[CHNOSZ-commits] r154 - in pkg/CHNOSZ: . inst vignettes

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

Author: jedick
Date: 2017-02-16 17:03:13 +0100 (Thu, 16 Feb 2017)
New Revision: 154

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
anintro.Rmd: add links to other vignettes


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-02-16 13:30:36 UTC (rev 153)
+++ pkg/CHNOSZ/DESCRIPTION	2017-02-16 16:03:13 UTC (rev 154)
@@ -1,6 +1,6 @@
 Date: 2017-02-16
 Package: CHNOSZ
-Version: 1.0.8-43
+Version: 1.0.8-44
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-02-16 13:30:36 UTC (rev 153)
+++ pkg/CHNOSZ/inst/NEWS	2017-02-16 16:03:13 UTC (rev 154)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-43 (2017-02-16)
+CHANGES IN CHNOSZ 1.0.8-44 (2017-02-16)
 ---------------------------------------
 
 DOCUMENTATION:

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2017-02-16 13:30:36 UTC (rev 153)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2017-02-16 16:03:13 UTC (rev 154)
@@ -828,7 +828,7 @@
 
 The <span style="color:green">`equilibrate()`</span> function in CHNOSZ automatically chooses between two methods for calculating equilibrium.
 ```{marginfigure}
-For more information, see the vignette <span style="color:blue">*Equilibrium in CHNOSZ*</span>.
+For more information, see the vignette [<span style="color:blue">*Equilibrium in CHNOSZ*</span>](equilibrium.pdf).
 ```
 The method based on the Boltzmann equation is fast, but is applicable only to systems where the coefficient on the balanced basis species in each of the formation reactions is one.
 The reaction-matrix method is slower, but can be applied to systems were the balanced basis species has reaction coefficients other than one.
@@ -1213,7 +1213,7 @@
 The metastable coexistence of the *residues* (i.e. per-residue formulas, or residue equivalents) of the same proteins spans a much smaller range of chemical activities.
 In CHNOSZ, the calculation of metastable equilibrium activities of the residue equivalents is referred to as *normalization*.
 ```{marginfigure}
-See the vignette <span style="color:blue">*Equilibrium in CHNOSZ*</span> for other examples using normalization.
+See the vignette [<span style="color:blue">*Equilibrium in CHNOSZ*</span>](equilibrium.pdf) for other examples using normalization.
 ```
 
 To take an example, let's look at the metastable equilibrium distribution of selected proteins in the ER-to-Golgi location of *S. cerevisiae* (yeast).
@@ -1407,7 +1407,7 @@
 We read a data file of amino acid compositions produced in that study, taking those labeled "transferase".
 Then we add the proteins and get their indices using <span style="color:red">`add.protein()`</span>, set the basis, calculate the affinities, and make a potential diagram with temperature and activity of dissolved hydrogen as variables:
 
-```{r bison_transferase, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, results="hide", message=FALSE, fig.cap='Potential diagram for metagenomically identified sequences of transferases in the outflow channel of Bison Pool hot spring. See also the vignette <span style="color:blue">*Hot-spring proteins in CHNOSZ*</span>.', cache=TRUE, pngquant=pngquant, timeit=timeit}
+```{r bison_transferase, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, results="hide", message=FALSE, fig.cap='Potential diagram for metagenomically identified sequences of transferases in the outflow channel of Bison Pool hot spring. See also the vignette [<span style="color:blue">*Hot-spring proteins in CHNOSZ*</span>](hotspring.pdf).', cache=TRUE, pngquant=pngquant, timeit=timeit}
 aa <- read.aa(system.file("extdata/protein/DS11.csv", package = "CHNOSZ"))
 aa <- aa[grep("transferase", aa$protein), ]
 ip <- add.protein(aa)
@@ -1916,12 +1916,12 @@
 
 ## Regressing thermodynamic data
 
-<span style="color:green">`EOSregress()`</span> and related functions can be used to regress "equation of state" parameters (e.g. coefficients in the HKF equations) from heat capacity and volumetric data. See <span style="color:blue">`?EOSregress`</span> and the vignette, [<span style="color:blue">*Regressing thermodynamic data*</span>](../eos-regress.html).
+<span style="color:green">`EOSregress()`</span> and related functions can be used to regress "equation of state" parameters (e.g. coefficients in the HKF equations) from heat capacity and volumetric data. See <span style="color:blue">`?EOSregress`</span> and the vignette, [<span style="color:blue">*Regressing thermodynamic data*</span>](eos-regress.html).
 
 ## Gibbs energy minimization
 
 <span style="color:green">`wjd()`</span> implements a Gibbs energy minimization using the method of steepest descent described by @WJD58.
-See <span style="color:blue">`?wjd`</span> as well as the vignette, <span style="color:blue">*Winding journey down (in Gibbs energy)*</span>.
+See <span style="color:blue">`?wjd`</span> as well as the vignette, [<span style="color:blue">*Winding journey down (in Gibbs energy)*</span>](wjd.pdf).
 
 ## Reaction paths (experimental feature) {#Reaction-paths-experimental-feature}