[CHNOSZ-commits] r454 - in pkg/CHNOSZ: . demo inst man vignettes

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

Author: jedick
Date: 2019-04-27 15:06:53 +0200 (Sat, 27 Apr 2019)
New Revision: 454

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/demo/aluminum.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/diagram.Rd
   pkg/CHNOSZ/vignettes/obigt.Rmd
Log:
fix some typos


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-04-23 05:21:07 UTC (rev 453)
+++ pkg/CHNOSZ/DESCRIPTION	2019-04-27 13:06:53 UTC (rev 454)
@@ -1,6 +1,6 @@
-Date: 2019-04-23
+Date: 2019-04-27
 Package: CHNOSZ
-Version: 1.3.2-1
+Version: 1.3.2-2
 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/demo/aluminum.R
===================================================================
--- pkg/CHNOSZ/demo/aluminum.R	2019-04-23 05:21:07 UTC (rev 453)
+++ pkg/CHNOSZ/demo/aluminum.R	2019-04-27 13:06:53 UTC (rev 454)
@@ -18,32 +18,31 @@
 thermo.plot.new(xlim = range(T), ylim = c(-3.5, -1.5), xlab = axis.label("T"), ylab = axis.label("SiO2"))
 points(xT, xlogaSiO2)
 basis(delete = TRUE)
-## first calculation: as in SUPCRT92
+## first calculation: CHNOSZ default
+# kaolinite from Berman, 1988
+# boehmite from Hemingway et al., 1991
+r1 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE) 
+## second calculation: minerals as in SUPCRT92
 add.obigt("SUPCRT92") # gets kaolinite and boehmite from HDNB78
-r1 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE) 
 # we need exceed.Ttr = TRUE because the T limit for boehmite is 500 K (Helgeson et al., 1978)
-## second calculation: CHNOSZ default
-# kaolinite from Berman, 1988
-# boehmite from Hemingway et al., 1991
-# SiO2 from Apps and Spycher, 2004
+r2 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE) 
 reset()
-r2 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE) 
-## third calculation: get SiO2(aq) from SHS89
+## third calculation: get SiO2(aq) from Apps and Spycher, 2004
 add.obigt("AS04")
 r3 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE) 
+reset()
 ## log activity of SiO2 is -ve logK
-lines(T, -r1$out$logK, col = "blue1", lty = 2)
-lines(T, -r2$out$logK, lwd = 1.5)
+lines(T, -r1$out$logK, lwd = 1.5)
+lines(T, -r2$out$logK, col = "blue1", lty = 2)
 lines(T, -r3$out$logK, col = "red", lty = 2)
 ## add points calculated using the SUPCRTBL package
 points(seq(125, 350, 25), -c(3.489, 3.217, 2.967, 2.734, 2.517, 2.314, 2.124, 1.946, 1.781, 1.628), pch = 4, col = "red")
 ## add legend and title
-title(main = describe.reaction(r1$reaction), cex.main = 1.1)
+title(main = describe.reaction(r2$reaction), cex.main = 1.1)
 legend("bottomright", lty = c(0, 2, 0, 1, 2), pch = c(1, NA, 4, NA, NA), lwd = c(1, 1, 1, 1.5, 1),
-       col = c("black", "black", "red", "black", "red"), bty = "n", cex = 0.9,
+       col = c("black", "blue", "red", "black", "red"), bty = "n", cex = 0.9,
        legend = c("Hemley et al., 1980", "SUPCRT92", "SUPCRTBL", "CHNOSZ", 'add.obigt("AS04")'))
 legend("topleft", c("Boehmite - Kaolinite", "After Zhu and Lu, 2009 Fig. A1"), bty = "n")
-reset()
 # Helgeson et al., 1978 (HDNB78): http://www.worldcat.org/oclc/13594862
 # Shock et al., 1989 (SHS89): doi:10.1016/0016-7037(89)90341-4
 # Berman, 1988 (Ber88): doi:10.1093/petrology/29.2.445

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-04-23 05:21:07 UTC (rev 453)
+++ pkg/CHNOSZ/inst/NEWS	2019-04-27 13:06:53 UTC (rev 454)
@@ -31,7 +31,7 @@
   2014.
 
 - Add argument 'plot.box' (default TRUE) to thermo.plot.new() and
-  'plot.line' (default FALSE) to thermo.axis() to prevent unecessary
+  'plot.line' (default FALSE) to thermo.axis() to prevent unnecessary
   plotting of axis lines. thermo.axis() also avoids plotting tick
   marks at the plot limits.
 

Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd	2019-04-23 05:21:07 UTC (rev 453)
+++ pkg/CHNOSZ/man/diagram.Rd	2019-04-27 13:06:53 UTC (rev 454)
@@ -265,7 +265,6 @@
 text(3, 21, describe.property(c("T", "P"), c(25, 1), oneline=TRUE))
 
 ## aqueous Al species, after Tagirov and Schott, 2001
-# this uses a HCL palette for the fill colors
 basis(c("Al+3", "F-", "H+", "O2", "H2O"))
 AlOH <- c("Al(OH)4-", "Al(OH)3", "Al(OH)2+", "AlOH+2")
 Al <- "Al+3"

Modified: pkg/CHNOSZ/vignettes/obigt.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.Rmd	2019-04-23 05:21:07 UTC (rev 453)
+++ pkg/CHNOSZ/vignettes/obigt.Rmd	2019-04-27 13:06:53 UTC (rev 454)
@@ -119,7 +119,7 @@
 
 * Data from SUPCRT92 which have been superseded by the Berman data are listed under **Optional Data** / **SUPCRT92**.
 
-* Superseded data from SLOP98 (inlucding Al, As, and Au species) are listed under **Optional Data** / **SLOP98**.
+* Superseded data from SLOP98 (including Al, As, and Au species) are listed under **Optional Data** / **SLOP98**.
 
 # Sources of data {.tabset .tabset-fade}