[CHNOSZ-commits] r844 - in pkg/CHNOSZ: . R inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jun 16 08:15:33 CEST 2024
Author: jedick
Date: 2024-06-16 08:15:32 +0200 (Sun, 16 Jun 2024)
New Revision: 844
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/diagram.R
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/man/diagram.Rd
Log:
Restore 'lines' to the output of diagram()
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2024-06-04 06:36:15 UTC (rev 843)
+++ pkg/CHNOSZ/DESCRIPTION 2024-06-16 06:15:32 UTC (rev 844)
@@ -1,6 +1,6 @@
Date: 2024-06-04
Package: CHNOSZ
-Version: 2.1.0-16
+Version: 2.1.0-17
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/diagram.R
===================================================================
--- pkg/CHNOSZ/R/diagram.R 2024-06-04 06:36:15 UTC (rev 843)
+++ pkg/CHNOSZ/R/diagram.R 2024-06-16 06:15:32 UTC (rev 844)
@@ -484,6 +484,7 @@
zs[is.na(zs)] <- 0
image(x = xs, y = ys, z = zs, col = c(fill.NA, fill), add = TRUE, breaks = breaks, useRaster = TRUE)
}
+
## Curve plot function
# 20091116 replaced plot.curve with plot.line; different name, same functionality, *much* faster
plot.line <- function(out, xlim, ylim, dotted, col, lwd, xrange) {
@@ -553,6 +554,7 @@
if(!is.null(xrange)) xs <- clipfun(xs, xrange)
lines(xs, ys, col = col, lwd = lwd)
}
+
## New line plotting function 20170122
contour.lines <- function(predominant, xlim, ylim, lty, col, lwd) {
# The x and y values
@@ -569,6 +571,10 @@
}
# The categories (species/groups/etc) on the plot
zvals <- na.omit(unique(as.vector(predominant)))
+
+ # Initialize list and counter for line x,y values 20240615
+ linesout <- list()
+ iout <- 1
if(is.null(lty.aq) & is.null(lty.cr)) {
@@ -585,6 +591,13 @@
for(k in 1:length(cLines)) {
# Draw the lines
lines(cLines[[k]][2:3], lty = lty[zvals[i]], col = col[zvals[i]], lwd = lwd[zvals[i]])
+
+ # Store the x and y values (list components 2 and 3)
+ linesout[[iout]] <- cLines[[k]][[2]]
+ names(linesout)[iout] <- paste0("x", k, "_", zvals[i])
+ linesout[[iout+1]] <- cLines[[k]][[3]]
+ names(linesout)[iout+1] <- paste0("y", k, "_", zvals[i])
+ iout <- iout + 2
}
}
# Mask species to prevent double-plotting contour lines
@@ -619,6 +632,14 @@
if(all(grepl("aq", eout$species$state[c(zvals[i], zvals[j])]))) mylty <- lty.aq
}
lines(cLines[[k]][2:3], lty = mylty, col = col[zvals[i]], lwd = lwd[zvals[i]])
+
+ # Store the x and y values (list components 2 and 3)
+ linesout[[iout]] <- cLines[[k]][[2]]
+ names(linesout)[iout] <- paste0("x", k, "_", zvals[i], ".", zvals[j])
+ linesout[[iout+1]] <- cLines[[k]][[3]]
+ names(linesout)[iout+1] <- paste0("y", k, "_", zvals[i], ".", zvals[j])
+ iout <- iout + 2
+
}
}
}
@@ -626,7 +647,13 @@
}
+ # Return x,y coordinates of lines padded to equal length
+ # https://stackoverflow.com/questions/34570860/adding-na-to-make-all-list-elements-equal-length 20181029
+ # For compatibility with R 3.1.0, don't use lengths() here 20190302
+ lapply(linesout, `length<-`, max(sapply(linesout, length)))
+
}
+
## To add labels
plot.names <- function(out, xs, ys, xlim, ylim, names, srt, min.area) {
# Calculate coordinates for field labels
@@ -716,6 +743,10 @@
# Add a title
if(!is.null(main)) title(main = main)
}
+
+ # Start with NA value for x,y locations of lines
+ linesout <- NA
+
if(identical(predominant, NA)) {
# No predominance matrix, so we're contouring properties
@@ -735,10 +766,8 @@
message("diagram: beyond range for saturation line of ", names[i])
next
}
-print(drawlabels)
if(drawlabels) contour(xs, ys, zs, add = TRUE, col = col, lty = lty, lwd = lwd, labcex = cex, levels = 0, labels = names[i], method = contour.method[i])
else contour(xs, ys, zs, add = TRUE, col = col, lty = lty, lwd = lwd, labcex = cex, levels = 0, labels = names[i], drawlabels = FALSE)
-print('hello')
}
} else {
# Contour solubilities (loga.balance), or properties using first species only
@@ -752,6 +781,7 @@
else contour(xs, ys, zs, add = TRUE, col = col, lty = lty, lwd = lwd, labcex = cex, levels = levels, drawlabels = FALSE)
}
}
+ # Keep the x,y coordinates of the names around to add to the output
pn <- list(namesx = NULL, namesy = NULL)
} else {
@@ -775,7 +805,7 @@
# font metric state and subsequent errors adding e.g. subscripted text to plot)
if(length(na.omit(unique(as.vector(zs)))) > 1) {
if(!is.null(dotted)) plot.line(zs, xlim.calc, ylim.calc, dotted, col, lwd, xrange = xrange)
- else contour.lines(predominant, xlim.calc, ylim.calc, lty = lty, col = col, lwd = lwd)
+ else linesout <- contour.lines(predominant, xlim.calc, ylim.calc, lty = lty, col = col, lwd = lwd)
}
# Re-draw the tick marks and axis lines in case the fill obscured them
has.color <- FALSE
@@ -786,8 +816,11 @@
thermo.axis()
box()
}
- } # Done with the 2D plot!
- out2D <- list(namesx = pn$namesx, namesy = pn$namesy)
+ }
+
+ # Done with the 2D plot!
+ out2D <- list(namesx = pn$namesx, namesy = pn$namesy, linesout = linesout)
+
} # end if(nd == 2)
} # end if(plot.it)
Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2024-06-04 06:36:15 UTC (rev 843)
+++ pkg/CHNOSZ/R/examples.R 2024-06-16 06:15:32 UTC (rev 844)
@@ -6,7 +6,7 @@
.ptime <- proc.time()
topics <- c("thermo", "examples",
"util.array", "util.data", "util.expression", "util.legend", "util.plot",
- "util.fasta", "util.formula", "util.misc", "util.seq", "util.units",
+ "util.formula", "util.misc", "util.seq", "util.units",
"util.water", "taxonomy", "info", "retrieve", "add.OBIGT", "protein.info",
"water", "IAPWS95", "subcrt", "Berman",
"makeup", "basis", "swap.basis", "species", "affinity",
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2024-06-04 06:36:15 UTC (rev 843)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2024-06-16 06:15:32 UTC (rev 844)
@@ -15,7 +15,7 @@
\newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{<I>C<sub>P</sub></I>}}{Cp}}}
\newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{Δ<I>G</I>°}}{ΔG°}}}
-\section{Changes in CHNOSZ version 2.1.0-15 (2024-05-22)}{
+\section{Changes in CHNOSZ version 2.1.0-17 (2024-06-15)}{
\itemize{
@@ -44,6 +44,10 @@
chromite (FeCr\s{2}O\s{4}) from
\href{https://doi.org/10.3133/b2131}{Robie and Hemingway (1995)}.
+ \item Add \file{demo/total_S.R} (total activity of S--pH diagram for Fe-S-O-C minerals).
+
+ \item Restore \code{lines} to the output of \code{diagram()} for the x and y values of predominance field boundaries.
+
}
}
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2024-06-04 06:36:15 UTC (rev 843)
+++ pkg/CHNOSZ/man/diagram.Rd 2024-06-16 06:15:32 UTC (rev 844)
@@ -206,6 +206,7 @@
For 2-D diagrams, \code{plotvals} corresponds to the values of affinity (from \code{eout$values}) divided by the respective balancing coefficients for each species.
For 2-D diagrams, the output also contains the matrices \code{predominant}, which identifies the predominant species in \code{eout$species} at each grid point, and \code{predominant.values}, which has the affinities of the predominant species divided by the balancing coefficients (if \code{eout} is the output of \code{affinity}) or the activities of the predominant species (if \code{eout} is the output of \code{equilibrate}).
The rows and columns of these matrices correspond to the \emph{x} and \emph{y} variables, respectively.
+ Finally, the output for 2-D diagrams contains a \code{lines} component, giving the x- and y-coordinates of the field boundaries computed using \code{\link{contourLines}}; the values are padded to equal length with NAs to faciliate exporting the results using \code{\link{write.csv}}.
}
More information about the CHNOSZ-commits
mailing list