diff --git a/DESCRIPTION b/DESCRIPTION index 56dc8e9..9203804 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Date: 2024-11-17 Package: CHNOSZ -Version: 2.1.0-20 +Version: 2.1.0-21 Title: Thermodynamic Calculations and Diagrams for Geochemistry Authors@R: c( person("Jeffrey", "Dick", , "j3ffdick@gmail.com", role = c("aut", "cre"), diff --git a/R/examples.R b/R/examples.R index 164ac50..6ee7d90 100644 --- a/R/examples.R +++ b/R/examples.R @@ -34,7 +34,7 @@ demos <- function(which = c("sources", "protein.equil", "affinity", "NaCl", "den "ORP", "ionize", "buffer", "protbuff", "glycinate", "mosaic", "copper", "arsenic", "solubility", "gold", "contour", "sphalerite", "minsol", "Shh", "saturation", "adenine", "DEW", "lambda", "potassium", "TCA", "aluminum", - "AD", "comproportionation", "Pourbaix", "E_coli", "yttrium", "rank.affinity", "uranium"), + "AD", "comproportionation", "Pourbaix", "E_coli", "yttrium", "rank.affinity", "uranyl"), save.png = FALSE) { # Run one or more demos from CHNOSZ with ask = FALSE, and return the value of the last one out <- NULL diff --git a/demo/00Index b/demo/00Index index e19139b..7ac447e 100644 --- a/demo/00Index +++ b/demo/00Index @@ -33,4 +33,4 @@ Pourbaix Eh-pH diagram for Fe-O-H with equisolubility lines E_coli Gibbs energy of biomass synthesis in E. coli rank.affinity Affinity ranking for proteins in yeast nutrient limitation yttrium logB.to.OBIGT fits at 800 and 1000 bar and Y speciation in NaCl solution at varying pH -uranium Total (carbonate|sulfate)-pH diagrams for uranium +uranyl Total (carbonate|sulfate)-pH diagrams for uranyl species diff --git a/demo/uranium.R b/demo/uranyl.R similarity index 93% rename from demo/uranium.R rename to demo/uranyl.R index 94f87e5..a04c43d 100644 --- a/demo/uranium.R +++ b/demo/uranyl.R @@ -1,5 +1,5 @@ -# CHNOSZ/demo/uranium.R -# Total (carbonate|sulfate)-pH diagrams for U, after Migdisov et al., 2024 +# CHNOSZ/demo/uranyl.R +# Total (carbonate|sulfate)-pH diagrams for uranyl species, after Migdisov et al., 2024 # 20241116 jmd library(CHNOSZ) diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd index 95c3264..283a9aa 100644 --- a/inst/NEWS.Rd +++ b/inst/NEWS.Rd @@ -15,7 +15,7 @@ \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{CP}}{Cp}}} \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{ΔG°}}{ΔG°}}} -\section{Changes in CHNOSZ version 2.1.0-20 (2024-11-17)}{ +\section{Changes in CHNOSZ version 2.1.0-21 (2024-11-17)}{ \itemize{ @@ -52,8 +52,8 @@ \item OBIGT: Fix sign of \emph{c} parameter for nesquehonite. Thanks to James Leong and Grayson Boyer. - \item Add \file{demo/uranium.R}, total (carbonate|sulfate)-pH diagrams - for uranium, after + \item Add \file{demo/uranyl.R}, total (carbonate|sulfate)-pH diagrams + for uranyl species, after \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}. } diff --git a/man/examples.Rd b/man/examples.Rd index 3f64e98..1bb3976 100644 --- a/man/examples.Rd +++ b/man/examples.Rd @@ -65,7 +65,7 @@ The demo(s) to run is/are specified by \code{which}; the default is to run them \item{E_coli}{Gibbs energy of biomass synthesis in \emph{E. coli} (LaRowe and Amend, 2016)} \item{rank.affinity}{Affinity ranking for proteins in yeast nutrient limitation (data from Tai et al., 2005)} \item{yttrium}{\code{\link{logB.to.OBIGT}} fits at 800 and 1000 bar and Y speciation in \code{\link{NaCl}} solution at varying pH (Guan et al., 2020)} - \item{uranium}{Total (carbonate|sulfate)-pH diagrams for uranium (Migdisov et al., 2024)} + \item{uranyl}{Total (carbonate|sulfate)-pH diagrams for uranyl species (Migdisov et al., 2024)} } For either function, if \code{save.png} is TRUE, the plots are saved in \code{\link{png}} files whose names begin with the names of the help topics or demos.