[CHNOSZ-commits] r614 - in pkg/CHNOSZ: . inst inst/extdata man vignettes

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

Author: jedick
Date: 2020-11-05 04:43:05 +0100 (Thu, 05 Nov 2020)
New Revision: 614

Removed:
   pkg/CHNOSZ/inst/extdata/supcrt/
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/TODO
   pkg/CHNOSZ/man/extdata.Rd
   pkg/CHNOSZ/vignettes/multi-metal.Rmd
Log:
Remove extdata/supcrt (scripts to read SUPCRT data files)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2020-11-04 01:29:33 UTC (rev 613)
+++ pkg/CHNOSZ/DESCRIPTION	2020-11-05 03:43:05 UTC (rev 614)
@@ -1,6 +1,6 @@
-Date: 2020-11-04
+Date: 2020-11-05
 Package: CHNOSZ
-Version: 1.3.6-87
+Version: 1.3.6-88
 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/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2020-11-04 01:29:33 UTC (rev 613)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2020-11-05 03:43:05 UTC (rev 614)
@@ -9,7 +9,7 @@
 \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 1.3.6-86 (2020-11-04)}{
+\section{Changes in CHNOSZ version 1.3.6-88 (2020-11-05)}{
 
   \subsection{MAJOR CHANGES}{
     \itemize{
@@ -256,6 +256,8 @@
       \item Change defaults in \code{mod.buffer()} to be more suitable for
       mineral buffers (\code{state = "cr"} and \code{logact = 0}).
 
+      \item Remove extdata/supcrt (scripts to read SUPCRT data files).
+
       \item Convert this NEWS file to Rd format.
 
     }

Modified: pkg/CHNOSZ/inst/TODO
===================================================================
--- pkg/CHNOSZ/inst/TODO	2020-11-04 01:29:33 UTC (rev 613)
+++ pkg/CHNOSZ/inst/TODO	2020-11-05 03:43:05 UTC (rev 614)
@@ -1,9 +1,5 @@
-- fix error in expr.species("AsO4---")
-
 - make a site for community uploaded data
 
-- refresh extdata/supcrt/compare.R
-
 - make separate directories for default and optional data files
 
 - diagram(): make error or warning for NA values of affinity

Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd	2020-11-04 01:29:33 UTC (rev 613)
+++ pkg/CHNOSZ/man/extdata.Rd	2020-11-05 03:43:05 UTC (rev 614)
@@ -55,14 +55,6 @@
       These are various subunits of the Poliovirus type 1 polyprotein (POLG_POL1M in UniProt).
   }
 
-
-  Files in \code{supcrt} contain scripts for reading and comparing SUPCRT files (including slop98.dat and newer slop files from GEOPIG (http://geopig.asu.edu)) with the database in CHNOSZ:
-  \itemize{
-    \item \code{read.supcrt.R} defines the function \code{read.supcrt} that can be used to read SUPCRT files.
-    \item \code{compare.R} uses \code{read.supcrt} to compare data in the SUPCRT file with that in \code{thermo()$OBIGT}.
-    \item \code{newnames.csv} maps names generated by \code{read.supcrt}, based on names present in the source SUPCRT files, to names used in \code{thermo()$OBIGT}.
-  }
-
   Files in \code{taxonomy} contain taxonomic data files:
   \itemize{
     \item \code{names.dmp} and \code{nodes.dmp} are excerpts of the taxonomy files available on the NCBI ftp site (\url{ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz}, accessed 2010-02-15). These files contain only the entries for \emph{Escherichia coli} K-12, \emph{Saccharomyces cerevisiae}, \emph{Homo sapiens}, \emph{Pyrococcus furisosus} and \emph{Methanocaldococcus jannaschii} (taxids 83333, 4932, 9606, 186497, 243232) and the higher-ranking nodes (genus, family, etc.) in the respective lineages. See \code{\link{taxonomy}} for examples that use these files.

Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd	2020-11-04 01:29:33 UTC (rev 613)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd	2020-11-05 03:43:05 UTC (rev 614)
@@ -99,7 +99,7 @@
 dS <- diagram(aS, add = TRUE, col = 4, col.names = 4)
 aCS <- flatten(dC, dS)
 diagram(aCS)
-legend("topright", legend = lTP(25, 1))
+legend("topright", legend = lTP(25, 1), bty = "n")
 ```
 
 The second diagram is just like the first, except the function `flatten()` is used to label the fields with names of species from both systems, and a legend is added to indicate the temperature and pressure.
@@ -275,7 +275,7 @@
 basis(c("VO+2", "Fe+2", "H2O", "e-", "H+"))
 species(c(iFe.aq, iFe.cr))$name
 species(1:length(iFe.aq), loga.Fe)
-aFe <- affinity(pH = c(0, 14), Eh = c(-1.5, 2))
+aFe <- affinity(pH = c(0, 14, 400), Eh = c(-1.5, 2, 400))
 dFe <- diagram(aFe, plot.it = FALSE)
 # V-bearing species
 species(c(iV.aq, iV.cr))$name