Commit 700d5756 by Eric Coissac

Rename procmod.frame procmod_frame

parent ee0efebb
...@@ -2,37 +2,37 @@ ...@@ -2,37 +2,37 @@
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)
S3method(as.data.frame,dist) S3method(as.data.frame,dist)
S3method(as.list,procmod.frame) S3method(as.list,procmod_frame)
S3method(as.procmod.frame,array) S3method(as.procmod_frame,array)
S3method(as.procmod.frame,list) 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)
export(corls) export(corls)
export(corls.partial) export(corls.partial)
export(corls.test) export(corls.test)
export(is.euclid) export(is.euclid)
export(is.procmod.frame) export(is.procmod_frame)
export(nmds) export(nmds)
export(ortho) export(ortho)
export(pca) export(pca)
export(pcoa) export(pcoa)
export(procmod.frame) export(procmod_frame)
export(protate) export(protate)
export(simulate_correlation) export(simulate_correlation)
export(simulate_matrix) export(simulate_matrix)
......
...@@ -51,7 +51,7 @@ NULL ...@@ -51,7 +51,7 @@ NULL
#' performs a Monte-Carlo Test on the sum of the singular values of a #' performs a Monte-Carlo Test on the sum of the singular values of a
#' procustean rotation (see \code{\link[ade4]{procuste.rtest}}). #' procustean rotation (see \code{\link[ade4]{procuste.rtest}}).
#' #'
#' @param ... the set of matrices or a \code{\link[ProcMod]{procmod.frame}} #' @param ... the set of matrices or a \code{\link[ProcMod]{procmod_frame}}
#' object. #' object.
#' @param permutations a list of control values for the permutations as returned #' @param permutations a list of control values for the permutations as returned
#' by the function \code{\link[permute]{how}}, or the number of #' by the function \code{\link[permute]{how}}, or the number of
...@@ -80,14 +80,14 @@ corls.test <- function(..., ...@@ -80,14 +80,14 @@ corls.test <- function(...,
if (length(xs) == 1) { if (length(xs) == 1) {
x <- xs[[1]] x <- xs[[1]]
if (is.procmod.frame(x)) { if (is.procmod_frame(x)) {
xs <- x xs <- x
} else { } else {
xs <- procmod.frame(x) xs <- procmod_frame(x)
} }
} }
else { else {
xs <- as.procmod.frame(xs) xs <- as.procmod_frame(xs)
} }
x_names <- names(xs) x_names <- names(xs)
...@@ -117,7 +117,7 @@ corls.test <- function(..., ...@@ -117,7 +117,7 @@ corls.test <- function(...,
replace = FALSE replace = FALSE
) )
rcov = varls(as.procmod.frame( rcov = varls(as.procmod_frame(
lapply( lapply(
1:nx, 1:nx,
function(j) xs[[j]][pmatrix[ps[j], ], ] function(j) xs[[j]][pmatrix[ps[j], ], ]
......
...@@ -66,7 +66,7 @@ registerDoParallel(1) ...@@ -66,7 +66,7 @@ registerDoParallel(1)
#' #'
#' The inputs must be numeric matrices or \code{\link[stats]{dist}} object. #' The inputs must be numeric matrices or \code{\link[stats]{dist}} object.
#' The set of input matrices can be aggregated un a #' The set of input matrices can be aggregated un a
#' \code{\link[ProcMod]{procmod.frame}}. #' \code{\link[ProcMod]{procmod_frame}}.
#' #'
#' Before computing the coefficients, matrices are projected into an #' Before computing the coefficients, matrices are projected into an
#' orthogonal space using the \code{\link[ProcMod]{ortho}} function. #' orthogonal space using the \code{\link[ProcMod]{ortho}} function.
...@@ -88,7 +88,7 @@ registerDoParallel(1) ...@@ -88,7 +88,7 @@ registerDoParallel(1)
#' \insertRef{Coissac-Eric:19:00}{ProcMod} #' \insertRef{Coissac-Eric:19:00}{ProcMod}
#' } #' }
#' #'
#' @param ... the set of matrices or a \code{\link[ProcMod]{procmod.frame}} #' @param ... the set of matrices or a \code{\link[ProcMod]{procmod_frame}}
#' object. #' object.
#' @param nrand number of randomisation used to estimate the mean #' @param nrand number of randomisation used to estimate the mean
#' covariance observed between two random matrix. #' covariance observed between two random matrix.
...@@ -131,7 +131,7 @@ registerDoParallel(1) ...@@ -131,7 +131,7 @@ registerDoParallel(1)
#' # compute the variance covariance matrix #' # compute the variance covariance matrix
#' varls(A, B, C) #' varls(A, B, C)
#' varls(A = A, B = B, C = C) #' varls(A = A, B = B, C = C)
#' data = procmod.frame(A = A, B = B, C = C) #' data = procmod_frame(A = A, B = B, C = C)
#' varls(data) #' varls(data)
#' #'
#' @author Eric Coissac #' @author Eric Coissac
...@@ -158,14 +158,14 @@ varls <- function(..., ...@@ -158,14 +158,14 @@ varls <- function(...,
if (length(xs) == 1) { if (length(xs) == 1) {
x <- xs[[1]] x <- xs[[1]]
if (is.procmod.frame(x)) { if (is.procmod_frame(x)) {
xs <- x xs <- x
} else { } else {
xs <- procmod.frame(x) xs <- procmod_frame(x)
} }
} }
else { else {
xs <- as.procmod.frame(xs) xs <- as.procmod_frame(xs)
} }
x_names <- names(xs) x_names <- names(xs)
......
...@@ -230,7 +230,7 @@ is.euclid <- function(distances, tol = 1e-07) { ...@@ -230,7 +230,7 @@ is.euclid <- function(distances, tol = 1e-07) {
} }
is.orthogonal <- function(x) { is.orthogonal <- function(x) {
stopifnot(is.procmod.frame(x)) stopifnot(is.procmod_frame(x))
!is.null(attr(x, "projected")) !is.null(attr(x, "projected"))
} }
...@@ -295,7 +295,7 @@ ortho.data.frame <- function(data, scale = FALSE, ...) { ...@@ -295,7 +295,7 @@ ortho.data.frame <- function(data, scale = FALSE, ...) {
#' @rdname ortho #' @rdname ortho
#' @export #' @export
ortho.procmod.frame <- function(data, ...) { ortho.procmod_frame <- function(data, ...) {
if (is.orthogonal(data)) { if (is.orthogonal(data)) {
return(data) return(data)
} }
......
...@@ -48,7 +48,7 @@ NULL ...@@ -48,7 +48,7 @@ NULL
#' @param nrows an interger value specifying the number of row #' @param nrows an interger value specifying the number of row
#' of the returned matrix #' of the returned matrix
#' @param contrasts see the \code{contrasts.arg} argument #' @param contrasts see the \code{contrasts.arg} argument
#' of the \code{\link[ProcMod]{procmod.frame}} #' of the \code{\link[ProcMod]{procmod_frame}}
#' constructor. #' constructor.
#' #'
#' @return a new numeric matrix with correct size. #' @return a new numeric matrix with correct size.
...@@ -166,20 +166,20 @@ NULL ...@@ -166,20 +166,20 @@ NULL
} }
#' The procmod.frame data structure. #' The procmod_frame data structure.
#' #'
#' A \code{procmod.frame} can be considered as the analog of a #' A \code{procmod_frame} can be considered as the analog of a
#' \code{data.frame} for vector data. In a \code{procmod.frame} #' \code{data.frame} for vector data. In a \code{procmod_frame}
#' each element, equivalent to a column in a \code{data.frame} #' each element, equivalent to a column in a \code{data.frame}
#' is a numeric matrix or a distance matrix object (\code{dist}). #' is a numeric matrix or a distance matrix object (\code{dist}).
#' Every element must describe the same number of individuals. #' Every element must describe the same number of individuals.
#' Therefore every numeric matrix must have the same number of row #' Therefore every numeric matrix must have the same number of row
#' (\code{nrow}) and every distance matrix must have the same size #' (\code{nrow}) and every distance matrix must have the same size
#' (\code{attr(d,"Size")}). A \code{procmod.frame} can simultaneously #' (\code{attr(d,"Size")}). A \code{procmod_frame} can simultaneously
#' contain both types of data, numeric and distance matrix. #' contain both types of data, numeric and distance matrix.
#' #'
#' @param ... a set of objects to aggregate into a #' @param ... a set of objects to aggregate into a
#' \code{procmod.frame}. These objects can be #' \code{procmod_frame}. These objects can be
#' numeric matrices, or dist objects. Every objects #' numeric matrices, or dist objects. Every objects
#' must have the same number of row. #' must have the same number of row.
#' #'
...@@ -188,12 +188,12 @@ NULL ...@@ -188,12 +188,12 @@ NULL
#' #'
#' @param check.rows a logical value. When set to \code{TRUE}, its #' @param check.rows a logical value. When set to \code{TRUE}, its
#' default value, the number of row of every elements of the #' default value, the number of row of every elements of the
#' \code{procmod.frame} are tested for equality. Otherwise no #' \code{procmod_frame} are tested for equality. Otherwise no
#' check is done. #' check is done.
#' #'
#' @param reorder.rows a logical value. When set to \code{TRUE}, its #' @param reorder.rows a logical value. When set to \code{TRUE}, its
#' default value, every elements of the #' default value, every elements of the
#' \code{procmod.frame} are reordered according to the \code{row.names} #' \code{procmod_frame} are reordered according to the \code{row.names}
#' order. Otherwise nothing is done. #' order. Otherwise nothing is done.
#' #'
#' @param contrasts.arg A list, whose entries are values #' @param contrasts.arg A list, whose entries are values
...@@ -202,7 +202,7 @@ NULL ...@@ -202,7 +202,7 @@ NULL
#' replacement function and whose names are the names #' replacement function and whose names are the names
#' of columns of data containing factors. #' of columns of data containing factors.
#' #'
#' @return a \code{procmod.frame} instance. #' @return a \code{procmod_frame} instance.
#' #'
#' @examples #' @examples
#' library(vegan) #' library(vegan)
...@@ -210,7 +210,7 @@ NULL ...@@ -210,7 +210,7 @@ NULL
#' data(eukaryotes) #' data(eukaryotes)
#' data(soil) #' data(soil)
#' #'
#' dataset <- procmod.frame(euk = vegdist(decostand(eukaryotes, #' dataset <- procmod_frame(euk = vegdist(decostand(eukaryotes,
#' method = "hellinger"), #' method = "hellinger"),
#' method = "euclidean"), #' method = "euclidean"),
#' bac = vegdist(decostand(bacteria, #' bac = vegdist(decostand(bacteria,
...@@ -227,7 +227,7 @@ NULL ...@@ -227,7 +227,7 @@ NULL
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
procmod.frame <- function(..., procmod_frame <- function(...,
row.names = NULL, row.names = NULL,
check.rows = TRUE, check.rows = TRUE,
reorder.rows = TRUE, reorder.rows = TRUE,
...@@ -297,7 +297,7 @@ procmod.frame <- function(..., ...@@ -297,7 +297,7 @@ procmod.frame <- function(...,
.siteNames(value[[i]]) <- NULL .siteNames(value[[i]]) <- NULL
} }
make_subS3Class(value, "procmod.frame") make_subS3Class(value, "procmod_frame")
} }
#' #'
...@@ -306,14 +306,14 @@ procmod.frame <- function(..., ...@@ -306,14 +306,14 @@ procmod.frame <- function(...,
#' @param x a R \code{object to test} #' @param x a R \code{object to test}
#' #'
#' @return a \code{logical} value equals to #' @return a \code{logical} value equals to
#' \code{TRUE} if \code{x} is a \code{procmod.frame}, #' \code{TRUE} if \code{x} is a \code{procmod_frame},
#' \code{FALSE} otherwise. #' \code{FALSE} otherwise.
#' #'
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
is.procmod.frame <- function(x) { is.procmod_frame <- function(x) {
inherits(x, "procmod.frame") inherits(x, "procmod_frame")
} }
#' #'
...@@ -325,31 +325,31 @@ is.procmod.frame <- function(x) { ...@@ -325,31 +325,31 @@ is.procmod.frame <- function(x) {
#' @param data a R object to coerce. #' @param data a R object to coerce.
#' @param ... supplementary parameters used in some #' @param ... supplementary parameters used in some
#' implementation of that method #' implementation of that method
#' @return a \code{procmod.frame} object #' @return a \code{procmod_frame} object
#' #'
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
as.procmod.frame <- function(data, ...) { as.procmod_frame <- function(data, ...) {
UseMethod("as.procmod.frame", data) UseMethod("as.procmod_frame", data)
} }
#' @rdname as.procmod.frame #' @rdname as.procmod_frame
#' @export #' @export
as.procmod.frame.list <- function(data, ...) { as.procmod_frame.list <- function(data, ...) {
data <- c(data, list(...)) data <- c(data, list(...))
do.call(procmod.frame, data) do.call(procmod_frame, data)
} }
#' @rdname as.procmod.frame #' @rdname as.procmod_frame
#' @export #' @export
as.procmod.frame.procmod.frame <- function(data, ...) { as.procmod_frame.procmod_frame <- function(data, ...) {
data data
} }
#' @rdname as.procmod.frame #' @rdname as.procmod_frame
#' @export #' @export
as.procmod.frame.array <- function(data, ...) { as.procmod_frame.array <- function(data, ...) {
di <- dim(data) di <- dim(data)
stopifnot(length(di) == 3) stopifnot(length(di) == 3)
...@@ -364,18 +364,18 @@ as.procmod.frame.array <- function(data, ...) { ...@@ -364,18 +364,18 @@ as.procmod.frame.array <- function(data, ...) {
data <- c(l, list(...)) data <- c(l, list(...))
do.call(procmod.frame, l) do.call(procmod_frame, l)
} }
# #' @rdname procmod.frame # #' @rdname procmod_frame
# #' @export # #' @export
# as.procmod.frame.pm <- function(data, ...) { # as.procmod_frame.pm <- function(data, ...) {
# vars.procmod(terms(data), data$model) # vars.procmod(terms(data), data$model)
# } # }
#' @rdname as.procmod.frame #' @rdname as.procmod_frame
#' @export #' @export
as.procmod.frame.matrix <- function(data, ...) { as.procmod_frame.matrix <- function(data, ...) {
l <- vector(mode = "list", length = ncol(data)) l <- vector(mode = "list", length = ncol(data))
for (i in seq_len(ncol(data))) { for (i in seq_len(ncol(data))) {
l[[i]] <- data[, i] l[[i]] <- data[, i]
...@@ -385,24 +385,24 @@ as.procmod.frame.matrix <- function(data, ...) { ...@@ -385,24 +385,24 @@ as.procmod.frame.matrix <- function(data, ...) {
names(l) <- colnames(data) names(l) <- colnames(data)
} }
as.procmod.frame(l) as.procmod_frame(l)
} }
#' Dimensions of a ProcMod Frame. #' Dimensions of a ProcMod Frame.
#' #'
#' @param x a \code{\link[ProcMod]{procmod.frame}} #' @param x a \code{\link[ProcMod]{procmod_frame}}
#' object #' object
#' #'
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
dim.procmod.frame <- function(x) dim.procmod_frame <- function(x)
return(c(.siteCount(x[[1]]), length(x))) return(c(.siteCount(x[[1]]), length(x)))
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
`[[<-.procmod.frame` <- function(x, i, value) { `[[<-.procmod_frame` <- function(x, i, value) {
cl <- class(x) cl <- class(x)
nrows <- .siteCount(x) nrows <- .siteCount(x)
class(x) <- "list" class(x) <- "list"
...@@ -447,7 +447,7 @@ dim.procmod.frame <- function(x) ...@@ -447,7 +447,7 @@ dim.procmod.frame <- function(x)
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
`$<-.procmod.frame` <- function(x, name, value) { `$<-.procmod_frame` <- function(x, name, value) {
x[[name]] <- value x[[name]] <- value
x x
...@@ -456,7 +456,7 @@ dim.procmod.frame <- function(x) ...@@ -456,7 +456,7 @@ dim.procmod.frame <- function(x)
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
`[.procmod.frame` <- function(x, i, j, `[.procmod_frame` <- function(x, i, j,
drop = TRUE) { drop = TRUE) {
has.j <- !missing(j) has.j <- !missing(j)
has.i <- !missing(i) has.i <- !missing(i)
...@@ -497,7 +497,7 @@ dim.procmod.frame <- function(x) ...@@ -497,7 +497,7 @@ dim.procmod.frame <- function(x)
if (drop && length(y) == 1L) { if (drop && length(y) == 1L) {
y <- y[[1]] y <- y[[1]]
} else { } else {
y <- make_subS3Class(y, "procmod.frame") y <- make_subS3Class(y, "procmod_frame")
attr(y, "row.names") <- rownames(y[[1]]) attr(y, "row.names") <- rownames(y[[1]])
} }
...@@ -507,7 +507,7 @@ dim.procmod.frame <- function(x) ...@@ -507,7 +507,7 @@ dim.procmod.frame <- function(x)
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
subset.procmod.frame <- function(x, subset, select, drop = FALSE, ...) { subset.procmod_frame <- function(x, subset, select, drop = FALSE, ...) {
r <- if (missing(subset)) { r <- if (missing(subset)) {
rep_len(TRUE, nrow(x)) rep_len(TRUE, nrow(x))
} else { } else {
...@@ -531,7 +531,7 @@ subset.procmod.frame <- function(x, subset, select, drop = FALSE, ...) { ...@@ -531,7 +531,7 @@ subset.procmod.frame <- function(x, subset, select, drop = FALSE, ...) {
#' @author Eric Coissac #' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima #' @author Christelle Gonindard-Melodelima
#' @export #' @export
as.list.procmod.frame <- function(x, ...) { as.list.procmod_frame <- function(x, ...) {
class(x) <- "list" class(x) <- "list"
x x
......
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/procmod_frame.R % Please edit documentation in R/procmod_frame.R
\name{as.procmod.frame} \name{as.procmod_frame}
\alias{as.procmod.frame} \alias{as.procmod_frame}
\alias{as.procmod.frame.list} \alias{as.procmod_frame.list}
\alias{as.procmod.frame.procmod.frame} \alias{as.procmod_frame.procmod_frame}
\alias{as.procmod.frame.array} \alias{as.procmod_frame.array}
\alias{as.procmod.frame.matrix} \alias{as.procmod_frame.matrix}
\title{Coerce to a ProcMod Frame.} \title{Coerce to a ProcMod Frame.}
\usage{ \usage{
as.procmod.frame(data, ...) as.procmod_frame(data, ...)
\method{as.procmod.frame}{list}(data, ...) \method{as.procmod_frame}{list}(data, ...)
\method{as.procmod.frame}{procmod.frame}(data, ...) \method{as.procmod_frame}{procmod_frame}(data, ...)
\method{as.procmod.frame}{array}(data, ...) \method{as.procmod_frame}{array}(data, ...)
\method{as.procmod.frame}{matrix}(data, ...) \method{as.procmod_frame}{matrix}(data, ...)
} }
\arguments{ \arguments{
\item{data}{a R object to coerce.} \item{data}{a R object to coerce.}
...@@ -25,7 +25,7 @@ as.procmod.frame(data, ...) ...@@ -25,7 +25,7 @@ as.procmod.frame(data, ...)
implementation of that method} implementation of that method}
} }
\value{ \value{
a \code{procmod.frame} object a \code{procmod_frame} object
} }
\description{ \description{
Conversion methods are proposed for \code{list}, Conversion methods are proposed for \code{list},
......
...@@ -8,7 +8,7 @@ corls.test(..., permutations = permute::how(nperm = 999), ...@@ -8,7 +8,7 @@ corls.test(..., permutations = permute::how(nperm = 999),
p.adjust.method = "holm") p.adjust.method = "holm")
} }
\arguments{ \arguments{
\item{...}{the set of matrices or a \code{\link[ProcMod]{procmod.frame}} \item{...}{the set of matrices or a \code{\link[ProcMod]{procmod_frame}}
object.} object.}
\item{permutations}{a list of control values for the permutations as returned \item{permutations}{a list of control values for the permutations as returned
......
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/procmod_frame.R % Please edit documentation in R/procmod_frame.R
\name{dim.procmod.frame} \name{dim.procmod_frame}
\alias{dim.procmod.frame} \alias{dim.procmod_frame}
\title{Dimensions of a ProcMod Frame.} \title{Dimensions of a ProcMod Frame.}
\usage{ \usage{
\method{dim}{procmod.frame}(x) \method{dim}{procmod_frame}(x)
} }
\arguments{ \arguments{
\item{x}{a \code{\link[ProcMod]{procmod.frame}} \item{x}{a \code{\link[ProcMod]{procmod_frame}}
object} object}
} }
\description{ \description{
......
...@@ -13,7 +13,7 @@ ...@@ -13,7 +13,7 @@
of the returned matrix} of the returned matrix}
\item{contrasts}{see the \code{contrasts.arg} argument \item{contrasts}{see the \code{contrasts.arg} argument
of the \code{\link[ProcMod]{procmod.frame}} of the \code{\link[ProcMod]{procmod_frame}}
constructor.} constructor.}
} }
\value{ \value{
......
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/procmod_frame.R % Please edit documentation in R/procmod_frame.R
\name{is.procmod.frame} \name{is.procmod_frame}
\alias{is.procmod.frame} \alias{is.procmod_frame}
\title{Check if an object is a ProcMod Frame.} \title{Check if an object is a ProcMod Frame.}
\usage{ \usage{
is.procmod.frame(x) is.procmod_frame(x)
} }
\arguments{ \arguments{
\item{x}{a R \code{object to test}} \item{x}{a R \code{object to test}}
} }
\value{ \value{
a \code{logical} value equals to a \code{logical} value equals to
\code{TRUE} if \code{x} is a \code{procmod.frame}, \code{TRUE} if \code{x} is a \code{procmod_frame},
\code{FALSE} otherwise. \code{FALSE} otherwise.
} }
\description{ \description{
......
...@@ -5,7 +5,7 @@ ...@@ -5,7 +5,7 @@
\alias{ortho.dist} \alias{ortho.dist}
\alias{ortho.matrix} \alias{ortho.matrix}
\alias{ortho.data.frame} \alias{ortho.data.frame}
\alias{ortho.procmod.frame} \alias{ortho.procmod_frame}
\title{Project a dataset in a euclidean space.} \title{Project a dataset in a euclidean space.}
\usage{ \usage{
ortho(data, ...) ortho(data, ...)
...@@ -16,7 +16,7 @@ ortho(data, ...) ...@@ -16,7 +16,7 @@ ortho(data, ...)
\method{ortho}{data.frame}(data, scale = FALSE, ...) \method{ortho}{data.frame}(data, scale = FALSE, ...)
\method{ortho}{procmod.frame}(data, ...) \method{ortho}{procmod_frame}(data, ...)
} }
\arguments{ \arguments{
\item{data}{a numeric matrix describing the points} \item{data}{a numeric matrix describing the points}
......
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/procmod_frame.R % Please edit documentation in R/procmod_frame.R
\name{procmod.frame} \name{procmod_frame}
\alias{procmod.frame} \alias{procmod_frame}
\title{The procmod.frame data structure.} \title{The procmod_frame data structure.}
\usage{ \usage{
procmod.frame(..., row.names = NULL, check.rows = TRUE, procmod_frame(..., row.names = NULL, check.rows = TRUE,
reorder.rows = TRUE, contrasts.arg = NULL) reorder.rows = TRUE, contrasts.arg = NULL)
} }
\arguments{ \arguments{
\item{...}{a set of objects to aggregate into a \item{...}{a set of objects to aggregate into a
\code{procmod.frame}. These objects can be \code{procmod_frame}. These objects can be
numeric matrices, or dist objects. Every objects numeric matrices, or dist objects. Every objects
must have the same number of row.} must have the same number of row.}