[CHNOSZ-commits] r591 - in pkg/CHNOSZ: . R vignettes

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

Author: jedick
Date: 2020-07-28 10:39:16 +0200 (Tue, 28 Jul 2020)
New Revision: 591

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/mix.R
   pkg/CHNOSZ/vignettes/multi-metal.Rmd
Log:
Fix for previous R versions (no 'simplify' argument in apply())


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2020-07-28 08:02:07 UTC (rev 590)
+++ pkg/CHNOSZ/DESCRIPTION	2020-07-28 08:39:16 UTC (rev 591)
@@ -1,6 +1,6 @@
 Date: 2020-07-28
 Package: CHNOSZ
-Version: 1.3.6-64
+Version: 1.3.6-65
 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/R/mix.R
===================================================================
--- pkg/CHNOSZ/R/mix.R	2020-07-28 08:02:07 UTC (rev 590)
+++ pkg/CHNOSZ/R/mix.R	2020-07-28 08:39:16 UTC (rev 591)
@@ -63,7 +63,7 @@
     # Remove combinations of a species with itself
     combs <- combs[combs[, 1] != combs[, 2], ]
     # Remove duplicated combinations
-    isdup <- duplicated(lapply(apply(combs, 1, sort, simplify = FALSE), paste))
+    isdup <- duplicated(paste(apply(combs, 1, sort)[1, ], apply(combs, 1, sort)[2, ]))
     combs <- combs[!isdup, ]
   }
   # Get species rows for each combination

Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd	2020-07-28 08:02:07 UTC (rev 590)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd	2020-07-28 08:39:16 UTC (rev 591)
@@ -294,7 +294,7 @@
 # 1:1 mixture (Fe:V)
 a11 <- mix(dFe, dV, dFeV, c(1, 1))
 d11 <- diagram(a11, fill = fill(a11), min.area = 0.01)
-water.lines(d11, col = 2)
+water.lines(d11, col = "orangered")
 
 # Calculate affinity of FeVO4
 species("FeVO4")
@@ -307,15 +307,15 @@
 image(aFeVO4_vs_stable, col = topo.colors(100, 0.7, TRUE), add = TRUE)
 par(opar)
 diagram(a11, add = TRUE, names = FALSE)
-water.lines(d11, col = 2)
+water.lines(d11, col = "orangered")
 thermo.axis()
 
 imax <- arrayInd(which.max(aFeVO4_vs_stable), dim(aFeVO4_vs_stable))
 pH <- d11$vals$pH[imax[1]]
 Eh <- d11$vals$Eh[imax[2]]
-points(pH, Eh, pch = 10, cex = 2, lwd = 2, col = 7)
+points(pH, Eh, pch = 10, cex = 2, lwd = 2, col = "gold")
 stable <- d11$names[d11$predominant[imax]]
-text(pH, Eh, stable, adj = c(0.5, -1), cex = 1.2, col = 7)
+text(pH, Eh, stable, adj = c(0.5, -1), cex = 1.2, col = "gold")
 ```
 
 We then compute the affinity for formation of a metastable material, in this case triclinic FeVO~4~, from the same basis species used to make the previous diagrams.
@@ -333,9 +333,9 @@
 imax <- arrayInd(which.max(aFeVO4_vs_stable), dim(aFeVO4_vs_stable))
 pH <- d11$vals$pH[imax[1]]
 Eh <- d11$vals$Eh[imax[2]]
-points(pH, Eh, pch = 10, cex = 2, lwd = 2, col = 7)
+points(pH, Eh, pch = 10, cex = 2, lwd = 2, col = "gold")
 stable <- d11$names[d11$predominant[imax]]
-text(pH, Eh, stable, adj = c(0.3, 2), cex = 1.2, col = 7)
+text(pH, Eh, stable, adj = c(0.3, 2), cex = 1.2, col = "gold")
 range(aFeVO4_vs_stable[d11$predominant == d11$predominant[imax]])
 ```