Merge pull request #34 from quicklizard99/feature/33-cpp-std

Feature/33 cpp std
quicklizard99 · Oct 8, 2016 · cfa0096 · cfa0096
2 parents 24a3503 + 2e6fe83
commit cfa0096
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: cheddar
 Type: Package
 Title: Analysis and Visualisation of Ecological Communities
-Version: 0.1-630
-Date: 2015-08-24
+Version: 0.1-631
+Date: 2016-10-10
 Author: Lawrence Hudson with contributions from Dan Reuman and Rob Emerson
 Maintainer: Lawrence Hudson <[email protected]>
 Description: Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.

diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2014-2015
+YEAR: 2014-2016
 COPYRIGHT HOLDER: Lawrence Hudson, Dan Reuman and Rob Emerson
diff --git a/build.sh b/build.sh
@@ -4,5 +4,5 @@ rm -rf build  && \
     mkdir build && \
     cd build && \
     R CMD build --compact-vignettes=gs .. && \
-    ~/local/R-devel/R.framework/Resources/bin/R CMD check --as-cran cheddar_${VERSION}.tar.gz && \
+    ~/local/R-devel/bin/R CMD check --as-cran cheddar_${VERSION}.tar.gz && \
     R CMD INSTALL --build --html cheddar_${VERSION}.tar.gz
diff --git a/man/cheddar.Rd b/man/cheddar.Rd
@@ -5,13 +5,13 @@
 \docType{package}
 \title{Analysis and visualisation of ecological communities}
 \description{
-Cheddar provides a flexible, extendable representation of an ecological 
-community and a range of functions for analysis and visualisation, focusing 
-on food web, body mass and numerical abundance data. It also allows inter-web 
-comparisons such as examining changes in community structure over 
-environmental, temporal or spatial gradients. 
+Cheddar provides a flexible, extendable representation of an ecological
+community and a range of functions for analysis and visualisation, focusing
+on food web, body mass and numerical abundance data. It also allows inter-web
+comparisons such as examining changes in community structure over
+environmental, temporal or spatial gradients.
 
-Details of differences between versions of Cheddar are in the the online 
+Details of differences between versions of Cheddar are in the the online
 release history:
 \href{https://github.com/quicklizard99/cheddar/blob/master/release_history.md}{https://github.com/quicklizard99/cheddar/blob/master/release_history.md}.
 }
@@ -21,7 +21,7 @@ release history:
     Package: \tab cheddar\cr
     Type: \tab Package\cr
     Version: \tab 0.1-630\cr
-    Date: \tab 2015-08-24\cr
+    Date: \tab 2016-10-10\cr
     License: \tab BSD 2 clause\cr
     }
 }
@@ -43,14 +43,14 @@ CPS(TL84)
 head(NPS(TL84))
 
 # Some computed node properties
-head(NPS(TL84, c('Log10M', 'Log10N', 'Log10Biomass', 
+head(NPS(TL84, c('Log10M', 'Log10N', 'Log10Biomass',
                  TL='PreyAveragedTrophicLevel', TS='TrophicSpecies')))
 
 # Properties of each trophic link
 head(TLPS(TL84))
 
 # Computed properties of each node in each link
-head(TLPS(TL84, node.properties=c('Log10M', 'Log10N', 'Log10Biomass', 
+head(TLPS(TL84, node.properties=c('Log10M', 'Log10N', 'Log10Biomass',
                                   'PreyAveragedTrophicLevel')))
 
 
@@ -60,7 +60,7 @@ data(pHWebs)
 # A data.frame of predictors and responses
 CollectionCPS(pHWebs, c('pH',
                         S='NumberOfNodes',
-                        L='NumberOfTrophicLinks', 
+                        L='NumberOfTrophicLinks',
                         C='DirectedConnectance',
                         Slope='NvMSlope'))
 }
diff --git a/release_history.md b/release_history.md
@@ -1,4 +1,13 @@
 #  Cheddar release history
+## 0.1-631 2016-10-10
+**Available on CRAN**
+#### Miscellaneous
+* [Issue 33](https://github.com/quicklizard99/cheddar/issues/33)
+  Declare use of C++ std namespace
+
+## 0.1-630 2015-08-24
+**Available on CRAN**
+* Non-code changes in order to comply with CRAN policies
 
 ## 0.1-629 2015-04-16
 **Available on CRAN**
@@ -22,7 +31,6 @@
 #### Bugs fixed
 * [Issue 31](https://github.com/quicklizard99/cheddar/issues/31)
   Missing Licence file
-
 #### Improvements
 * [Issue 30](https://github.com/quicklizard99/cheddar/issues/30)
   Indicate that there are too many trophic chains to compute
@@ -41,113 +49,101 @@
 * [Issue 24](https://github.com/quicklizard99/cheddar/issues/24)
   Function to produce a site by species matrix from a collection
 * [Issue 27](https://github.com/quicklizard99/cheddar/issues/27)
-  PredationMatrixToLinks should be able to extract a link property 
+  PredationMatrixToLinks should be able to extract a link property
 * [Issue 28](https://github.com/quicklizard99/cheddar/issues/28)
   Quantitative web stats a la Bersier et al 2002 Ecology
 
 ## 0.1-622 Released 2013-03-19
 **Available on CRAN**
-
 #### Improvements
 * [Issue 21](https://github.com/quicklizard99/cheddar/issues/21)
   Some units tests are testing equality of computed values
 
 ## 0.1-621 Released 2013-03-09
 #### Improvements
-* A first attempt at fixing 
+* A first attempt at fixing
   [Issue 21](https://github.com/quicklizard99/cheddar/issues/21)
   Some units tests are testing equality of computed values
 
 ## 0.1-620 Released 2013-01-22
 #### Bugs fixed
 * [Issue 17](https://github.com/quicklizard99/cheddar/issues/17)
   The title for PlotAuppervAlower plots is odd
-
 #### Improvements
-* [Issue 15](https://github.com/quicklizard99/cheddar/issues/15) 
+* [Issue 15](https://github.com/quicklizard99/cheddar/issues/15)
   MinimiseSumDietGaps and MinimiseSumConsumerGaps do not replicate
-* [Issue 16](https://github.com/quicklizard99/cheddar/issues/16) 
+* [Issue 16](https://github.com/quicklizard99/cheddar/issues/16)
   PlotPredationMatrix does not permit different resource and consumer orderings
 * [Issue 18](https://github.com/quicklizard99/cheddar/issues/18)
   A function to calculate log N versus log M convex hull
 * [Issue 19](https://github.com/quicklizard99/cheddar/issues/19)
   Pyramid functions lack flexibility
 * [Issue 20](https://github.com/quicklizard99/cheddar/issues/20)
   PlotNvM() and friends always shows nodes that lack X and/or Y
-
 #### Miscellaneous
 * Fixed some typos in vignettes
 
 ## 0.1-619 Released 2012-11-22
 **Available on CRAN**
-
 #### Miscellaneous
-* Fixed problem with example code in help pages LoadCommunity / SaveCommunity 
+* Fixed problem with example code in help pages LoadCommunity / SaveCommunity
 and LoadCollection / SaveCollection
 
 ## 0.1-618 Released 2012-11-20
 **Available on CRAN**
-
 #### Bugs fixed
-* [Issue 13](https://github.com/quicklizard99/cheddar/issues/13) 
+* [Issue 13](https://github.com/quicklizard99/cheddar/issues/13)
   Plot pyramid functions fail for some communities
-
 #### Improvements
 * [Issue 11](https://github.com/quicklizard99/cheddar/issues/11)
-  PredationMatrixToLinks requires a square predation matrix with 
+  PredationMatrixToLinks requires a square predation matrix with
   ncol=nrow=number of nodes enhancement
 * [Issue 12]() Improvements to enumerating trophic chains
 * [Issue 14]() LoadCommunity and SaveCommunity restrict options
 
 ## 0.1-617 Released 2012-10-25
-
 #### Bugs fixed
 * [Issue 10](https://github.com/quicklizard99/cheddar/issues/10)
   AggregateCommunities fails for certain communities
 
 ## 0.1-616 Released 2012-09-24
 **Available on CRAN**
-
 #### Miscellaneous
 * Fixed some minor mistakes in help files
 * Added some missing journal names in vignette references
 
 ## 0.1-615 Released 2012-09-24
-
 #### Bugs fixed
 * [Issue 2](https://github.com/quicklizard99/cheddar/issues/2)
-  MinimiseSumDietGaps and MinimiseSumConsumerGaps returns community with 
+  MinimiseSumDietGaps and MinimiseSumConsumerGaps returns community with
   incorrect title
-* [Issue 4](https://github.com/quicklizard99/cheddar/issues/4) 
+* [Issue 4](https://github.com/quicklizard99/cheddar/issues/4)
   Graph legend produced by FormatLM() does not show r squared correctly on a Mac
 * [Issue 5](https://github.com/quicklizard99/cheddar/issues/5)
   Columns returned by CollectionCPS() show empy categories as 'V1'
 * [Issue 6](https://github.com/quicklizard99/cheddar/issues/6)
-  NvMSlopeByClass() and friends should give NA for categories where all nodes 
+  NvMSlopeByClass() and friends should give NA for categories where all nodes
   have N and/or M of NA
-
 #### Improvements
 * [Issue 3](https://github.com/quicklizard99/cheddar/issues/3)
   Inconsistent references style in vignettes
 * [Issue 7](https://github.com/quicklizard99/cheddar/issues/7)
   ImportExport vignette needs more export examples enhancement
 * [Issue 8](https://github.com/quicklizard99/cheddar/issues/8)
-  SumMByClass(), SumNByClass() and SumBiomassByClass() do not allow 
+  SumMByClass(), SumNByClass() and SumBiomassByClass() do not allow
   user-control of NA behaviour
 * [Issue 9](https://github.com/quicklizard99/cheddar/issues/9)
   PlotNPS() always shows nodes that lack X and/or Y
-
 #### Miscellaneous
 * Added information about link strengths to PlotsAndStats vignette
-* Added genus and species node properties to communities that have 
-  classification: Broadstone, Millstream, SkipwithPond, TL84, TL86 and 
+* Added genus and species node properties to communities that have
+  classification: Broadstone, Millstream, SkipwithPond, TL84, TL86 and
   YthanEstuary
-* Citeable sources for classification for Broadstone, Millstream, SkipwithPond, 
+* Citeable sources for classification for Broadstone, Millstream, SkipwithPond,
   TL84, TL86 and YthanEstuary
 
 ## 0.1-614 Released 2012-07-23
 **First release available on CRAN**
-
 #### Bugs fixed
 * [Issue 1](https://github.com/quicklizard99/cheddar/issues/1)
   Does not build on Solaris - C99 function isfinite() not present