Commit 6e42ea2c by Eric Coissac

renames types procmod.corls et procmod.varls to procmod_corls, and procmod_varls

parent 31bf9388
# Generated by roxygen2: do not edit by hand # Generated by roxygen2: do not edit by hand
S3method("$",procmod.corls) S3method("$",procmod_corls)
S3method("$",procmod.varls) S3method("$",procmod_varls)
S3method("$<-",procmod_frame) S3method("$<-",procmod_frame)
S3method("[",procmod_frame) S3method("[",procmod_frame)
S3method("[[<-",procmod_frame) S3method("[[<-",procmod_frame)
...@@ -12,14 +12,14 @@ S3method(as_procmod_frame,list) ...@@ -12,14 +12,14 @@ S3method(as_procmod_frame,list)
S3method(as_procmod_frame,matrix) S3method(as_procmod_frame,matrix)
S3method(as_procmod_frame,procmod_frame) S3method(as_procmod_frame,procmod_frame)
S3method(dim,procmod_frame) S3method(dim,procmod_frame)
S3method(names,procmod.corls) S3method(names,procmod_corls)
S3method(names,procmod.varls) S3method(names,procmod_varls)
S3method(ortho,data.frame) S3method(ortho,data.frame)
S3method(ortho,dist) S3method(ortho,dist)
S3method(ortho,matrix) S3method(ortho,matrix)
S3method(ortho,procmod_frame) S3method(ortho,procmod_frame)
S3method(print,procmod.corls) S3method(print,procmod_corls)
S3method(print,procmod.varls) S3method(print,procmod_varls)
S3method(subset,procmod_frame) S3method(subset,procmod_frame)
export(as_procmod_frame) export(as_procmod_frame)
export(bicenter) export(bicenter)
......
...@@ -102,7 +102,7 @@ registerDoParallel(1) ...@@ -102,7 +102,7 @@ registerDoParallel(1)
#' \code{"BH"}, \code{"BY"}, \code{"fdr"}, \code{"none"}. #' \code{"BH"}, \code{"BY"}, \code{"fdr"}, \code{"none"}.
#' The default is,set to \code{"holm"}. #' The default is,set to \code{"holm"}.
#' #'
#' @return a \code{procmod.varls} object which corresponds to a numeric #' @return a \code{procmod_varls} object which corresponds to a numeric
#' matrix annotated by several attributes. #' matrix annotated by several attributes.
#' #'
#' The following attribute is always added: #' The following attribute is always added:
...@@ -257,7 +257,7 @@ varls <- function(..., ...@@ -257,7 +257,7 @@ varls <- function(...,
colnames(cov_xxs) <- x_names colnames(cov_xxs) <- x_names
rownames(cov_xxs) <- x_names rownames(cov_xxs) <- x_names
make_subS3Class(cov_xxs, "procmod.varls") make_subS3Class(cov_xxs, "procmod_varls")
} }
...@@ -279,7 +279,7 @@ corls <- function(..., nrand = 100, ...@@ -279,7 +279,7 @@ corls <- function(..., nrand = 100,
attr(rls, "nrand") <- attr(cov, "nrand") attr(rls, "nrand") <- attr(cov, "nrand")
} }
make_subS3Class(rls, "procmod.corls") make_subS3Class(rls, "procmod_corls")
} }
#' @rdname varls #' @rdname varls
...@@ -294,12 +294,12 @@ corls.partial <- function(..., nrand = 100) { ...@@ -294,12 +294,12 @@ corls.partial <- function(..., nrand = 100) {
attr(rp, "nrand") <- attr(rls, "nrand") attr(rp, "nrand") <- attr(rls, "nrand")
attr(rp, "rcovls") <- attr(rls, "rcovls") attr(rp, "rcovls") <- attr(rls, "rcovls")
make_subS3Class(rp, "procmod.corls") make_subS3Class(rp, "procmod_corls")
} }
#' Print procrustean variance / covariance matrix. #' Print procrustean variance / covariance matrix.
#' #'
#' @param x a \code{procmod.varls} #' @param x a \code{procmod_varls}
#' object #' object
#' @param ... other parameters passed to other functions #' @param ... other parameters passed to other functions
#' #'
...@@ -308,7 +308,7 @@ corls.partial <- function(..., nrand = 100) { ...@@ -308,7 +308,7 @@ corls.partial <- function(..., nrand = 100) {
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
print.procmod.varls <- function(x, ...) { print.procmod_varls <- function(x, ...) {
class(x) <- "matrix" class(x) <- "matrix"
attr(x, "nrand") <- NULL attr(x, "nrand") <- NULL
attr(x, "rcovls") <- NULL attr(x, "rcovls") <- NULL
...@@ -319,14 +319,14 @@ print.procmod.varls <- function(x, ...) { ...@@ -319,14 +319,14 @@ print.procmod.varls <- function(x, ...) {
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
`$.procmod.varls` <- function(x, name) { `$.procmod_varls` <- function(x, name) {
attr(x,name) attr(x,name)
} }
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
names.procmod.varls <- function(x) { names.procmod_varls <- function(x) {
n <- names(attributes(x)) n <- names(attributes(x))
bn <- grep(pattern = "^(dim|class)", bn <- grep(pattern = "^(dim|class)",
x = n) x = n)
...@@ -336,7 +336,7 @@ names.procmod.varls <- function(x) { ...@@ -336,7 +336,7 @@ names.procmod.varls <- function(x) {
#' Print procrustean correlation matrix. #' Print procrustean correlation matrix.
#' #'
#' @param x a \code{procmod.corls} #' @param x a \code{procmod_corls}
#' object #' object
#' @param ... other parameters passed to other functions #' @param ... other parameters passed to other functions
#' #'
...@@ -345,7 +345,7 @@ names.procmod.varls <- function(x) { ...@@ -345,7 +345,7 @@ names.procmod.varls <- function(x) {
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
print.procmod.corls <- function(x, ...) { print.procmod_corls <- function(x, ...) {
class(x) <- "matrix" class(x) <- "matrix"
attr(x, "nrand") <- NULL attr(x, "nrand") <- NULL
attr(x, "rcovls") <- NULL attr(x, "rcovls") <- NULL
...@@ -357,7 +357,7 @@ print.procmod.corls <- function(x, ...) { ...@@ -357,7 +357,7 @@ print.procmod.corls <- function(x, ...) {
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
`$.procmod.corls` <- function(x, name) { `$.procmod_corls` <- function(x, name) {
attr(x,name) attr(x,name)
} }
...@@ -365,7 +365,7 @@ print.procmod.corls <- function(x, ...) { ...@@ -365,7 +365,7 @@ print.procmod.corls <- function(x, ...) {
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
names.procmod.corls <- function(x) { names.procmod_corls <- function(x) {
n <- names(attributes(x)) n <- names(attributes(x))
bn <- grep(pattern = "^(dim|class)", bn <- grep(pattern = "^(dim|class)",
x = n) x = n)
......
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/covls.R % Please edit documentation in R/covls.R
\name{print.procmod.corls} \name{print.procmod_corls}
\alias{print.procmod.corls} \alias{print.procmod_corls}
\title{Print procrustean correlation matrix.} \title{Print procrustean correlation matrix.}
\usage{ \usage{
\method{print}{procmod.corls}(x, ...) \method{print}{procmod_corls}(x, ...)
} }
\arguments{ \arguments{
\item{x}{a \code{procmod.corls} \item{x}{a \code{procmod_corls}
object} object}
\item{...}{other parameters passed to other functions} \item{...}{other parameters passed to other functions}
......
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/covls.R % Please edit documentation in R/covls.R
\name{print.procmod.varls} \name{print.procmod_varls}
\alias{print.procmod.varls} \alias{print.procmod_varls}
\title{Print procrustean variance / covariance matrix.} \title{Print procrustean variance / covariance matrix.}
\usage{ \usage{
\method{print}{procmod.varls}(x, ...) \method{print}{procmod_varls}(x, ...)
} }
\arguments{ \arguments{
\item{x}{a \code{procmod.varls} \item{x}{a \code{procmod_varls}
object} object}
\item{...}{other parameters passed to other functions} \item{...}{other parameters passed to other functions}
......
...@@ -30,7 +30,7 @@ belongsone of the folowing values: \code{"holm"}, ...@@ -30,7 +30,7 @@ belongsone of the folowing values: \code{"holm"},
The default is,set to \code{"holm"}.} The default is,set to \code{"holm"}.}
} }
\value{ \value{
a \code{procmod.varls} object which corresponds to a numeric a \code{procmod_varls} object which corresponds to a numeric
matrix annotated by several attributes. matrix annotated by several attributes.
The following attribute is always added: The following attribute is always added:
......
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