[CHNOSZ-commits] r200 - in pkg/CHNOSZ: . inst man vignettes

Thu May 4 13:28:40 CEST 2017

Author: jedick
Date: 2017-05-04 13:28:39 +0200 (Thu, 04 May 2017)
New Revision: 200

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/revisit.Rd
   pkg/CHNOSZ/man/util.misc.Rd
   pkg/CHNOSZ/man/util.plot.Rd
   pkg/CHNOSZ/man/wjd.Rd
   pkg/CHNOSZ/vignettes/anintro.Rmd
   pkg/CHNOSZ/vignettes/vig.bib
Log:
minor documentation changes #5


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================

--- pkg/CHNOSZ/DESCRIPTION	2017-05-04 03:43:04 UTC (rev 199)
+++ pkg/CHNOSZ/DESCRIPTION	2017-05-04 11:28:39 UTC (rev 200)
@@ -1,24 +1,23 @@
 Date: 2017-05-04
 Package: CHNOSZ
-Version: 1.0.8-88
+Version: 1.0.8-89
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
 Depends: R (>= 3.1.0)
 Suggests: limSolve, testthat, knitr, rmarkdown, tufte, RSVGTipsDevice
 Imports: grDevices, graphics, stats, utils, colorspace
-Description: Tools for thermodynamic calculations in compositional biology and
-  low-temperature geochemistry. Thermodynamic properties are taken from a database
-  including aqueous species, minerals, and biomolecules, or from amino acid group
-  additivity for proteins. High-temperature properties are calculated using the
-  revised Helgeson-Kirkham-Flowers equations of state for aqueous species. Functions
-  are provided to define a system using basis species, automatically balance reactions,
-  calculate the chemical affinities of reactions for selected species, and plot the
-  results on potential diagrams or equilibrium activity diagrams. Experimental functions
-  calculate activity coefficients for aqueous species or optimize multiple thermodynamic
-  variables using an objective function for chemical activities.
+Description: An integrated set of tools for thermodynamic calculations in compositional
+  biology and geochemistry. Thermodynamic properties are taken from a database for minerals
+  and inorganic and organic aqueous species including biomolecules, or from amino acid
+  group additivity for proteins. High-temperature properties are calculated using the
+  revised Helgeson-Kirkham-Flowers equations of state for aqueous species. Functions are
+  provided to define a system using basis species, automatically balance reactions,
+  calculate the chemical affinities of reactions for selected species, and plot the results
+  on potential diagrams or equilibrium activity diagrams. Experimental features are
+  available to calculate activity coefficients for aqueous species or for multidimensional
+  optimization of thermodynamic variables using an objective function.
 License: GPL (>= 2)
 BuildResaveData: no
-ZipData: no
 VignetteBuilder: knitr
 URL: http://www.chnosz.net/, http://chnosz.r-forge.r-project.org/

Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2017-05-04 03:43:04 UTC (rev 199)
+++ pkg/CHNOSZ/inst/CHECKLIST	2017-05-04 11:28:39 UTC (rev 200)
@@ -33,10 +33,7 @@
 
 - update list of documentation topics in examples() with any new ones
 
-- especially on Windows:  
-  - data files are uncompressed on installation? (from BuildResaveData: no)
-    (so that users can copy and modify the thermodynamic database)
-  - anim.*() produce pngs / movies (ImageMagick dependency)?
+- especially on Windows: anim.*() produce pngs / movies (ImageMagick dependency)?
 
 - check for stale URLs in Rd files
 
@@ -52,3 +49,6 @@
     - Secondary thermodynamic modeling (less often-used functions e.g. revisit)
     - Extra thermodynamic modeling (out-of-workflow functions e.g. transfer)
     - Protein thermodynamic modeling (protein-specific functions e.g. ionize.aa)
+
+- although Rd files could use the \doi macro, it generates a largish (ca. 265K)
+  build/partial.rdb file; just use \url for now.

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-05-04 03:43:04 UTC (rev 199)
+++ pkg/CHNOSZ/inst/NEWS	2017-05-04 11:28:39 UTC (rev 200)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-88 (2017-05-04)
+CHANGES IN CHNOSZ 1.0.8-89 (2017-05-04)
 ---------------------------------------
 
 DOCUMENTATION:
@@ -156,7 +156,7 @@
 - Correct charge (-2) of NAD(red)-2 in biotic_aq.csv. Thanks to Peter
   Canovas.
 
-- Also correct charge (-2) of MgATP-2.
+- Correct charge (-2) of MgATP-2.
 
 - subcrt() returns `loggam` using the common logarithm; add
   test-nonideal.R to check for consistency between loggam and logK

Modified: pkg/CHNOSZ/man/revisit.Rd
===================================================================
--- pkg/CHNOSZ/man/revisit.Rd	2017-05-04 03:43:04 UTC (rev 199)
+++ pkg/CHNOSZ/man/revisit.Rd	2017-05-04 11:28:39 UTC (rev 200)
@@ -69,7 +69,7 @@
 In this case, plotting is disabled, since the names of the variables are not in the input.
 
 \samp{revisit} is a partial anagram of \samp{diversity}, which was the provisional name of the function but was changed in CHNOSZ-0.9.
-While the \code{diversity} function (in \pkg{vegan}) operates on a matrix with (biological) species on the columns, \code{revisit} operates on a list with (chemical) species as the elements of the list.
+While the \code{diversity} function (in \CRANpkg{vegan}) operates on a matrix with (biological) species on the columns, \code{revisit} operates on a list with (chemical) species as the elements of the list.
 The name of the \samp{H} output value is the conventional symbol for the Shannon diversity index, which was the first target statistic to be implemented in \code{revisit}.
 
 }

Modified: pkg/CHNOSZ/man/util.misc.Rd
===================================================================
--- pkg/CHNOSZ/man/util.misc.Rd	2017-05-04 03:43:04 UTC (rev 199)
+++ pkg/CHNOSZ/man/util.misc.Rd	2017-05-04 11:28:39 UTC (rev 200)
@@ -41,10 +41,6 @@
 If any of those species are proteins, the function gets their lengths using \code{protein.length}.
 }
 
-\value{
-  Numeric returns are made by \code{dPdTtr}, \code{Ttr}, \code{spearman}, \code{mod.obigt} Functions with no (or unspecified) returns are \code{thermo.plot.new}, \code{thermo.postscript}, \code{label.plot} and \code{water.lines}.
-}
-
 \examples{\dontshow{data(thermo)}
 ## properties of phase transitions
 si <- info("enstatite")

Modified: pkg/CHNOSZ/man/util.plot.Rd
===================================================================
--- pkg/CHNOSZ/man/util.plot.Rd	2017-05-04 03:43:04 UTC (rev 199)
+++ pkg/CHNOSZ/man/util.plot.Rd	2017-05-04 11:28:39 UTC (rev 200)
@@ -11,7 +11,7 @@
 \title{Functions to Create and Modify Plots}
 
 \description{
-  Initialize a new plot window using preset parameters, open a postcript file for plotting, add an axis or title to a plot, generate labels for plot axes and for identification of subplots and physical and chemical conditions, add stability lines for water to a diagram, get colors for set of values.
+  Initialize a new plot window using preset parameters, add an axis or title to a plot, generate labels for axes and subplots, add stability lines for water, get colors for a set of numeric values.
 }
 
 
@@ -94,7 +94,7 @@
 The spacing of the last (bottom) line from the edge of the plot is specified by \code{line}.
 This function exists to facilitate using \code{\link{expression}}s in multiline titles (see \code{\link{revisit}} for an example.) 
 
-\code{ZC.col} returns colors from a diverging palette (red - light grey - blue) corresponding to the values in \code{z}.
+\code{ZC.col} uses \CRANpkg{colorspace}) to generate colors from a diverging palette (red - light grey - blue) corresponding to the values in \code{z}.
 Red is associated with lower values of \code{z}.
 This function is intended to generate colors for distinguishing average oxidation state of carbon \code{\link{ZC}}, but any numeric values can be supplied.
 

Modified: pkg/CHNOSZ/man/wjd.Rd
===================================================================
--- pkg/CHNOSZ/man/wjd.Rd	2017-05-04 03:43:04 UTC (rev 199)
+++ pkg/CHNOSZ/man/wjd.Rd	2017-05-04 11:28:39 UTC (rev 200)
@@ -95,7 +95,7 @@
 Often, when investigating an equilibrium problem, the stoichiometric constraints are expressed most readily in terms of bulk composition -- numbers of moles of each element.
 \code{guess} is a function to make initial guesses about the numbers of moles of all species in the system subject to the positivity constraints.
 Its system-specific arguments are the stoichiometric matrix \code{A} (as defined above for \code{wjd}) and the bulk composition vector \code{B}, giving the number of moles of each element, in the same order that the elements appear in \code{A}.
-The first \code{method} available in \code{guess} generates the \sQuote{central} solution of the system of linear equations using the \code{\link[limSolve]{xranges}} function from \pkg{limSolve}. The central solution is the mean of ranges of unknowns. The inequality constraint, or minimum number of moles of any species, is given by \code{minX}.
+The first \code{method} available in \code{guess} generates the \sQuote{central} solution of the system of linear equations using the \code{\link[limSolve]{xranges}} function from \CRANpkg{limSolve}. The central solution is the mean of ranges of unknowns. The inequality constraint, or minimum number of moles of any species, is given by \code{minX}.
 
 The second method for \code{guess} \sQuote{stoich} (and the default for \code{run.guess} and \code{run.wjd}) is to test successive combinations of species whose elemental compositions are linearly independent.
 The linearly independent combinations tested are all those from \code{\link{invertible.combs}} if \code{ic} is NULL, or only those identified by \code{ic}.

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2017-05-04 03:43:04 UTC (rev 199)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2017-05-04 11:28:39 UTC (rev 200)
@@ -1198,7 +1198,7 @@
 ```
 
 By projecting the compositions of proteins into the `QEC` set of basis species, *n*̅<sub>`r o2`</sub> emerges as a strong indicator of oxidation state, while *n*̅<sub>`r h2o`</sub> is a relatively uncorrelated (i.e. independent) compositional variable.
-These independent variables make it easier to distinguish the effects of oxidation and hydration state in proteomic datasets [@Dic17].
+These independent variables make it easier to distinguish the effects of oxidation and hydration state in proteomic datasets [@Dic17a].
 
 ## Normalization to residues
 

Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib	2017-05-04 03:43:04 UTC (rev 199)
+++ pkg/CHNOSZ/vignettes/vig.bib	2017-05-04 11:28:39 UTC (rev 200)
@@ -638,13 +638,6 @@
   number      = {UCRL-MA-110662 PT I},
 }
 
- at Article{Dic17,
-  author        = {Dick, Jeffrey M.},
-  journal       = {PeerJ},
-  title         = {{C}hemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress},
-  year          = {2017},
-}
-
 @Article{SVI12,
   author        = {Sabatini, Antonio and Vacca, Alberto and Iotti, Stefano},
   journal       = {PLoS ONE},

