[CHNOSZ-commits] r188 - in pkg/CHNOSZ: . R inst man tests/testthat

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

Author: jedick
Date: 2017-04-27 04:30:51 +0200 (Thu, 27 Apr 2017)
New Revision: 188

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/diagram.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/diagram.Rd
   pkg/CHNOSZ/tests/testthat/test-diagram.R
Log:
diagram(): add 'col.NA' argument


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-04-25 11:19:56 UTC (rev 187)
+++ pkg/CHNOSZ/DESCRIPTION	2017-04-27 02:30:51 UTC (rev 188)
@@ -1,6 +1,6 @@
-Date: 2017-04-25
+Date: 2017-04-27
 Package: CHNOSZ
-Version: 1.0.8-76
+Version: 1.0.8-77
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R	2017-04-25 11:19:56 UTC (rev 187)
+++ pkg/CHNOSZ/R/diagram.R	2017-04-27 02:30:51 UTC (rev 188)
@@ -20,7 +20,7 @@
   # line styles
   lty=NULL, lwd=par("lwd"), dotted=NULL, 
   # colors
-  col=par("col"), col.names=par("col"), fill=NULL, 
+  col=par("col"), col.names=par("col"), fill=NULL, col.NA="black",
   # labels
   names=NULL, main=NULL, legend.x=NA, format.names=TRUE, adj=0.5, dy=0,
   # plotting controls
@@ -315,8 +315,10 @@
         zs <- out
         for(i in 1:nrow(zs)) zs[i,] <- out[nrow(zs)+1-i,]
         zs <- t(zs)
-        breaks <- c(0,1:nspecies) + 0.5
-        image(x=xs, y=ys, z=zs, col=fill, add=TRUE, breaks=breaks, useRaster=TRUE)
+        breaks <- c(-1, 0, 1:nspecies) + 0.5
+        # use col.NA for NA values
+        zs[is.na(zs)] <- 0
+        image(x=xs, y=ys, z=zs, col=c(col.NA, fill), add=TRUE, breaks=breaks, useRaster=TRUE)
       }
       ## curve plot function
       # 20091116 replaced plot.curve with plot.line; different

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-04-25 11:19:56 UTC (rev 187)
+++ pkg/CHNOSZ/inst/NEWS	2017-04-27 02:30:51 UTC (rev 188)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-76 (2017-04-25)
+CHANGES IN CHNOSZ 1.0.8-77 (2017-04-27)
 ---------------------------------------
 
 DOCUMENTATION:
@@ -161,8 +161,8 @@
   the bug report and test.
 
 - NaN values from equilibrate() are now preserved by diagram(),
-  producing unlabeled blank (white) fields rather than being
-  mistakenly labeled with the first species.
+  producing unlabeled fields rather than being mistakenly labeled with
+  the first species. Thanks to Grayson Boyer for the bug report.
 
 OTHER CHANGES:
 

Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd	2017-04-25 11:19:56 UTC (rev 187)
+++ pkg/CHNOSZ/man/diagram.Rd	2017-04-27 02:30:51 UTC (rev 188)
@@ -14,7 +14,7 @@
     ylog=TRUE, xlim=NULL, ylim=NULL, xlab=NULL, ylab=NULL,
     cex=par("cex"), cex.names=1, cex.axis=par("cex"),
     lty=NULL, lwd=par("lwd"), dotted=NULL,
-    col=par("col"), col.names=par("col"), fill=NULL,
+    col=par("col"), col.names=par("col"), fill=NULL, col.NA="black",
     names=NULL, main=NULL, legend.x=NA, format.names=TRUE, adj=0.5, dy=0,
     add=FALSE, plot.it=TRUE, tplot=TRUE, ...)
   strip(affinity, ispecies = NULL, col = NULL, ns = NULL, 
@@ -48,6 +48,7 @@
   \item{col}{character, color of activity lines (1D diagram) or predominance field boundaries (2D diagram), or colors of bars in a strip diagram (\code{strip})}
   \item{col.names}{character, colors for labels of species}
   \item{fill}{character, colors used to fill predominance fields}
+  \item{col.NA}{character, color for grid points with NA values}
   \item{names}{character, names of species for activity lines or predominance fields}
   \item{main}{character, a main \code{\link{title}} for the plot; \code{NULL} means to plot no title}
   \item{legend.x}{character, description of legend placement passed to \code{\link{legend}}}

Modified: pkg/CHNOSZ/tests/testthat/test-diagram.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-diagram.R	2017-04-25 11:19:56 UTC (rev 187)
+++ pkg/CHNOSZ/tests/testthat/test-diagram.R	2017-04-27 02:30:51 UTC (rev 188)
@@ -85,3 +85,16 @@
   #expect_equal(diagram(a), diagram(a, plot.it=FALSE))
   expect_warning(diagram(a, what="CO2", plot.it=FALSE), "showing only first species in 2-D property diagram")
 })
+
+test_that("NaN values from equilibrate() are preserved (as NA in predominance calculation)", {
+  # example provided by Grayson Boyer 20170411
+  basis(c("H2", "O2", "CO2"), c(-7.19, -60, -2.65))
+  species(c("n-hexadecanol", "n-hexadecanoic acid", "n-octadecanol", "n-octadecanoic acid"), c("liq", "liq", "liq", "liq"))
+  a <- affinity("H2" = c(-12, 0), "O2" = c(-90, -50), T=30)
+  e <- equilibrate(a, balance = 1)
+  d <- diagram(e, plot.it = FALSE)
+  # equilibrate() here with default "boltzmann" method produces
+  # NaN at very high O2 + low H2 or very low O2 + high H2 
+  expect_equal(d$predominant[1, 128], as.numeric(NA))
+  expect_equal(d$predominant[128, 1], as.numeric(NA))
+})