[CHNOSZ-commits] r258 - in pkg/CHNOSZ: . inst vignettes

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

Author: jedick
Date: 2017-10-14 17:09:27 +0200 (Sat, 14 Oct 2017)
New Revision: 258

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/vignettes/obigt.Rmd
Log:
reduce size of obigt.html


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-10-14 07:02:09 UTC (rev 257)
+++ pkg/CHNOSZ/DESCRIPTION	2017-10-14 15:09:27 UTC (rev 258)
@@ -1,6 +1,6 @@
 Date: 2017-10-14
 Package: CHNOSZ
-Version: 1.1.0-56
+Version: 1.1.0-57
 Title: Thermodynamic Calculations for Geobiochemistry
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-10-14 07:02:09 UTC (rev 257)
+++ pkg/CHNOSZ/inst/NEWS	2017-10-14 15:09:27 UTC (rev 258)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.0-56 (2017-10-14)
+CHANGES IN CHNOSZ 1.1.0-57 (2017-10-14)
 ---------------------------------------
 
 MAJOR CHANGES:
@@ -14,7 +14,7 @@
   calculateDensity(), calculateGibbsofWater(), calculateEpsilon(),
   calculateQ().
 
-- The computational setting for water (thermo$opt$par) can now be set
+- The computational setting for water (thermo$opt$water) can now be set
   using water("DEW"), water("IAPWS"), etc.
 
 - Usage of the DEW model is shown in the new demo DEW.R. This demo also
@@ -155,6 +155,11 @@
 - Remove read.expr() and extdata/abundance/ISR+08.csv (protein abundance
   in E. coli).
 
+- Reduce the size of obigt.html by ~450 KB. This was done by 1) using
+  rmarkdown with files in rmd/h/bootstrap-3.3.5/fonts/ replaced with
+  empty files (291 KB), and 2) changing the theme from "cosmo" to
+  "default" (151 KB).
+
 CHANGES IN CHNOSZ 1.1.0 (2017-05-04)
 ------------------------------------
 

Modified: pkg/CHNOSZ/vignettes/obigt.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.Rmd	2017-10-14 07:02:09 UTC (rev 257)
+++ pkg/CHNOSZ/vignettes/obigt.Rmd	2017-10-14 15:09:27 UTC (rev 258)
@@ -1,11 +1,9 @@
 ---
 title: "Thermodynamic data in [CHNOSZ](http://www.chnosz.net)"
 output:
-# change to html_document for full version
   html_document:
     mathjax: null
-# uncomment the next two lines for full version
-    theme: cosmo
+    theme: default
     css: obigt.css
 vignette: >
   %\VignetteIndexEntry{Thermodynamic data in CHNOSZ}
@@ -15,8 +13,6 @@
 # so that these appear in the bibliography
 nocite: | 
   @SPRONS92, @SLOP98, @SLOP07, @SLOP15, @CHNOSZ, @JOH92, @WP02, @CWM89, @PRPG97, @TH88, @Kul06, @Sho09
-# 20170212: comment the csl line to build package on R-Forge, to avoid
-# getting an error there (pandoc-citeproc: error while parsing the XML string)
 csl: elementa.csl
 ---
 
@@ -125,17 +121,17 @@
 
 # Recent additions (late 2017)
 
-* Mineral data using the [Berman (1988)](https://doi.org/10.1093/petrology/29.2.445) equations are listed under **Solids** / **Berman**.
+* Mineral data using the [Berman (1988)](https://doi.org/10.1093/petrology/29.2.445) equations are listed under [**Solids** / **Berman**](#berman-107).
 
-* Aqueous species data intended for use with the [Deep Earth Water](http://www.dewcommunity.org/) model are listed under **Optional Data** / **DEW**.
+* Aqueous species data intended for use with the [Deep Earth Water](http://www.dewcommunity.org/) model are listed under [**Optional Data** / **DEW**](#dew-199).
 
-# Sources of data {.tabset .tabset-fade}
+# Sources of data {.tabset .tabset-fade .tabset-sticky}
 
 <!-- uncomment for full version -->
 Use the tabs below to select a section for viewing.
 Select "All at once" to show all sections.
 
-## Aqueous species {.tabset .tabset-pills}
+## Aqueous species {.tabset .tabset-pills .tabset-sticky}
 
 ### `r setfile("H2O_aq.csv")`
 ```{r H2O_aq, results="asis", echo=FALSE}
@@ -181,7 +177,7 @@
 ```{r reflist, results="asis", echo=FALSE}
 ```
 
-## Solids {.tabset .tabset-pills}
+## Solids {.tabset .tabset-pills .tabset-sticky}
 
 ### `r setfile("inorganic_cr.csv")`
 ```{r inorganic_cr, results="asis", echo=FALSE}
@@ -206,13 +202,13 @@
 ```{r reflist, results="asis", echo=FALSE}
 ```
 
-## Liquids {.tabset .tabset-pills}
+## Liquids {.tabset .tabset-pills .tabset-sticky}
 
 ### `r setfile("organic_liq.csv")`
 ```{r reflist, results="asis", echo=FALSE}
 ```
 
-## Gases {.tabset .tabset-pills}
+## Gases {.tabset .tabset-pills .tabset-sticky}
 
 ### `r setfile("inorganic_gas.csv")`
 ```{r reflist, results="asis", echo=FALSE}
@@ -222,7 +218,7 @@
 ```{r reflist, results="asis", echo=FALSE}
 ```
 
-## Optional Data {.tabset .tabset-pills}
+## Optional Data {.tabset .tabset-pills .tabset-sticky}
 
 ```{r Optional_Data, results="asis", echo=FALSE}
 cat("These files contain optional data updates that are not loaded by default (using `data(thermo)`). To load these data, run `add.obigt('CHNOSZ')` or `add.obigt('DEW')`.\n\n")