[CHNOSZ-commits] r204 - in pkg/CHNOSZ: . inst man vignettes

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

Author: jedick
Date: 2017-06-06 16:35:05 +0200 (Tue, 06 Jun 2017)
New Revision: 204

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/basis.Rd
   pkg/CHNOSZ/vignettes/anintro.Rmd
   pkg/CHNOSZ/vignettes/vig.bib
Log:
update links for 2017 PeerJ paper


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-06-04 17:28:46 UTC (rev 203)
+++ pkg/CHNOSZ/DESCRIPTION	2017-06-06 14:35:05 UTC (rev 204)
@@ -1,6 +1,6 @@
-Date: 2017-06-04
+Date: 2017-06-06
 Package: CHNOSZ
-Version: 1.1.0-2
+Version: 1.1.0-3
 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	2017-06-04 17:28:46 UTC (rev 203)
+++ pkg/CHNOSZ/inst/NEWS	2017-06-06 14:35:05 UTC (rev 204)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.0-2 (2017-06-04)
+CHANGES IN CHNOSZ 1.1.0-3 (2017-06-06)
 --------------------------------------
 
 - water.lines() now works for diagrams of Eh, pe, logfO2, logaO2,

Modified: pkg/CHNOSZ/man/basis.Rd
===================================================================
--- pkg/CHNOSZ/man/basis.Rd	2017-06-04 17:28:46 UTC (rev 203)
+++ pkg/CHNOSZ/man/basis.Rd	2017-06-06 14:35:05 UTC (rev 204)
@@ -80,7 +80,7 @@
 \references{
 Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. \emph{PeerJ} \bold{4}:e2238. \url{https://doi.org/10.7717/peerj.2238}
 
-Dick, J. M. (2017) Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. \emph{bioRxiv} \url{https://doi.org/10.1101/097667}
+Dick, J. M. (2017) Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. \emph{PeerJ} \bold{5}:e3421 \url{https://doi.org/10.7717/peerj.3421}
 }
 
 \examples{

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2017-06-04 17:28:46 UTC (rev 203)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2017-06-06 14:35:05 UTC (rev 204)
@@ -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 [@Dic17a].
+These independent variables make it easier to distinguish the effects of oxidation and hydration state in proteomic datasets [@Dic17].
 
 ## Normalization to residues
 

Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib	2017-06-04 17:28:46 UTC (rev 203)
+++ pkg/CHNOSZ/vignettes/vig.bib	2017-06-06 14:35:05 UTC (rev 204)
@@ -530,14 +530,6 @@
   url       = {http://www.worldcat.org/oclc/18559968},
 }
 
- at Article{Dic17a,
-  author        = {Dick, Jeffrey M.},
-  journal       = {bioRxiv},
-  title         = {{C}hemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress},
-  year          = {2017},
-  doi           = {10.1101/097667},
-}
-
 @Article{HW97,
   author    = {Hn\v{e}dkovsk\'y, Lubom\'ir and Wood, Robert H.},
   journal   = {Journal of Chemical Thermodynamics},
@@ -638,6 +630,14 @@
   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},
+  url           = {https://peerj.com/articles/3421},
+}
+
 @Article{SVI12,
   author        = {Sabatini, Antonio and Vacca, Alberto and Iotti, Stefano},
   journal       = {PLoS ONE},