[CHNOSZ-commits] r316 - in pkg/CHNOSZ: . inst vignettes

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2018-04-20 16:45:18 +0200 (Fri, 20 Apr 2018)
New Revision: 316

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/vignettes/anintro.Rmd
   pkg/CHNOSZ/vignettes/obigt.Rmd
Log:
update DESCRIPTION and reduce vignette size


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2018-04-11 14:43:37 UTC (rev 315)
+++ pkg/CHNOSZ/DESCRIPTION	2018-04-20 14:45:18 UTC (rev 316)
@@ -1,6 +1,6 @@
-Date: 2018-04-11
+Date: 2018-04-20
 Package: CHNOSZ
-Version: 1.1.3-23
+Version: 1.1.3-24
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
@@ -15,11 +15,14 @@
 Suggests: limSolve, testthat, knitr, rmarkdown, tufte, RSVGTipsDevice
 Imports: grDevices, graphics, stats, utils
 Description: An integrated set of tools for thermodynamic calculations in geochemistry and compositional
-  biology. Thermodynamic properties are taken from a database for minerals and inorganic and
-  organic aqueous species including biomolecules, or from amino acid group additivity for proteins
-  (Dick et al., 2006 <doi:10.5194/bg-3-311-2006>). High-temperature properties are calculated
-  using the Berman-Brown (1985) <doi:10.1007/BF00379451> equations for minerals and the
-  revised Helgeson-Kirkham-Flowers (1981) <doi:10.2475/ajs.281.10.1249> equations of state for
+  biology. The thermodynamic properties of liquid water are calculated using Fortran code from
+  SUPCRT92 (Johnson et al., 1992 <doi:10.1016/0098-3004(92)90029-Q>) or an implementation
+  in R of the IAPWS-95 formulation (Wagner and Pruß, 2002 doi:10.1063/1.1461829).
+  Thermodynamic properties of other species are taken from a database for minerals and inorganic
+  and organic aqueous species including biomolecules, or from amino acid group additivity for
+  proteins (Dick et al., 2006 <doi:10.5194/bg-3-311-2006>). High-temperature properties are
+  calculated using the Berman-Brown (1985) <doi:10.1007/BF00379451> equations for minerals
+  and the revised Helgeson-Kirkham-Flowers (1981) <doi:10.2475/ajs.281.10.1249> equations for
   aqueous species. The HKF equations are augmented with the Deep Earth Water (DEW) model
   (Sverjensky et al., 2014 <doi:10.1016/j.gca.2013.12.019>) and estimates of parameters in the
   extended Debye-Hückel equation (Manning et al., 2013 <doi:10.2138/rmg.2013.75.5>)

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2018-04-11 14:43:37 UTC (rev 315)
+++ pkg/CHNOSZ/inst/NEWS	2018-04-20 14:45:18 UTC (rev 316)
@@ -14,7 +14,7 @@
   Al-bearing minerals, as well as calcite, dolomite, hematite, and
   magnetite) are in the file extdata/OBIGT/SUPCRT92.csv, which can be
   loaded with add.obigt("SUPCRT92"). This is used in some examples for
-  comparing the datasets (see ?berman and demo(go-IU.R)), but should not
+  comparing the datasets (see ?berman and demo("go-IU")), but should not
   be needed by most users.
 
 - In thermo$obigt, the minerals using the Berman equations are
@@ -27,8 +27,8 @@
   winTWQ).
 
 - Multipliers on values in the Berman data files (extdata/Berman/*.csv)
-  have been removed, except for 10^5, 10^5, 10^5, and 10^8 on v1 to v4
-  (to be consistent with the winTWQ data format).
+  have been removed, except for 10^5, 10^5, 10^5, and 10^8 on v1 to v4,
+  to be consistent with the winTWQ data format.
 
 - berman() now reads data from a user-supplied file specified in
   thermo$opt$Berman.
@@ -61,7 +61,7 @@
 
 - TODO: fix overly long message for info("SiO2").
 
-- In equilibrate(), accept a length > 1 'normalize' argument in order
+- In equilibrate(), accept a length > 1 'normalize' argument to
   normalize the chemical formulas of only the selected species.
 
 - Export thermo.axis(), as it is useful for adding major and minor tick

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2018-04-11 14:43:37 UTC (rev 315)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2018-04-20 14:45:18 UTC (rev 316)
@@ -67,8 +67,8 @@
   # save space by using a lower resolution
   dpi <- 50
 } else {
-  pngquant <- "--speed=1 --quality=0-50"
-  dpi <- 72
+  pngquant <- "--speed=1 --quality=0-25"
+  dpi <- 50
 }
 
 ## http://stackoverflow.com/questions/23852753/knitr-with-gridsvg
@@ -1868,7 +1868,7 @@
 ```{r smoker_plot, eval=FALSE, echo=23:25}
 ```
 
-```{r smoker_plot, fig.fullwidth=TRUE, fig.width=9, fig.height=5, small.mar=TRUE, dpi=100, out.width="85%", echo=FALSE, message=FALSE, results="hide", cache=TRUE, fig.cap="Optimization of a thermodynamic model for relative abundances of amino acids in a 270 °C black smoker fluid using 1, 2, or 3 variables (left to right).", pngquant=pngquant, timeit=timeit}
+```{r smoker_plot, fig.fullwidth=TRUE, fig.width=9, fig.height=5, small.mar=TRUE, dpi=dpi, out.width="85%", echo=FALSE, message=FALSE, results="hide", cache=TRUE, fig.cap="Optimization of a thermodynamic model for relative abundances of amino acids in a 270 °C black smoker fluid using 1, 2, or 3 variables (left to right).", pngquant=pngquant, timeit=timeit}
 ```
 
 The calculation using <span style="color:red">`findit()`</span>, in which the added variable log*a*<sub>`r h2o`</sub> optimizes to ca. -2.4, shows that measured concentrations of 6 amino acids fall within 1--2 log units of the relative abundances in metastable equilibrium.

Modified: pkg/CHNOSZ/vignettes/obigt.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.Rmd	2018-04-11 14:43:37 UTC (rev 315)
+++ pkg/CHNOSZ/vignettes/obigt.Rmd	2018-04-20 14:45:18 UTC (rev 316)
@@ -5,6 +5,7 @@
     mathjax: null
     theme: default
     css: obigt.css
+    highlight: null
 vignette: >
   %\VignetteIndexEntry{Thermodynamic data in CHNOSZ}
   %\VignetteEngine{knitr::rmarkdown}