[CHNOSZ-commits] r801 - in pkg/CHNOSZ: . demo inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Sep 1 07:29:36 CEST 2023
Author: jedick
Date: 2023-09-01 07:29:35 +0200 (Fri, 01 Sep 2023)
New Revision: 801
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/demo/DEW.R
pkg/CHNOSZ/demo/NaCl.R
pkg/CHNOSZ/demo/Shh.R
pkg/CHNOSZ/demo/TCA.R
pkg/CHNOSZ/demo/adenine.R
pkg/CHNOSZ/demo/affinity.R
pkg/CHNOSZ/demo/buffer.R
pkg/CHNOSZ/demo/copper.R
pkg/CHNOSZ/demo/dehydration.R
pkg/CHNOSZ/demo/density.R
pkg/CHNOSZ/demo/ionize.R
pkg/CHNOSZ/demo/lambda.R
pkg/CHNOSZ/demo/protbuff.R
pkg/CHNOSZ/demo/protein.equil.R
pkg/CHNOSZ/demo/rank.affinity.R
pkg/CHNOSZ/demo/sources.R
pkg/CHNOSZ/inst/NEWS.Rd
Log:
Add file names to demos
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/DESCRIPTION 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,6 +1,6 @@
-Date: 2023-08-22
+Date: 2023-09-01
Package: CHNOSZ
-Version: 2.0.0-20
+Version: 2.0.0-21
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/demo/DEW.R
===================================================================
--- pkg/CHNOSZ/demo/DEW.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/DEW.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/DEW.R
# Demo for the Deep Earth Water (DEW) model in CHNOSZ 20170927
library(CHNOSZ)
Modified: pkg/CHNOSZ/demo/NaCl.R
===================================================================
--- pkg/CHNOSZ/demo/NaCl.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/NaCl.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/NaCl.R
## NaCl dissocation logK f(T,P)
## after Shock et al., 1992, Fig. 1
## (Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (1992)
Modified: pkg/CHNOSZ/demo/Shh.R
===================================================================
--- pkg/CHNOSZ/demo/Shh.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/Shh.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/Shh.R
# Compare affinities of Sonic hedgehog and transcription factors involved in dorsal-ventral patterning
# (Dick, 2015. Chemical integration of proteins in signaling and development. https://doi.org/10.1101/015826)
library(CHNOSZ)
Modified: pkg/CHNOSZ/demo/TCA.R
===================================================================
--- pkg/CHNOSZ/demo/TCA.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/TCA.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,4 +1,4 @@
-# TCA.R 20171010
+# CHNOSZ/demo/TCA.R 20171010
# Reproduce Fig. 6 in Canovas and Shock, 2016:
# Plots of the standard partial molal Gibbs energy of reaction for each step in
# the citric acid cycle for temperatures to 500 degrees C and pressures to 5 kbar.
Modified: pkg/CHNOSZ/demo/adenine.R
===================================================================
--- pkg/CHNOSZ/demo/adenine.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/adenine.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,4 +1,4 @@
-# CHNOSZ/demos/adenine.R
+# CHNOSZ/demo/adenine.R
# Plot thermodynamic data and model fits for aqueous adenine 20170725
library(CHNOSZ)
Modified: pkg/CHNOSZ/demo/affinity.R
===================================================================
--- pkg/CHNOSZ/demo/affinity.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/affinity.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/affinity.R
## Affinities of metabolic reactions
## After Amend and Shock, 2001, Fig. 7
## Amend, J. P. and Shock, E. L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria.
Modified: pkg/CHNOSZ/demo/buffer.R
===================================================================
--- pkg/CHNOSZ/demo/buffer.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/buffer.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,4 +1,4 @@
-# demos/buffer.R
+# CHNOSZ/demo/buffer.R
# Calculate buffered activities of basis species using two methods
# Ater Figure 6 of Schulte and Shock, 1995 (doi:10.1007/BF01581580)
library(CHNOSZ)
Modified: pkg/CHNOSZ/demo/copper.R
===================================================================
--- pkg/CHNOSZ/demo/copper.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/copper.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/copper.R
## Eh-pH diagrams for copper-water-glycine
## After Fig. 2 of Aksu and Doyle, 2001
## (Aksu, S. and Doyle, F. M., 2001. Electrochemistry of copper in aqueous glycine
Modified: pkg/CHNOSZ/demo/dehydration.R
===================================================================
--- pkg/CHNOSZ/demo/dehydration.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/dehydration.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/dehydration.R
# Plot temperature dependence of log K for some dehydration reactions
library(CHNOSZ)
Modified: pkg/CHNOSZ/demo/density.R
===================================================================
--- pkg/CHNOSZ/demo/density.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/density.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/density.R
# Make T-P diagram for H2O, colored according to density
library(CHNOSZ)
Modified: pkg/CHNOSZ/demo/ionize.R
===================================================================
--- pkg/CHNOSZ/demo/ionize.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/ionize.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/ionize.R
## ionize.aa(): Contour plots of net charge and ionization properties of LYSC_CHICK
library(CHNOSZ)
Modified: pkg/CHNOSZ/demo/lambda.R
===================================================================
--- pkg/CHNOSZ/demo/lambda.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/lambda.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/lambda.R
# Plot effects of lambda transition in quartz
# After Berman 1988 Figs. 1 and 2
library(CHNOSZ)
Modified: pkg/CHNOSZ/demo/protbuff.R
===================================================================
--- pkg/CHNOSZ/demo/protbuff.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/protbuff.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/protbuff.R
## Buffer + ionization: Metastablilities of
## thiol peroxidases from model bactera
## (ECOLI, BACSU mesophile; AQUAE thermophile,
Modified: pkg/CHNOSZ/demo/protein.equil.R
===================================================================
--- pkg/CHNOSZ/demo/protein.equil.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/protein.equil.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/protein.equil.R
## Steps in calculation of chemical activities of two proteins
## in metastable equilibrium, after Dick and Shock, 2011
library(CHNOSZ)
Modified: pkg/CHNOSZ/demo/rank.affinity.R
===================================================================
--- pkg/CHNOSZ/demo/rank.affinity.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/rank.affinity.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/rank.affinity.R
## Affinity ranking for proteins coded by differentially expressed
## genes in response to carbon limitation in yeast
# Demo written on 20220620
Modified: pkg/CHNOSZ/demo/sources.R
===================================================================
--- pkg/CHNOSZ/demo/sources.R 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/demo/sources.R 2023-09-01 05:29:35 UTC (rev 801)
@@ -1,3 +1,4 @@
+# CHNOSZ/demo/sources.R
## Cross-checking sources
library(CHNOSZ)
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2023-08-21 23:56:37 UTC (rev 800)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2023-09-01 05:29:35 UTC (rev 801)
@@ -33,8 +33,9 @@
appropriate argument names for basis species and adjusts the labels for
the diagram (\dQuote{total C}, \dQuote{total S}, etc.).
- \item Fix bug where \code{exceed.Ttr} argument in \code{subcrt()} was
- stuck at FALSE for automatically balanced reactions.
+ \item Fix bug in \code{subcrt()} for \code{exceed.Ttr} not applied to
+ automatically balanced reactions (it was stuck on FALSE regardless of the
+ argument value).
}
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