[Vegan-commits] r1759 - in pkg/gravy: . R man

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

Author: jarioksa
Date: 2011-08-25 15:28:35 +0200 (Thu, 25 Aug 2011)
New Revision: 1759

Added:
   pkg/gravy/NAMESPACE
Modified:
   pkg/gravy/DESCRIPTION
   pkg/gravy/R/zzz.R
   pkg/gravy/man/HOF.Rd
   pkg/gravy/man/betadiversity.Rd
   pkg/gravy/man/hillscale.Rd
   pkg/gravy/man/nichelap.Rd
Log:
gravy got a NAMESPACE

Modified: pkg/gravy/DESCRIPTION
===================================================================
--- pkg/gravy/DESCRIPTION	2011-08-25 12:46:28 UTC (rev 1758)
+++ pkg/gravy/DESCRIPTION	2011-08-25 13:28:35 UTC (rev 1759)
@@ -1,11 +1,11 @@
 Package: gravy
 Title: Gradient Analysis of Vegetation
-Version: 0.1-3
-Date: September 2, 2010
+Version: 0.2-0
+Date: August 25, 2011
 Author: Jari Oksanen
 Maintainer: Jari Oksanen <jari.oksanen at oulu.fi>
 Suggests: lattice 
-Description: Gravy is an experimental package of tools for gradient analysis
+Description: Gravy is an experimental package of tools for gradient analysis 
  of community data. The functions will be incorporated in `vegan' when they
  are close of being satisfactory. At the moment, using `gravy' may require an 
  adventurous mind and good knowledge of methods and R.  

Added: pkg/gravy/NAMESPACE
===================================================================
--- pkg/gravy/NAMESPACE	                        (rev 0)
+++ pkg/gravy/NAMESPACE	2011-08-25 13:28:35 UTC (rev 1759)
@@ -0,0 +1,54 @@
+## compiled code
+useDynLib(gravy)
+
+## Export
+
+export(GaussPara, HOF, betadiversity, betahill, boxgradient,
+gaussgradient, gradscale, hillscale, nichelap, plotGrad)
+
+## Do NOT export the following internal functions:
+
+## export(HOF1, gradder.HOF, pick.model, scale01, ssHOF)
+
+## S3 methods
+import(stats)
+import(graphics)
+
+# GaussPara: gravy
+S3method(GaussPara, HOF.frame)
+S3method(GaussPara, HOF)
+S3method(GaussPara, optop.HOF)
+S3method(GaussPara, tol.HOF)
+# HOF: gravy
+S3method(HOF, data.frame)
+S3method(HOF, default)
+# as.matrix: base
+S3method(as.matrix, nichelap.HOF.frame)
+# betadiversity: gravy
+S3method(betadiversity, HOF.frame)
+# coef, deviance, df.residual, fitted, logLik: stats
+S3method(coef, HOF)
+S3method(deviance, HOF)
+S3method(df.residual, HOF)
+S3method(fitted, HOF)
+S3method(logLik, HOF)
+# nichelap: gravy
+S3method(nichelap, HOF.frame)
+S3method(nichelap, HOF)
+# plot: graphics
+S3method(plot, HOF.frame)
+S3method(plot, HOF)
+S3method(plot, betadiversity)
+S3method(plot, hillscale)
+# predict: stats
+S3method(predict, HOF)
+# print: base
+S3method(print, GaussPara.HOF.frame)
+S3method(print, GaussPara.HOF)
+S3method(print, HOF.frame)
+S3method(print, HOF)
+S3method(print, betadiversity)
+S3method(print, hillscale)
+S3method(print, nichelap.HOF.frame)
+# residuals: stats
+S3method(residuals, HOF)

Modified: pkg/gravy/R/zzz.R
===================================================================
--- pkg/gravy/R/zzz.R	2011-08-25 12:46:28 UTC (rev 1758)
+++ pkg/gravy/R/zzz.R	2011-08-25 13:28:35 UTC (rev 1759)
@@ -1,4 +1,8 @@
-.First.lib <- function(lib, pkg) {
-    library.dynam("gravy", pkg, lib)
+.onAttach <- function(lib, pkg) {
+    packageStartupMessage("This is gravy ",
+                          utils::packageDescription("gravy",
+                                                    field="Version"),
+                          appendLF = TRUE)
+
 }
 

Modified: pkg/gravy/man/HOF.Rd
===================================================================
--- pkg/gravy/man/HOF.Rd	2011-08-25 12:46:28 UTC (rev 1758)
+++ pkg/gravy/man/HOF.Rd	2011-08-25 13:28:35 UTC (rev 1759)
@@ -7,12 +7,8 @@
 \alias{plot.HOF}
 \alias{plot.HOF.frame}
 \alias{predict.HOF}
-\alias{print.HOF}
-\alias{print.HOF.frame}
 \alias{GaussPara.HOF}
 \alias{GaussPara.HOF.frame}
-\alias{print.GaussPara.HOF}
-\alias{print.GaussPara.HOF.frame}
 
 \title{ Fits Huisman-Olff-Fresco (HOF) Response Models for Species
   along an Ecological Gradient. }

Modified: pkg/gravy/man/betadiversity.Rd
===================================================================
--- pkg/gravy/man/betadiversity.Rd	2011-08-25 12:46:28 UTC (rev 1758)
+++ pkg/gravy/man/betadiversity.Rd	2011-08-25 13:28:35 UTC (rev 1759)
@@ -1,7 +1,6 @@
 \name{betadiversity}
 \alias{betadiversity}
 \alias{betadiversity.HOF.frame}
-\alias{print.betadiversity}
 \alias{plot.betadiversity}
 
 \title{Estimates Beta Diversity as the instantaneous rate of change at

Modified: pkg/gravy/man/hillscale.Rd
===================================================================
--- pkg/gravy/man/hillscale.Rd	2011-08-25 12:46:28 UTC (rev 1758)
+++ pkg/gravy/man/hillscale.Rd	2011-08-25 13:28:35 UTC (rev 1759)
@@ -2,7 +2,6 @@
 \alias{hillscale}
 \alias{betahill}
 \alias{plot.hillscale}
-\alias{print.hillscale}
 
 \title{Hill indices of Beta diversity and gradient scaling to constant
   Hill index 2 }

Modified: pkg/gravy/man/nichelap.Rd
===================================================================
--- pkg/gravy/man/nichelap.Rd	2011-08-25 12:46:28 UTC (rev 1758)
+++ pkg/gravy/man/nichelap.Rd	2011-08-25 13:28:35 UTC (rev 1759)
@@ -1,9 +1,7 @@
 \name{nichelap}
 \alias{nichelap}
-\alias{nichelap.default}
 \alias{nichelap.HOF}
 \alias{nichelap.HOF.frame}
-\alias{print.nichelap.HOF.frame}
 \alias{as.matrix.nichelap.HOF.frame}
 
 \title{Overlap of Two Species Responses along a Gradient. }