Merge pull request #3 from friendly/roxygen

Roxygen

.Rbuildignore

@@ -11,3 +11,6 @@ README.md
 ^docs$
 ^pkgdown$
 .nojekyll
+man-old/
+NAMESPACE-old
+.build-steps.R

DESCRIPTION

@@ -1,18 +1,31 @@
 Package: candisc
 Type: Package
 Title: Visualizing Generalized Canonical Discriminant and Canonical Correlation Analysis
-Version: 0.8-6
-Date: 2021-10-06
-Depends: R (>= 3.5.0), car, heplots (>= 0.8-6), graphics, stats 
-Suggests: rgl, corrplot,
+Version: 0.9.0
+Date: 2024-05-05
+Depends: R (>= 3.5.0), heplots (>= 0.8-6)
+Imports: car, graphics, stats
+Suggests: 
+    rgl,
+    carData,
+    corrplot,
     knitr,
     rmarkdown,
-    MASS, rpart, rpart.plot
+    MASS, 
+    rpart, 
+    rpart.plot
 LazyLoad: yes
 LazyData: yes
-Authors@R: c(person(given = "Michael", family = "Friendly", role=c("aut", "cre"), email="friendly@yorku.ca"),
-             person(given = "John", family = "Fox", role="aut"))
-Author: Michael Friendly [aut, cre], John Fox [aut]
+Authors@R: c(
+            person(given = "Michael", 
+                   family = "Friendly", 
+                   role=c("aut", "cre"), 
+                   email="friendly@yorku.ca",
+                   comment = c(ORCID = "0000-0002-3237-0941")),
+            person(given = "John", 
+                   family = "Fox", role="aut",
+                   comment = c(ORCID = "0000-0002-1196-8012"))
+            )
 Maintainer: Michael Friendly <friendly@yorku.ca>
 Language: en-US
 Description: Functions for computing and visualizing 
@@ -27,6 +40,8 @@ Description: Functions for computing and visualizing
 	visualizations of terms in an 'mlm' via the 'plot.candisc' and 'heplot.candisc' methods. Related plots are
 	now provided for canonical correlation analysis when all predictors are quantitative.
 License: GPL (>= 2)
-Packaged: 10/9/2008 6:12PM; Michael Friendly
+Encoding: UTF-8
 VignetteBuilder: knitr
+URL: https://github.com/friendly/candisc/, https://friendly.github.io/candisc/
 BugReports: https://github.com/friendly/candisc/issues
+RoxygenNote: 7.3.1

NAMESPACE

@@ -1,55 +1,78 @@
-# last modified 6 October 2007 by J. Fox
-# last modified 22 April 2009 by M. Friendly
-
-import(car)
-
-import(heplots)
-import(graphics)
-import(stats)
-importFrom("grDevices", "palette")
-importFrom("utils", "menu")
-
-export(candisc, candiscList, dataIndex,
-	cancor, vectors, Wilks, scores, redundancy, vecscale, can_lm, varOrder)
-#S3method(can_lm, mlm)
-S3method(candisc, mlm)
-S3method(candiscList, mlm)
-S3method(coef, candisc)
-S3method(plot, candisc)
-S3method(plot, candiscList)
-S3method(print, candisc)
-S3method(print, candiscList)
-S3method(summary, candisc)
-S3method(summary, candiscList)
-
-# the following may be moved to the heplots package
-S3method(heplot, candisc)
-S3method(heplot3d, candisc)
-S3method(heplot, candiscList)
-S3method(heplot3d, candiscList)
-
-# new for cancor
-S3method(cancor, default)
-S3method(cancor, formula)
-S3method(print, cancor)
-S3method(summary, cancor)
-S3method(coef, cancor)
-S3method(Wilks, cancor)
-S3method(Wilks, candisc)
-S3method(heplot, cancor)
-S3method(scores, cancor)
-S3method(print, cancor.redundancy)
-S3method(plot, cancor)
-S3method(heplot3d, cancor)
-
-S3method(varOrder, mlm)
-S3method(varOrder, data.frame)
-
-
-
-
-
-
-
-
-
+# Generated by roxygen2: do not edit by hand
+
+S3method(Wilks,cancor)
+S3method(Wilks,candisc)
+S3method(cancor,default)
+S3method(cancor,formula)
+S3method(candisc,mlm)
+S3method(candiscList,mlm)
+S3method(coef,cancor)
+S3method(coef,candisc)
+S3method(heplot,cancor)
+S3method(heplot,candisc)
+S3method(heplot,candiscList)
+S3method(heplot3d,cancor)
+S3method(heplot3d,candisc)
+S3method(heplot3d,candiscList)
+S3method(plot,cancor)
+S3method(plot,candisc)
+S3method(plot,candiscList)
+S3method(predictor.names,default)
+S3method(print,cancor)
+S3method(print,cancor.redundancy)
+S3method(print,candisc)
+S3method(print,candiscList)
+S3method(scores,cancor)
+S3method(summary,cancor)
+S3method(summary,candisc)
+S3method(summary,candiscList)
+S3method(varOrder,data.frame)
+S3method(varOrder,default)
+S3method(varOrder,mlm)
+export(Wilks)
+export(can_lm)
+export(cancor)
+export(candisc)
+export(candiscList)
+export(dataIndex)
+export(predictor.names)
+export(redundancy)
+export(scores)
+export(varOrder)
+export(vecscale)
+export(vectors)
+importFrom(car,Anova)
+importFrom(car,dataEllipse)
+importFrom(car,loessLine)
+importFrom(car,showLabels)
+importFrom(grDevices,palette)
+importFrom(graphics,abline)
+importFrom(graphics,arrows)
+importFrom(graphics,boxplot)
+importFrom(graphics,layout)
+importFrom(graphics,lines)
+importFrom(graphics,par)
+importFrom(graphics,points)
+importFrom(graphics,polygon)
+importFrom(graphics,symbols)
+importFrom(graphics,text)
+importFrom(heplots,heplot)
+importFrom(heplots,heplot3d)
+importFrom(stats,aggregate)
+importFrom(stats,complete.cases)
+importFrom(stats,contrasts)
+importFrom(stats,cor)
+importFrom(stats,cov)
+importFrom(stats,cov.wt)
+importFrom(stats,formula)
+importFrom(stats,lsfit)
+importFrom(stats,model.frame)
+importFrom(stats,model.matrix)
+importFrom(stats,model.response)
+importFrom(stats,model.weights)
+importFrom(stats,pf)
+importFrom(stats,qchisq)
+importFrom(stats,terms)
+importFrom(stats,update)
+importFrom(stats,var)
+importFrom(utils,menu)

NAMESPACE-old

@@ -0,0 +1,55 @@
+# last modified 6 October 2007 by J. Fox
+# last modified 22 April 2009 by M. Friendly
+
+import(car)
+
+import(heplots)
+import(graphics)
+import(stats)
+importFrom("grDevices", "palette")
+importFrom("utils", "menu")
+
+export(candisc, candiscList, dataIndex,
+	cancor, vectors, Wilks, scores, redundancy, vecscale, can_lm, varOrder)
+#S3method(can_lm, mlm)
+S3method(candisc, mlm)
+S3method(candiscList, mlm)
+S3method(coef, candisc)
+S3method(plot, candisc)
+S3method(plot, candiscList)
+S3method(print, candisc)
+S3method(print, candiscList)
+S3method(summary, candisc)
+S3method(summary, candiscList)
+
+# the following may be moved to the heplots package
+S3method(heplot, candisc)
+S3method(heplot3d, candisc)
+S3method(heplot, candiscList)
+S3method(heplot3d, candiscList)
+
+# new for cancor
+S3method(cancor, default)
+S3method(cancor, formula)
+S3method(print, cancor)
+S3method(summary, cancor)
+S3method(coef, cancor)
+S3method(Wilks, cancor)
+S3method(Wilks, candisc)
+S3method(heplot, cancor)
+S3method(scores, cancor)
+S3method(print, cancor.redundancy)
+S3method(plot, cancor)
+S3method(heplot3d, cancor)
+
+S3method(varOrder, mlm)
+S3method(varOrder, data.frame)
+
+
+
+
+
+
+
+
+

NEWS.md

@@ -1,3 +1,10 @@
+## Version 0.9.0 (2024-05-05)
+
+* Created `pkgdown` site, https://friendly.github.io/candisc/
+* Convert documentation to roxygen
+* Extend description of candisc/cancor methods
+* Added `diabetes` vignette giving more discursive examples 
+
 ## Version 0.8-6 (2021-10-06)
 
 * Fix JSS URLs -> DOI

R/.build-steps.R

@@ -0,0 +1,29 @@
+Sys.setenv(RGL_USE_NULL = TRUE)
+
+# get list of possibly misspelled words
+wds <- spelling::spell_check_package()
+cat(paste(wds[, "word"], collapse = "\n"))
+# to add all words
+update_wordlist()
+
+# check reverse dependencies
+devtools::revdep()
+# [1] "Guerry"               "heplots"              "KnowBR"               "MorphoTools2"        
+# [5] "MultivariateAnalysis" "smacof"               "SurveyCC"
+
+# revdep
+#remotes::install_github("r-lib/revdepcheck")
+#library(revdepcheck)
+revdepcheck::revdep_check(num_workers = 4)
+
+
+library(devtools)
+
+# prepare pkgdown site
+build_readme()
+pkgdown::build_site()
+
+devtools::build()
+devtools::build_vignettes()
+
+devtools::check_win_devel()

R/Wilks.cancor.R

@@ -1,7 +1,42 @@
+#' Wilks Lambda Tests for Canonical Correlations
+#' 
+#' Tests the sequential hypotheses that the \eqn{i}th canonical correlation and
+#' all that follow it are zero, \deqn{\rho_i = \rho_{i+1} = \cdots = 0}
+#' 
+#' Wilks' Lambda values are calculated from the eigenvalues and converted to F
+#' statistics using Rao's approximation.
+#' 
+#' @aliases Wilks Wilks.cancor Wilks.candisc
+#' @param object An object of class \code{"cancor""} or \code{"candisc""}
+#' @param \dots Other arguments passed to methods (not used)
+#' @return A data.frame (of class \code{"anova"}) containing the test
+#' statistics 
+#' @author Michael Friendly
+#' @seealso \code{\link{cancor}}, ~~~
+#' @references Mardia, K. V., Kent, J. T. and Bibby, J. M. (1979).
+#' \emph{Multivariate Analysis}. London: Academic Press.
+#' @keywords htest
+#' @examples
+#' 
+#' data(Rohwer, package="heplots")
+#' X <- as.matrix(Rohwer[,6:10])  # the PA tests
+#' Y <- as.matrix(Rohwer[,3:5])   # the aptitude/ability variables
+#' 
+#' cc <- cancor(X, Y, set.names=c("PA", "Ability"))
+#' Wilks(cc)
+#' 
+#' iris.mod <- lm(cbind(Petal.Length, Sepal.Length, Petal.Width, Sepal.Width) ~ Species, data=iris)
+#' iris.can <- candisc(iris.mod, data=iris)
+#' Wilks(iris.can)
+#' 
+#' 
+#' @export Wilks
 Wilks <- function (object, ...) {
 	UseMethod("Wilks")
 }
 
+#' @describeIn Wilks \code{"cancor"} method.
+#' @export
 Wilks.cancor <- function(object, ...) {
 # tests of canonical dimensions
 
@@ -45,6 +80,8 @@ tests
 # Rao's F approximation for canonical discriminant analysis
 # using code from Martina Vandebroek <martina.vandebroek@kuleuven.be>
 
+#' @describeIn Wilks \code{print()} method for \code{"candisc"} objects.
+#' @export
 Wilks.candisc <- function(object, ...) {
 
   ev <- object$eigenvalues

R/can_lm.R

@@ -1,14 +1,31 @@
 #' Transform a Multivariate Linear model mlm to a Canonical Representation
 
+#' @description
+#' 
 #' This function uses \code{\link{candisc}} to transform the responses in a
 #' multivariate linear model to scores on canonical variables for a given term and then uses
 #' those scores as responses in a linear (lm) or multivariate linear model (mlm).
-
+#'
+#' The function constructs a model formula of the form \code{Can ~ terms} where
+#' Can is the canonical score(s) and terms are the terms in the original mlm,
+#' then runs lm() with that formula.
+#' 
+#' 
 #' @param mod A \code{mlm} object
 #' @param term One term in that model
-#' @param ... Arguments passed to \code{\link{candisc}}
+#' @param \dots Arguments passed to \code{\link{candisc}}
 #' @return A \code{lm} object if \code{term} is a rank 1 hypothesis, otherwise a \code{mlm} object
-
+#' @author Michael Friendly
+#' @seealso \code{\link{candisc}}, \code{\link{cancor}}
+#' @examples
+#' 
+#' iris.mod <- lm(cbind(Petal.Length, Sepal.Length, Petal.Width, Sepal.Width) ~ Species, data=iris)
+#' iris.can <- can_lm(iris.mod, "Species")
+#' iris.can
+#' car::Anova(iris.mod)
+#' car::Anova(iris.can)
+#' 
+#' @export can_lm
 can_lm <- function(mod, term, ...) {
   if (!(inherits(mod, "mlm"))) stop("model must be a mlm")
   term.names <- gsub(" ", "", labels(terms(mod)))