mvabund v3.11.3

.Rhistory

@@ -0,0 +1,6 @@
+library(Rcpp)
+compileAttributes()
+q()
+library(Rcpp)
+compileAttributes()
+q()

DESCRIPTION

@@ -0,0 +1,23 @@
+Package: mvabund
+Title: Statistical Methods for Analysing Multivariate Abundance Data
+Version: 3.11.3
+Date: 2015-09-01
+Author: Yi Wang, Ulrike Naumann, Stephen Wright and David Warton
+Maintainer: David Warton <David.Warton@unsw.edu.au>
+Description: A set of tools for displaying, modeling and analysing
+        multivariate abundance data in community ecology. See
+        'mvabund-package.Rd' for details of overall package organization.
+        The package is implemented with the Gnu Scientific Library
+        (http://www.gnu.org/software/gsl/) and Rcpp
+        (http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ classes.
+Depends: R (>= 3.0.0)
+Imports: Rcpp, MASS, methods, stats, tweedie, statmod, parallel
+LinkingTo: Rcpp, RcppGSL
+License: LGPL (>= 2.1)
+Repository: R-Forge
+Packaged: 2015-08-26 00:41:47 UTC; ywang
+NeedsCompilation: yes
+Date/Publication: 2015-08-17 02:08:55
+Repository/R-Forge/Project: mvabund
+Repository/R-Forge/Revision: 133
+Repository/R-Forge/DateTimeStamp: 2015-08-17 02:08:55

NAMESPACE

@@ -0,0 +1,94 @@
+useDynLib(mvabund)
+
+export(RcppVersion,
+       as.mvabund,
+       anova.manylm, 
+       anova.manyglm,
+       anova.manyany,
+       anova.traitglm,
+       boxplot.mvabund, 
+       boxplot.mvformula,
+       best.r.sq,
+       cv.glm1path,
+       deviance.manylm,
+       extend.x.formula, 
+       formulaUnimva,
+       glm1,
+       glm1path,
+       is.mvabund,
+       is.mvformula,
+       mvabund, 
+       mvformula,
+       manylm, 
+       manyglm, 
+       manyany,
+       predict.manylm,
+       predict.manyglm,
+       predict.traitglm,
+       print.manyglm,
+       print.anova.manyany,
+       print.anova.manylm, 
+       print.summary.manylm, 
+       print.anova.manyglm, 
+       print.summary.manyglm, 
+       print.mvformula,
+       plotMvaFactor, 
+       plotFormulafeature, 
+       plot.glm1path,
+       plot.mvabund,
+       plot.manylm,
+       plot.manyglm,
+       plot.manyany,
+       plot.mvformula,
+       ridgeParamEst,
+       residuals.glm1path,
+       residuals.manyany, 
+       residuals.manyglm, 
+       summary.manylm,
+       summary.manyglm,
+       shiftpoints,
+       traitglm,
+       unabund       
+       )
+
+exportClasses(mvabund, mvformula)
+
+exportMethods(meanvar.plot)
+
+import(Rcpp, MASS, graphics, methods, tweedie, statmod, parallel)
+importFrom(stats,dpois, ppois, qpois, rpois)
+importFrom(stats,dbinom, pbinom, qbinom, rbinom)
+importFrom(stats,dnbinom, pnbinom, qnbinom, rnbinom)
+
+S3method(extractAIC, manyglm)
+S3method(logLik, manyglm)
+S3method(logLik, manylm)
+S3method(logLik, manyany)
+S3method(anova, manyany)
+S3method(anova, manyglm)
+S3method(anova, manylm)
+S3method(anova, traitglm)
+S3method(summary, manyglm)
+S3method(summary, manylm)
+S3method(predict, manyglm)
+S3method(predict, manylm)
+S3method(predict, traitglm)
+S3method(deviance, manylm)
+S3method(residuals, manyany)
+S3method(residuals, manyglm)
+S3method(residuals, glm1path)
+S3method(plot, manyany)
+S3method(plot, manyglm)
+S3method(plot, manylm)
+S3method(plot, mvabund)
+S3method(plot, mvformula)
+S3method(plot, glm1path)
+S3method(boxplot, mvabund)
+S3method(boxplot, mvformula)
+S3method(print, anova.manyany)
+S3method(print, anova.manyglm)
+S3method(print, anova.manylm)
+S3method(print, manyglm)
+S3method(print, mvformula)
+S3method(print, summary.manyglm)
+S3method(print, summary.manylm)

R/AllClass.R

@@ -0,0 +1,20 @@
+# CLASSES in the mvabund package
+
+# basic objects
+setClass("mvabund" ) 
+setClass("formulaUnimva" )
+setClass("mvformula")
+
+# Model classes
+setClass("glm1path" ) 
+setClass("manylm")
+setClass("manyglm")
+setClass("traitglm" ) 
+
+# summary classes
+setClass("summary.manylm")
+setClass("summary.manyglm")
+
+# anova classes
+setClass("anova.manylm")
+setClass("anova.manyglm")

R/RcppExports.R

@@ -0,0 +1,23 @@
+# This file was generated by Rcpp::compileAttributes
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+RtoAnovaCpp <- function(rparam, Y, X, isXvarIn, bIDsexp) {
+    .Call('mvabund_RtoAnovaCpp', PACKAGE = 'mvabund', rparam, Y, X, isXvarIn, bIDsexp)
+}
+
+RtoGlmAnova <- function(sparam, rparam, Y, X, O, isXvarIn, bIDsexp, lambda) {
+    .Call('mvabund_RtoGlmAnova', PACKAGE = 'mvabund', sparam, rparam, Y, X, O, isXvarIn, bIDsexp, lambda)
+}
+
+RtoGlm <- function(rparam, Y, X, O) {
+    .Call('mvabund_RtoGlm', PACKAGE = 'mvabund', rparam, Y, X, O)
+}
+
+RtoGlmSmry <- function(sparam, rparam, Y, X, O, bIDsexp, lambda) {
+    .Call('mvabund_RtoGlmSmry', PACKAGE = 'mvabund', sparam, rparam, Y, X, O, bIDsexp, lambda)
+}
+
+RtoSmryCpp <- function(rparam, Y, X, bIDsexp) {
+    .Call('mvabund_RtoSmryCpp', PACKAGE = 'mvabund', rparam, Y, X, bIDsexp)
+}
+

R/RcppVersion.R

@@ -0,0 +1,14 @@
+RcppVersion <- function() {
+
+    version <- installed.packages()["Rcpp","Version"]
+
+    ## Print version of this package
+    cat('\nRcpp package Version ', version, '\n')
+
+    ## Print version of Rcpp/RcppTemplate used to build this package
+    licenseFile <- system.file(".", "LICENSE-Rcpp.txt", package="Rcpp")
+    con <- file(licenseFile, "r")
+    writeLines(readLines(con)[1:4])
+    close(con)
+    invisible(NULL)
+}