[CHNOSZ-commits] r621 - in pkg/CHNOSZ: . man vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Nov 10 11:40:16 CET 2020 

Author: jedick
Date: 2020-11-10 11:40:16 +0100 (Tue, 10 Nov 2020)
New Revision: 621

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/man/diagram.Rd
   pkg/CHNOSZ/man/examples.Rd
   pkg/CHNOSZ/vignettes/anintro.Rmd
   pkg/CHNOSZ/vignettes/eos-regress.Rmd
Log:
More URL fixes


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2020-11-10 07:40:30 UTC (rev 620)
+++ pkg/CHNOSZ/DESCRIPTION	2020-11-10 10:40:16 UTC (rev 621)
@@ -1,6 +1,6 @@
 Date: 2020-11-10
 Package: CHNOSZ
-Version: 1.3.6-94
+Version: 1.3.6-95
 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/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd	2020-11-10 07:40:30 UTC (rev 620)
+++ pkg/CHNOSZ/man/diagram.Rd	2020-11-10 10:40:16 UTC (rev 621)
@@ -295,7 +295,7 @@
 
 \references{
 
-Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. \emph{J. Electrochem. Soc.} \bold{148}, B51--B57. \url{https://doi.org/10.1149/1.1344532}
+Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. \emph{J. Electrochem. Soc.} \bold{148}, B51--B57.
 
 Dick, J. M. (2019) CHNOSZ: Thermodynamic calculations and diagrams for geochemistry. \emph{Front. Earth Sci.} \bold{7}:180. \url{https://doi.org/10.3389/feart.2019.00180}
 

Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd	2020-11-10 07:40:30 UTC (rev 620)
+++ pkg/CHNOSZ/man/examples.Rd	2020-11-10 10:40:16 UTC (rev 621)
@@ -91,7 +91,7 @@
 
 Akinfiev, N. N. and Zotov, A. V. (2001) Thermodynamic description of chloride, hydrosulfide, and hydroxo complexes of Ag(I), Cu(I), and Au(I) at temperatures of 25-500\degC and pressures of 1-2000 bar. \emph{Geochem. Int.} \bold{39}, 990--1006.
 
-Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. \emph{J. Electrochem. Soc.} \bold{148}, B51--B57. \url{https://doi.org/10.1149/1.1344532}
+Aksu, S. and Doyle, F. M. (2001) Electrochemistry of copper in aqueous glycine solutions. \emph{J. Electrochem. Soc.} \bold{148}, B51--B57.
 
 Amend, J. P. and Shock, E. L. (1998) Energetics of amino acid synthesis in hydrothermal ecosystems. \emph{Science} \bold{281}, 1659--1662. \url{https://doi.org/10.1126/science.281.5383.1659}
 

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2020-11-10 07:40:30 UTC (rev 620)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2020-11-10 10:40:16 UTC (rev 621)
@@ -117,7 +117,7 @@
 
 # Overview
 
-This vignette was made for version `r sessionInfo()$otherPkgs$CHNOSZ$Version` of CHNOSZ, a package for the [R software environment](http://www.r-project.org/).
+This vignette was made for version `r sessionInfo()$otherPkgs$CHNOSZ$Version` of CHNOSZ, a package for the [R software environment](https://www.r-project.org/).
 For more information on R, see "[An Introduction to R](https://cran.r-project.org/manuals.html)" and the [contributed documentation](https://cran.r-project.org/other-docs.html) for R.
 
 CHNOSZ has been developed since 2006 as a tool for thermodynamic calculations in geochemistry and compositional biology.

Modified: pkg/CHNOSZ/vignettes/eos-regress.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/eos-regress.Rmd	2020-11-10 07:40:30 UTC (rev 620)
+++ pkg/CHNOSZ/vignettes/eos-regress.Rmd	2020-11-10 10:40:16 UTC (rev 621)
@@ -445,7 +445,7 @@
 For example, the almost 200 cal/mol offset in Δ<i>G</i>° at 350 °C corresponds to a difference in log<i>K</i> of only -0.07.
 
 The following example uses the `H4SiO4` from Stefánsson (2001) to make an activity diagram for the K<sub>2</sub>O-Al<sub>2</sub>O<sub>3</sub>-SiO<sub>2</sub>-H<sub>2</sub>O system.
-This is similar to diagrams found, for example, on p. 361 of [Garrels and Christ, 1965](http://www.worldcat.org/oclc/517586) and Figure 3 of [Steinmann et al., 1994](http://ccm.geoscienceworld.org/content/42/2/197), but is quantitatively a closer match to the diagram in the [User's Guide to PHREEQC](https://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/html/final-75.html).
+This is similar to diagrams found, for example, on p. 361 of [Garrels and Christ, 1965](https://www.worldcat.org/oclc/517586) and Figure 3 of [Steinmann et al., 1994](http://ccm.geoscienceworld.org/content/42/2/197), but is quantitatively a closer match to the diagram in the [User's Guide to PHREEQC](https://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc/html/final-75.html).
 
 ```{r activity_diagram, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, echo=TRUE, results="hide", message=FALSE, dpi=dpi, out.width="100%", cache=TRUE, fig.cap="Activity diagram for K<sub>2</sub>O-Al<sub>2</sub>O<sub>3</sub>-SiO<sub>2</sub>-H<sub>2</sub>O.", pngquant=pngquant}
 basis(c("Al+3", "H4SiO4", "K+", "H2O", "H+", "O2"))

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