.org/oclc/583263}
}
+ at Article{HKF81,
+ author = {Helgeson, Harold C. and Kirkham, David H. and Flowers, George C.},
+ journal = {American Journal of Science},
+ title = {{T}heoretical prediction of the thermodynamic behavior of aqueous electrolytes at high pressures and temperatures: {IV}. {C}alculation of activity coefficients, osmotic coefficients, and apparent molal and standard and relative partial molal properties to 600°{C} and 5 {K}b},
+ year = {1981},
+ volume = {281},
+ number = {10},
+ pages = {1249--1516},
+ doi = {10.2475/ajs.281.10.1249},
+ size = {268 p.},
+}
+
@Article{HFG+03,
author = {Huh, Won-Ki and Falvo, James V. and Gerke, Luke C. and Carroll, Adam S. and Howson, Russell W. and Weissman, Jonathan S. and O'Shea, Erin K.},
journal = {Nature},
@@ -324,7 +336,7 @@
@Article{JOH92,
author = {Johnson, James W. and Oelkers, Eric H. and Helgeson, Harold C.},
journal = {Computers \& Geosciences},
- title = {{SUPCRT}92: {A} software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000$^\circ${C}},
+ title = {SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000°C},
year = {1992},
volume = {18},
number = {7},
@@ -342,6 +354,17 @@
doi = {10.1016/j.gca.2011.11.041},
}
+ at Article{MSS13,
+ author = {Manning, Craig E. and Shock, Everett L. and Sverjensky, Dimitri A.},
+ journal = {Reviews in Mineralogy and Geochemistry},
+ title = {The chemistry of carbon in aqueous fluids at crustal and upper-mantle conditions: Experimental and theoretical constraints},
+ year = {2013},
+ volume = {75},
+ number = {1},
+ pages = {109-148},
+ doi = {10.2138/rmg.2013.75.5},
+}
+
@Article{MIS+08,
author = {Markowitz, Victor M. and Ivanova, Natalia N. and Szeto, Ernest and Palaniappan, Krishna and Chu, Ken and Dalevi, Daniel and Chen, I-Min A. and Grechkin, Yuri and Dubchak, Inna and Anderson, Iain and Lykidis, Athanasios and Mavromatis, Konstantinos and Hugenholtz, Philip and Kyrpides, Nikos C.},
journal = {Nucleic Acids Research},
@@ -469,6 +492,17 @@
doi = {10.1007/BF01581580},
}
+ at Article{SSW01,
+ author = {Schulte, Mitchell D. and Shock, Everett L. and Wood, Robert H.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{T}he temperature dependence of the standard-state thermodynamic properties of aqueous nonelectrolytes},
+ year = {2001},
+ volume = {65},
+ number = {21},
+ pages = {3919--3930},
+ doi = {10.1016/S0016-7037(01)00717-7},
+}
+
@Article{See96,
author = {Seewald, Jeffrey S.},
journal = {Materials Research Society Symposium Proceedings},
@@ -504,6 +538,17 @@
doi = {10.1016/0016-7037(90)90429-O},
}
+ at Article{SOJSH92,
+ author = {Shock, Everett L. and Oelkers, Eric H. and Johnson, James W. and Sverjensky, Dimitri A. and Helgeson, Harold C.},
+ journal = {Journal of the Chemical Society, Faraday Transactions},
+ title = {{C}alculation of the thermodynamic properties of aqueous species at high pressures and temperatures: {E}ffective electrostatic radii, dissociation constants, and standard partial molal properties to 1000 °{C} and 5 kbar},
+ year = {1992},
+ volume = {88},
+ number = {6},
+ pages = {803 -- 826},
+ doi = {10.1039/FT9928800803},
+}
+
@Article{SWM+05,
author = {Spear, John R. and Walker, Jeffrey J. and McCollom, Thomas M. and Pace, Norman R.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
@@ -536,6 +581,17 @@
doi = {10.1016/S0016-7037(01)00705-0},
}
+ at Article{TH88,
+ author = {Tanger, IV, John C. and Helgeson, Harold C.},
+ journal = {American Journal of Science},
+ title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {R}evised equations of state for the standard partial molal properties of ions and electrolytes},
+ year = {1988},
+ volume = {288},
+ number = {1},
+ pages = {19--98},
+ doi = {10.2475/ajs.288.1.19},
+}
+
@Article{WJD58,
author = {White, W. B. and Johnson, S. M. and Dantzig, G. B.},
journal = {Journal of Chemical Physics},
@@ -573,3 +629,53 @@
issn = {1474-760X},
}
+ at Article{HW97,
+ author = {Hn\v{e}dkovsk\'y, Lubom\'ir and Wood, Robert H.},
+ journal = {Journal of Chemical Thermodynamics},
+ title = {{A}pparent molar heat capacities of aqueous solutions of {CH}4, {CO}2, {H}2{S}, and {NH}3 at temperatures from 304 {K} to 704 {K} at a pressure of 28 {MP}a},
+ year = {1997},
+ volume = {29},
+ number = {7},
+ pages = {731--747},
+ doi = {10.1006/jcht.1997.0192},
+ issn = {0021-9614},
+}
+
+ at Article{MKDW15,
+ author = {Miron, George D. and Kulik, Dmitrii A. and Dmytrieva, Svitlana V. and Wagner, Thomas},
+ journal = {Applied Geochemistry},
+ title = {{GEMSFITS}: {C}ode package for optimization of geochemical model parameters and inverse modeling},
+ year = {2015},
+ volume = {55},
+ number = {0},
+ pages = {28 - 45},
+ note = {Geochemical Speciation Codes and Databases},
+ doi = {10.1016/j.apgeochem.2014.10.013},
+ issn = {0883-2927},
+}
+
+ at Article{Shv15,
+ author = {Shvarov, Yuri},
+ journal = {Applied Geochemistry},
+ title = {{A} suite of programs, {O}ptim{A}, {O}ptim{B}, {O}ptim{C}, and {O}ptim{S} compatible with the {U}nitherm database, for deriving the thermodynamic properties of aqueous species from solubility, potentiometry and spectroscopy measurements},
+ year = {2015},
+ volume = {55},
+ number = {0},
+ pages = {17 - 27},
+ note = {Geochemical Speciation Codes and Databases},
+ doi = {10.1016/j.apgeochem.2014.11.021},
+ issn = {0883-2927},
+}
+
+ at Article{HWM96,
+ author = {Hn\v{e}dkovsk\'y, Lubom\'ir and Wood, Robert H. and Majer, Vladimir},
+ journal = {Journal of Chemical Thermodynamics},
+ title = {{V}olumes of aqueous solutions of {CH}4, {CO}2, {H}2{S}, and {NH}3 at temperatures from 298.15 {K} to 705 {K} and pressures to 35 {MP}a},
+ year = {1996},
+ volume = {28},
+ number = {2},
+ pages = {125 -- 142},
+ doi = {10.1006/jcht.1996.0011},
+ issn = {0021-9614},
+}
+
Modified: pkg/CHNOSZ/vignettes/vig.css
===================================================================
--- pkg/CHNOSZ/vignettes/vig.css 2017-01-31 15:07:36 UTC (rev 124)
+++ pkg/CHNOSZ/vignettes/vig.css 2017-02-02 17:17:22 UTC (rev 125)
@@ -1,5 +1,26 @@
-html { font-size: 14px; }
+html {
+ font-size: 14px;
+}
-body { font-family: ‘Times New Roman’, Times, serif; }
+body {
+ font-family: ‘Times New Roman’, Times, serif;
+}
-li { padding: 0.25rem 0; }
+li {
+ padding: 0.25rem 0;
+}
+
+/* zero margin around pre blocks (looks more like R console output) */
+pre {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+
+/* for CHNOSZ links */
+h1 a:link {
+ color: red;
+}
+
+h3 a:link {
+ color: red;
+}
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