[Analogue-commits] r230 - in pkg: . R

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

Author: gsimpson
Date: 2011-08-23 10:49:26 +0200 (Tue, 23 Aug 2011)
New Revision: 230

Added:
   pkg/NAMESPACE
Modified:
   pkg/R/zzz.R
Log:
adds a name space

Added: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	                        (rev 0)
+++ pkg/NAMESPACE	2011-08-23 08:49:26 UTC (rev 230)
@@ -0,0 +1,177 @@
+## compiled code
+useDynLib(analogue)
+
+## Imports
+##
+## vegan
+importFrom(vegan, pasteCall, eigenvals, tolerance)
+## lattice
+importFrom(lattice, densityplot, histogram, panel.refline, panel.grid,
+           panel.lines, panel.points, panel.polygon, panel.abline,
+           trellis.par.get)
+## stats
+import(stats)
+## utils
+importFrom(utils, head, tail)
+## graphics
+import(graphics)
+
+## Exports
+export(analog, bayesF, bootstrap, chooseTaxa, cma, crossval, deshrink, dissim,
+       dissimilarities, distance, fuse, getK, gradientDist, join, logitreg,
+       mat, mcarlo, minDC, optima, panel.Loess, panel.Stratiplot, pcr,
+       performance, prcurve, ##randomWA,
+       reconPlot, residLen, RMSEP, roc,
+       smoothSpline, Stratiplot, stdError, timetrack, tran, varExpl, wa,
+       "setK<-", Hellinger, ChiSquare)
+
+### S3 Methods
+##
+## main user-visible functions
+S3method(analog, default)
+S3method(bootstrap, default)
+S3method(bootstrap, mat)
+S3method(bootstrap, wa)
+S3method(chooseTaxa, default)
+S3method(cma, analog)
+S3method(cma, default)
+S3method(cma, predict.mat)
+S3method(cma, mat)
+S3method(crossval, wa)
+S3method(densityplot, residLen)
+S3method(dissimilarities, analog)
+S3method(dissimilarities, mat)
+S3method(distance, default)
+S3method(distance, join)
+S3method(eigenvals, pcr)
+S3method(fuse, dist)
+S3method(fuse, matrix)
+S3method(getK, default)
+S3method(getK, mat)
+S3method(getK, bootstrap.mat)
+S3method(getK, predict.mat)
+S3method(gradientDist, default)
+S3method(gradientDist, cca)
+S3method(gradientDist, prcurve)
+S3method(head, join)
+S3method(hist, residLen)
+S3method(histogram, residLen)
+S3method(logitreg, default)
+S3method(logitreg, analog)
+S3method(mat, default)
+S3method(mat, formula)
+S3method(mcarlo, default)
+S3method(mcarlo, mat)
+S3method(mcarlo, analog)
+S3method(minDC, default)
+S3method(minDC, predict.mat)
+S3method(minDC, analog)
+S3method(minDC, wa)
+S3method(optima, default)
+S3method(pcr, default)
+S3method(pcr, formula)
+S3method(performance, bootstrap.wa)
+S3method(performance, predict.wa)
+S3method(performance, pcr)
+S3method(performance, wa)
+S3method(RMSEP, default)
+S3method(RMSEP, mat)
+S3method(RMSEP, bootstrap.mat)
+S3method(RMSEP, bootstrap.wa)
+##S3method(randomWA, default)
+S3method(roc, default)
+S3method(roc, analog)
+S3method(roc, mat)
+S3method(stdError, mat)
+S3method(stdError, predict.mat)
+S3method("setK<-", default)
+S3method("setK<-", mat)
+S3method(tail, join)
+S3method(tolerance, default)
+S3method(tran, default)
+S3method(tran, formula)
+S3method(varExpl, default)
+S3method(varExpl, cca)
+S3method(varExpl, prcurve)
+S3method(wa, default)
+S3method(wa, formula)
+## fitted, predict, coef etc
+S3method(coef, pcr)
+S3method(coef, wa)
+S3method(fitted, pcr)
+S3method(fitted, bootstrap.mat)
+S3method(fitted, mat)
+S3method(fitted, timetrack)
+S3method(fitted, wa)
+S3method(predict, mat)
+S3method(predict, wa)
+S3method(residuals, bootstrap.mat)
+S3method(residuals, mat)
+S3method(residuals, pcr)
+## plotting
+S3method(plot, minDC)
+S3method(plot, bayesF)
+S3method(plot, cma)
+S3method(plot, dissimilarities)
+S3method(plot, gradientDist)
+S3method(lines, gradientDist)
+S3method(points, gradientDist)
+S3method(plot, logitreg)
+S3method(plot, mat)
+S3method(plot, mcarlo)
+S3method(plot, prcurve)
+S3method(plot, residLen)
+S3method(plot, roc)
+S3method(plot, timetrack)
+S3method(plot, wa)
+S3method(reconPlot, default)
+S3method(reconPlot, predict.mat)
+S3method(reconPlot, predict.wa)
+S3method(screeplot, bootstrap.mat)
+S3method(screeplot, mat)
+S3method(screeplot, pcr)
+S3method(Stratiplot, default)
+S3method(Stratiplot, formula)
+## print
+S3method(print, analog)
+S3method(print, bayesF)
+S3method(print, bootstrap.mat)
+S3method(print, bootstrap.wa)
+S3method(print, cma)
+S3method(print, crossval)
+S3method(print, fitted.bootstrap.mat)
+S3method(print, fitted.mat)
+S3method(print, logitreg)
+S3method(print, mat)
+S3method(print, mcarlo)
+S3method(print, minDC)
+S3method(print, optima)
+S3method(print, pcr)
+S3method(print, performance)
+S3method(print, predict.mat)
+S3method(print, predict.wa)
+S3method(print, residLen)
+S3method(print, residuals.bootstrap.mat)
+S3method(print, residuals.mat)
+S3method(print, roc)
+S3method(print, summary.analog)
+S3method(print, summary.bootstrap.mat)
+S3method(print, summary.cma)
+S3method(print, summary.logitreg)
+S3method(print, summary.mat)
+S3method(print, summary.predict.mat)
+S3method(print, summary.roc)
+S3method(print, timetrack)
+S3method(print, tolerance)
+S3method(print, wa)
+## summary
+S3method(summary, analog)
+S3method(summary, bootstrap.mat)
+S3method(summary, cma)
+S3method(summary, logitreg)
+S3method(summary, mat)
+S3method(summary, predict.mat)
+S3method(summary, roc)
+## utilities
+S3method(as.data.frame, optima)
+S3method(as.data.frame, tolerance)

Modified: pkg/R/zzz.R
===================================================================
--- pkg/R/zzz.R	2011-08-23 08:48:37 UTC (rev 229)
+++ pkg/R/zzz.R	2011-08-23 08:49:26 UTC (rev 230)
@@ -1,4 +1,11 @@
-.First.lib <- function(lib, pkg)  {
+## .First.lib <- function(lib, pkg)  {
+##     library.dynam("analogue", pkg, lib)
+##     packageStartupMessage("This is analogue ",
+##                           utils::packageDescription("analogue",
+##                                                     field="Version"),
+##                           appendLF = TRUE)
+## }
+.onAttach <- function(lib, pkg)  {
     library.dynam("analogue", pkg, lib)
     packageStartupMessage("This is analogue ",
                           utils::packageDescription("analogue",