[CHNOSZ-commits] r778 - in pkg/CHNOSZ: . inst man

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

Author: jedick
Date: 2023-03-11 14:34:27 +0100 (Sat, 11 Mar 2023)
New Revision: 778

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/man/add.OBIGT.Rd
   pkg/CHNOSZ/man/ionize.aa.Rd
Log:
Fix up a couple of examples


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2023-03-10 14:57:39 UTC (rev 777)
+++ pkg/CHNOSZ/DESCRIPTION	2023-03-11 13:34:27 UTC (rev 778)
@@ -1,6 +1,6 @@
-Date: 2023-03-10
+Date: 2023-03-11
 Package: CHNOSZ
-Version: 1.9.9-69
+Version: 1.9.9-70
 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/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2023-03-10 14:57:39 UTC (rev 777)
+++ pkg/CHNOSZ/inst/CHECKLIST	2023-03-11 13:34:27 UTC (rev 778)
@@ -1,6 +1,6 @@
 ****************************
 Release checklist for CHNOSZ
-    (updated 2023-03-02)
+    (updated 2023-03-10)
 ****************************
 
 - Run examples() and demos() and inspect their output (especially plots)
@@ -19,7 +19,7 @@
 - Add BibTeX references to vignettes/OBIGT.bib
   (used in the OBIGT.Rmd vignette).
 
-- Add references *and notes* to extdata/OBIGT/refs.csv
+- Add references and notes to extdata/OBIGT/refs.csv
   (also used in the OBIGT.Rmd vignette and thermo.refs()).
 
 - Check output of demo/sources.R to make sure all references
@@ -38,16 +38,6 @@
   co <- check.OBIGT()
   write.csv(co, "OBIGT_check.csv", row.names = FALSE, na = "")
 
-******************
-Updating vignettes
-******************
-
-- Customize rmarkdown installation (in R local library)
-
-  - To enable page offset from anchor position in OBIGT.Rmd:
-    remove padding-top: 10px; from h2 in
-    rmarkdown/templates/html_vignette/resources/vignette.css
-
 ***************
 R compatibility
 ***************
@@ -59,7 +49,7 @@
   LC_CTYPE=en_US R CMD check CHNOSZ_x.x.x.tar.gz
 
 - Backwards compatibility: build and check the package with the
-  *minimum* R version (from the DESCRIPTION file)
+  minimum R version (from the DESCRIPTION file)
 
 *************
 Documentation 

Modified: pkg/CHNOSZ/man/add.OBIGT.Rd
===================================================================
--- pkg/CHNOSZ/man/add.OBIGT.Rd	2023-03-10 14:57:39 UTC (rev 777)
+++ pkg/CHNOSZ/man/add.OBIGT.Rd	2023-03-11 13:34:27 UTC (rev 778)
@@ -133,7 +133,7 @@
 OBIGT()
 
 # Another use of add.OBIGT(): calculate Delta G of
-# H4SiO4 = SiO2 + 2H2O using different data for SiO2.
+# H4SiO4 = SiO2 + 2H2O using various sources of data for SiO2.
 # First, get H4SiO4 from Stefansson, 2001
 add.OBIGT("AS04", "H4SiO4")
 T <- seq(0, 350, 10)
@@ -148,9 +148,13 @@
 # Add title and legend
 title(main = describe.reaction(s1$reaction))
 stxt <- lapply(c("H4SiO4", "SiO2", "SiO2"), expr.species)
-legend("top", legend = as.expression(stxt), bty = "n")
-legend("topright", c("Stef\u00e1nsson, 2001", "Shock et al., 1989",
-  "Apps and Spycher, 2004"), lty = c(0, 1, 2), bty = "n")
+legend("top", c("Shock et al., 1989", "Apps and Spycher, 2004"),
+  title = as.expression(expr.species("SiO2")), lty = c(1, 2))
+legend("topright", "Stef\u00e1nsson, 2001",
+  title = as.expression(expr.species("H4SiO4")))
+abline(h = 0, lty = 3, col = 8)
+# Take-home message: SiO2 from Ste01 is compatible with H4SiO4 from Ste01
+# at low T, but SiO2 from Shock et al., 1989 (the default in OBIGT) isn't
 OBIGT()
 }
 

Modified: pkg/CHNOSZ/man/ionize.aa.Rd
===================================================================
--- pkg/CHNOSZ/man/ionize.aa.Rd	2023-03-10 14:57:39 UTC (rev 777)
+++ pkg/CHNOSZ/man/ionize.aa.Rd	2023-03-11 13:34:27 UTC (rev 778)
@@ -40,7 +40,7 @@
 # Cp of non-ionized protein
 Cp.nonion <- subcrt("LYSC_CHICK", T = T)$out[[1]]$Cp
 plot(T, Cp.nonion, xlab = axis.label("T"), type = "l",
-  ylab = axis.label("Cp"), ylim = c(5000, 8000))
+  ylab = axis.label("Cp"), ylim = c(20000, 35000))
 # Cp of ionization and ionized protein
 aa <- pinfo(pinfo("LYSC_CHICK"))
 for(pH in c(5, 9, 3)) {
@@ -50,10 +50,10 @@
 }
 # Makhatadze and Privalov's group contributions
 T <- c(5, 25, 50, 75, 100, 125)
-points(T, convert(MP90.cp("LYSC_CHICK", T), "cal"))
+points(T, MP90.cp("LYSC_CHICK", T))
 # Privalov and Makhatadze's experimental values
 e <- read.csv(system.file("extdata/cpetc/PM90.csv", package = "CHNOSZ"))
-points(e$T, convert(e$LYSC_CHICK, "cal"), pch = 16)
+points(e$T, e$LYSC_CHICK, pch = 16)
 legend("bottomright", pch = c(16, 1, NA, NA), lty = c(NA, NA, 1, 2),
   legend = c("PM90 experiment", "MP90 groups", 
   "DLH06 groups no ion", "DLH06 groups ionized"))