[CHNOSZ-commits] r731 - in pkg/CHNOSZ: . R inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jun 20 11:04:39 CEST 2022
Author: jedick
Date: 2022-06-20 11:04:39 +0200 (Mon, 20 Jun 2022)
New Revision: 731
Added:
pkg/CHNOSZ/R/stack_mosaic.R
pkg/CHNOSZ/man/stack_mosaic.Rd
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/NAMESPACE
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/man/mosaic.Rd
pkg/CHNOSZ/vignettes/multi-metal.Rmd
Log:
Add stack_mosaic()
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2022-06-20 05:41:11 UTC (rev 730)
+++ pkg/CHNOSZ/DESCRIPTION 2022-06-20 09:04:39 UTC (rev 731)
@@ -1,6 +1,6 @@
Date: 2022-06-20
Package: CHNOSZ
-Version: 1.9.9-23
+Version: 1.9.9-24
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/NAMESPACE
===================================================================
--- pkg/CHNOSZ/NAMESPACE 2022-06-20 05:41:11 UTC (rev 730)
+++ pkg/CHNOSZ/NAMESPACE 2022-06-20 09:04:39 UTC (rev 731)
@@ -58,7 +58,9 @@
# added 20220324
"logB_to_OBIGT",
# added 20220416
- "rank_affinity"
+ "rank_affinity",
+# added 20220620
+ "stack_mosaic", "add_alpha"
)
# Load shared objects
@@ -68,7 +70,7 @@
# Imports from default packages
importFrom("grDevices", "dev.cur", "dev.off", "extendrange",
"heat.colors", "png", "rainbow", "topo.colors", "dev.list",
- "contourLines")
+ "contourLines", "col2rgb", "rgb")
importFrom("graphics", "abline", "axTicks", "axis", "barplot", "box",
"contour", "image", "legend", "lines", "mtext", "par", "plot",
"plot.new", "plot.window", "points", "rect", "text", "title")
Added: pkg/CHNOSZ/R/stack_mosaic.R
===================================================================
--- pkg/CHNOSZ/R/stack_mosaic.R (rev 0)
+++ pkg/CHNOSZ/R/stack_mosaic.R 2022-06-20 09:04:39 UTC (rev 731)
@@ -0,0 +1,56 @@
+# CHNOSZ/stack_mosaic.R
+
+# Function to create mosaic stack 20220617
+# Adapted from vignettes/multi-metal.Rmd
+# col: Colors for species1, species2, and species12
+# (default of NA for col[3] means to plot species12 boundaries with color for species2)
+# ...: Arguments for mosaic() (incl. affinity() arguments)
+stack_mosaic <- function(bases, species1, species2, species12, names = NULL, col = list(4, 3, 6), col.names = list(4, 3, 6),
+ fill = NULL, dx = list(0, 0, 0), dy = list(0, 0, 0), srt = list(0, 0, 0), lwd = list(1, 1, 1), lty = list(1, 1, 1), ...) {
+
+ # Default is to use semi-transparent fill for bimetallic species
+ if(is.null(fill)) fill <- list(NA, NA, add_alpha(col.names[3], "50"))
+
+ # Load species1 (first metal-bearing species)
+ species(species1)
+ # Calculate affinity of species1 while speciating bases (e.g. aqueous S species)
+ mosaic1 <- mosaic(bases, ...)
+ # Show predominance fields
+ diagram1 <- diagram(mosaic1$A.species, names = names[[1]], col = col[[1]], col.names = col.names[[1]], fill = fill[[1]],
+ dx = dx[[1]], dy = dy[[1]], srt = srt[[1]], lwd = lwd[[1]], lty = lty[[1]])
+
+ # Load species12 (bimetallic species) and species2 (second metal-bearing species)
+ species(c(species12, species2))
+ # Speciate bases again (NULL)
+ # Take the predominant members of species1 (diagram1$predominant)
+ mosaic2 <- mosaic(list(bases, species1), stable = list(NULL, diagram1$predominant), ...)
+ # Set colors
+ col <- c(rep_len(col[[3]], length(species12)), rep_len(col[[2]], length(species2)))
+ col.names <- c(rep_len(col.names[[3]], length(species12)), rep_len(col.names[[2]], length(species2)))
+ # For NULL names, use the species names
+ if(is.null(names[[3]])) names[[3]] <- species12
+ if(is.null(names[[2]])) names[[2]] <- species2
+ names <- c(names[[3]], names[[2]])
+ # Set other parameters
+ dx <- c(rep_len(dx[[3]], length(species12)), rep_len(dx[[2]], length(species2)))
+ dy <- c(rep_len(dy[[3]], length(species12)), rep_len(dy[[2]], length(species2)))
+ srt <- c(rep_len(srt[[3]], length(species12)), rep_len(srt[[2]], length(species2)))
+ lwd <- c(rep_len(lwd[[3]], length(species12)), rep_len(lwd[[2]], length(species2)))
+ lty <- c(rep_len(lty[[3]], length(species12)), rep_len(lty[[2]], length(species2)))
+ fill <- c(rep_len(fill[[3]], length(species12)), rep_len(fill[[2]], length(species2)))
+ diagram2 <- diagram(mosaic2$A.species, add = TRUE, names = names, col = col, col.names = col.names, fill = fill,
+ dx = dx, dy = dy, srt = srt, lwd = lwd, lty = lty)
+
+ out <- list(diagram1, diagram2)
+ invisible(out)
+
+}
+
+# Function to add transparency to given color 20220223
+add_alpha <- function(col, alpha) {
+ x <- col2rgb(col)
+ newcol <- rgb(x[1], x[2], x[3], maxColorValue = 255)
+ newcol <- paste0(newcol, alpha)
+ newcol
+}
+
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2022-06-20 05:41:11 UTC (rev 730)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2022-06-20 09:04:39 UTC (rev 731)
@@ -10,7 +10,7 @@
\newcommand{\s}{\ifelse{latex}{\eqn{_{#1}}}{\ifelse{html}{\out{<sub>#1</sub>}}{#1}}}
\newcommand{\S}{\ifelse{latex}{\eqn{^{#1}}}{\ifelse{html}{\out{<sup>#1</sup>}}{^#1}}}
-\section{Changes in CHNOSZ version 1.9.9-22 (2022-06-20)}{
+\section{Changes in CHNOSZ version 1.9.9-24 (2022-06-20)}{
\subsection{MAJOR CHANGE}{
\itemize{
@@ -59,33 +59,31 @@
}
}
- \subsection{NEW FEATURES: PROTEINS}{
+ \subsection{NEW FEATURES: DIAGRAMS}{
\itemize{
- \item Add an \strong{as.residue} argument to \code{add.protein()} to
- normalize amino acid compositions by protein length.
+ \item Add \code{stack_mosaic()} to create stacked mosaic diagrams, where
+ the species formed in the first layer become the basis species for the
+ species formed in the second layer. This function implements the main
+ steps for making mosaic diagrams for bimetallic systems described in
+ \strong{multi-metal.Rmd}.
- \item Add a check to \code{add.protein()} that all new protein IDs
- (protein name + organism name) are unique.
-
- \item Add function and demo for \code{rank_affinity()} to calculate (sums
- of ranks of affinities for species in designated groups) normalized by
- number of species in each group. The output of the new function can be
- used by \code{diagram()}.
-
}
}
- \subsection{OTHER CHANGES}{
+ \subsection{NEW FEATURES: PROTEINS}{
\itemize{
- \item Add a \strong{zap} argument to \code{mod.OBIGT()} to clear
- parameters of preexisting species (used by \code{logB_to_OBIGT()}).
+ \item Add function and demo for \code{rank_affinity()} to calculate means
+ of affinity rankings for specified groups of proteins, intended for
+ evolutionary comparisons. The output of the new function can be used by
+ \code{diagram()}.
- \item Change default for \code{affinity()} to \code{loga.protein = 0}
- (was -3).
+ \item Add an \strong{as.residue} argument to \code{add.protein()} to
+ normalize amino acid compositions by protein length.
- \item Change license from GPL (>= 2) to GPL-3.
+ \item Add a check to \code{add.protein()} that all new protein IDs
+ (protein name + organism name) are unique.
}
}
@@ -117,14 +115,14 @@
\item \code{diagram()}: Improve handling of length > 2 \code{col},
\code{lty} and \code{lwd} arguments for predominance diagrams. Because
- field boundaries are drawn for the first species, then removing that
- species before drawing boundaries for the second species, etc., species
- for which different-colored or -styled lines are desired should be placed
- at the top of the species list. This change makes possible one less call
- to \code{diagram()} in the Mosaic Stacking sections in
+ field boundaries are drawn for the first species, then that species is
+ removed before drawing boundaries for the second species, and so on,
+ species for which different-colored or -styled lines are desired should
+ be placed at the top of the species list. This change makes possible one
+ less call to \code{diagram()} in the Mosaic Stacking sections in
\strong{multi-metal.Rmd}, and now the entire chalcopyrite field in Mosaic
- Stacking 2 is bounded by a thick orange line, instead of just the
- border shared with bornite.
+ Stacking 2 is bounded by a thick orange line, instead of just the border
+ shared with bornite.
\item Improve handling of non-integer coefficients in
\code{expr.species()}. The result for FeS1.33 was previously equivalent
@@ -133,6 +131,20 @@
}
}
+ \subsection{OTHER CHANGES}{
+ \itemize{
+
+ \item Add a \strong{zap} argument to \code{mod.OBIGT()} to clear
+ parameters of preexisting species (used by \code{logB_to_OBIGT()}).
+
+ \item Change default for \code{affinity()} to \code{loga.protein = 0}
+ (was -3).
+
+ \item Change license from GPL (>= 2) to GPL-3.
+
+ }
+ }
+
}
\section{Changes in CHNOSZ version 1.4.3 (2022-02-20)}{
Modified: pkg/CHNOSZ/man/mosaic.Rd
===================================================================
--- pkg/CHNOSZ/man/mosaic.Rd 2022-06-20 05:41:11 UTC (rev 730)
+++ pkg/CHNOSZ/man/mosaic.Rd 2022-06-20 09:04:39 UTC (rev 731)
@@ -55,6 +55,7 @@
\seealso{
\code{demo("mosaic")}, which extends the example below with carbonate species in order to plot a siderite field.
To calculate mineral solubilities with mosaic calculations that account for ligand speciation, use \code{bases} as the first argument to \code{\link{solubility}}.
+\code{\link{stack_mosaic}} implements calculations for bimetallic systems.
}
\examples{
Added: pkg/CHNOSZ/man/stack_mosaic.Rd
===================================================================
--- pkg/CHNOSZ/man/stack_mosaic.Rd (rev 0)
+++ pkg/CHNOSZ/man/stack_mosaic.Rd 2022-06-20 09:04:39 UTC (rev 731)
@@ -0,0 +1,106 @@
+\encoding{UTF-8}
+\name{stack_mosaic}
+\alias{stack_mosaic}
+\alias{add_alpha}
+\title{Stacked mosaic diagram}
+\description{
+Create a stacked mosaic diagram, where the species formed in the first layer become the basis species for the species formed in the second layer.
+The species in each layer are usually minerals with different metals; any bimetallic species are added to the second layer.
+}
+
+\usage{
+ stack_mosaic(bases, species1, species2, species12, names = NULL,
+ col = list(4, 3, 6), col.names = list(4, 3, 6), fill = NULL,
+ dx = list(0, 0, 0), dy = list(0, 0, 0), srt = list(0, 0, 0),
+ lwd = list(1, 1, 1), lty = list(1, 1, 1), ...)
+ add_alpha(col, alpha)
+}
+
+\arguments{
+ \item{bases}{basis species to be changed for each layer (commonly S-bearing aqueous species)}
+ \item{species1}{species (minerals and/or aqueous species) with metal 1}
+ \item{species2}{species with metal 2}
+ \item{species12}{bimetallic species}
+ \item{names}{character, species names (or chemical formulas) for labeling fields}
+ \item{col}{line color}
+ \item{col.names}{text color}
+ \item{fill}{field color}
+ \item{dx}{label x-offset}
+ \item{dy}{label y-offset}
+ \item{srt}{label rotation}
+ \item{lwd}{line width}
+ \item{lty}{line type}
+ \item{...}{arguments for \code{\link{mosaic}} and \code{\link{affinity}}}
+ \item{alpha}{character, hexadecimal value of color transparency (alpha)}
+}
+
+\details{
+\code{stack_mosaic} creates a stacked mosaic diagram following steps that are described in detail in the vignette \viglink{multi-metal}.
+Briefly, the first layer of the diagram is made by speciating the species in \code{bases} across the diagram to form the first set of species in \code{species1}.
+Then, both \code{bases} \emph{and} \code{species1} (the stable species at each point on the diagram) are used to form the second set of species, consisting of both \code{species2} \emph{and} \code{species12}.
+
+The plot parameters \code{col}, \code{col.names}, \code{fill}, \code{dx}, \code{dy}, \code{srt}, \code{lwd}, and \code{lty} should be length-3 lists (not vectors).
+The values of elements 1--3 of the list are recycled to the number of species in \code{species1}, \code{species2}, and \code{species12}, respectively.
+
+For \code{fill}, the default is to use no fill except for \code{species12}, where the fill color is taken from \code{col.names} with added transparency.
+The default definition of \code{fill} is \code{list(NA, NA, add_alpha(col.names[3], "50"))}.
+\code{add_alpha} adds transparency to a color by appending the value of \code{alpha} to the hexadecimal representation of the color given in \code{col}.
+}
+
+\section{Warning}{
+The bimetallic species in \code{species12} are shown as part of the second layer, although their formation is sensitive to the presence of stable species in the first layer.
+It follows that changing the order of layers (i.e., swapping \code{species1} and \code{species2}) can affect the depiction of mineral assemblages that have \code{species12}.
+Only one of the alternatives is thermodynamically correct, but currently there is no check to determine which one it is.
+}
+
+\value{
+A list of length two containing the output of each of the \code{\link{diagram}} calls use to make the diagram.
+}
+
+\examples{
+# Define temperature (degrees C), pressure (bar), pH and logfO2 ranges
+T <- 200
+P <- "Psat"
+res <- 200
+pH <- c(0, 14, res)
+O2 <- c(-48, -33, res)
+
+# Define system: Fe-Cu-O-S-Cl
+# NOTE: the basis species must include the first species listed
+# in each of bases, species1, and species2 below
+basis(c("pyrite", "Cu", "Cl-", "H2S", "H2O", "oxygen", "H+"))
+basis("H2S", -2)
+# Calculate solution composition for 1 mol/kg NaCl
+NaCl <- NaCl(T = T, P = P, m_tot=1)
+basis("Cl-", log10(NaCl$m_Cl))
+
+# Define arguments for stack_mosaic: Speciate aqueous sulfur
+bases <- c("H2S", "HS-", "HSO4-", "SO4-2")
+# Calculate stabilities of Fe-bearing minerals first
+species1 <- c("pyrite", "pyrrhotite", "magnetite", "hematite")
+# Calculate stabilities of Cu-bearing and FeCu-bearing minerals second
+species2 <- c("copper", "cuprite", "tenorite", "chalcocite", "covellite")
+species12 <- c("chalcopyrite", "bornite")
+# Use abbreviations for Fe-bearing minerals and formulas for Cu-bearing minerals
+names1 <- c("Py", "Po", "Mag", "Hem")
+names2 <- info(info(species2))$formula
+names12 <- info(info(species12))$formula
+names <- list(names1, names2, names12)
+# Adjust x-position for one species (chalcocite, Cu2S)
+dx <- list(c(0, 0, 0, 0), c(0, 0, 0, 1, 0), c(0, 0))
+# Use thick dashed lines for the bimetallic species
+lwd <- list(1, 1, 2)
+lty <- list(1, 1, 2)
+
+# Make the diagram
+stack_mosaic(bases, species1, species2, species12, names = names,
+ dx = dx, lwd = lwd, lty = lty,
+ pH = pH, O2 = O2, T = T, P = P, IS = NaCl$IS)
+# Add legend and title
+lTP <- lex(lTP(T, P))
+db <- describe.basis(ibasis = c(3:4))
+legend("topright", c(lTP, db), bg = "white")
+title("Fe-Cu-S-O-H-Cl", font.main = 1)
+}
+
+\concept{Extended workflow}
Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd 2022-06-20 05:41:11 UTC (rev 730)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd 2022-06-20 09:04:39 UTC (rev 731)
@@ -446,6 +446,8 @@
## Mosaic Stacking 1
+*For a function that implements the workflow described below, see `stack_mosaic()` (added in CHNOSZ 2.0.0).*
+
A mosaic diagram shows the effects of changing basis species on the stabilities of minerals.
The Fe-S-O-H system is a common example: the speciation of aqueous sulfur species affects the stabilities of iron oxides and sulfides.
Examples of mosaic diagrams with Fe or other single metals are given elsewhere.
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