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LECASofts
ProcMod
Commits
6e42ea2c
Commit
6e42ea2c
authored
Oct 01, 2019
by
Eric Coissac
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Plain Diff
renames types procmod.corls et procmod.varls to procmod_corls, and procmod_varls
parent
31bf9388
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Showing
5 changed files
with
27 additions
and
27 deletions
+27
-27
NAMESPACE
NAMESPACE
+6
-6
covls.R
R/covls.R
+12
-12
print.procmod_corls.Rd
man/print.procmod_corls.Rd
+4
-4
print.procmod_varls.Rd
man/print.procmod_varls.Rd
+4
-4
varls.Rd
man/varls.Rd
+1
-1
No files found.
NAMESPACE
View file @
6e42ea2c
# Generated by roxygen2: do not edit by hand
S3method("$",procmod
.
corls)
S3method("$",procmod
.
varls)
S3method("$",procmod
_
corls)
S3method("$",procmod
_
varls)
S3method("$<-",procmod_frame)
S3method("[",procmod_frame)
S3method("[[<-",procmod_frame)
...
...
@@ -12,14 +12,14 @@ S3method(as_procmod_frame,list)
S3method(as_procmod_frame,matrix)
S3method(as_procmod_frame,procmod_frame)
S3method(dim,procmod_frame)
S3method(names,procmod
.
corls)
S3method(names,procmod
.
varls)
S3method(names,procmod
_
corls)
S3method(names,procmod
_
varls)
S3method(ortho,data.frame)
S3method(ortho,dist)
S3method(ortho,matrix)
S3method(ortho,procmod_frame)
S3method(print,procmod
.
corls)
S3method(print,procmod
.
varls)
S3method(print,procmod
_
corls)
S3method(print,procmod
_
varls)
S3method(subset,procmod_frame)
export(as_procmod_frame)
export(bicenter)
...
...
R/covls.R
View file @
6e42ea2c
...
...
@@ -102,7 +102,7 @@ registerDoParallel(1)
#' \code{"BH"}, \code{"BY"}, \code{"fdr"}, \code{"none"}.
#' 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.
#'
#' The following attribute is always added:
...
...
@@ -257,7 +257,7 @@ varls <- function(...,
colnames
(
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,
attr
(
rls
,
"nrand"
)
<-
attr
(
cov
,
"nrand"
)
}
make_subS3Class
(
rls
,
"procmod
.
corls"
)
make_subS3Class
(
rls
,
"procmod
_
corls"
)
}
#' @rdname varls
...
...
@@ -294,12 +294,12 @@ corls.partial <- function(..., nrand = 100) {
attr
(
rp
,
"nrand"
)
<-
attr
(
rls
,
"nrand"
)
attr
(
rp
,
"rcovls"
)
<-
attr
(
rls
,
"rcovls"
)
make_subS3Class
(
rp
,
"procmod
.
corls"
)
make_subS3Class
(
rp
,
"procmod
_
corls"
)
}
#' Print procrustean variance / covariance matrix.
#'
#' @param x a \code{procmod
.
varls}
#' @param x a \code{procmod
_
varls}
#' object
#' @param ... other parameters passed to other functions
#'
...
...
@@ -308,7 +308,7 @@ corls.partial <- function(..., nrand = 100) {
#' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima
#' @export
print.procmod
.
varls
<-
function
(
x
,
...
)
{
print.procmod
_
varls
<-
function
(
x
,
...
)
{
class
(
x
)
<-
"matrix"
attr
(
x
,
"nrand"
)
<-
NULL
attr
(
x
,
"rcovls"
)
<-
NULL
...
...
@@ -319,14 +319,14 @@ print.procmod.varls <- function(x, ...) {
#' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima
#' @export
`$.procmod
.
varls`
<-
function
(
x
,
name
)
{
`$.procmod
_
varls`
<-
function
(
x
,
name
)
{
attr
(
x
,
name
)
}
#' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima
#' @export
names.procmod
.
varls
<-
function
(
x
)
{
names.procmod
_
varls
<-
function
(
x
)
{
n
<-
names
(
attributes
(
x
))
bn
<-
grep
(
pattern
=
"^(dim|class)"
,
x
=
n
)
...
...
@@ -336,7 +336,7 @@ names.procmod.varls <- function(x) {
#' Print procrustean correlation matrix.
#'
#' @param x a \code{procmod
.
corls}
#' @param x a \code{procmod
_
corls}
#' object
#' @param ... other parameters passed to other functions
#'
...
...
@@ -345,7 +345,7 @@ names.procmod.varls <- function(x) {
#' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima
#' @export
print.procmod
.
corls
<-
function
(
x
,
...
)
{
print.procmod
_
corls
<-
function
(
x
,
...
)
{
class
(
x
)
<-
"matrix"
attr
(
x
,
"nrand"
)
<-
NULL
attr
(
x
,
"rcovls"
)
<-
NULL
...
...
@@ -357,7 +357,7 @@ print.procmod.corls <- function(x, ...) {
#' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima
#' @export
`$.procmod
.
corls`
<-
function
(
x
,
name
)
{
`$.procmod
_
corls`
<-
function
(
x
,
name
)
{
attr
(
x
,
name
)
}
...
...
@@ -365,7 +365,7 @@ print.procmod.corls <- function(x, ...) {
#' @author Eric Coissac
#' @author Christelle Gonindard-Melodelima
#' @export
names.procmod
.
corls
<-
function
(
x
)
{
names.procmod
_
corls
<-
function
(
x
)
{
n
<-
names
(
attributes
(
x
))
bn
<-
grep
(
pattern
=
"^(dim|class)"
,
x
=
n
)
...
...
man/print.procmod
.
corls.Rd
→
man/print.procmod
_
corls.Rd
View file @
6e42ea2c
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/covls.R
\name{print.procmod
.
corls}
\alias{print.procmod
.
corls}
\name{print.procmod
_
corls}
\alias{print.procmod
_
corls}
\title{Print procrustean correlation matrix.}
\usage{
\method{print}{procmod
.
corls}(x, ...)
\method{print}{procmod
_
corls}(x, ...)
}
\arguments{
\item{x}{a \code{procmod
.
corls}
\item{x}{a \code{procmod
_
corls}
object}
\item{...}{other parameters passed to other functions}
...
...
man/print.procmod
.
varls.Rd
→
man/print.procmod
_
varls.Rd
View file @
6e42ea2c
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/covls.R
\name{print.procmod
.
varls}
\alias{print.procmod
.
varls}
\name{print.procmod
_
varls}
\alias{print.procmod
_
varls}
\title{Print procrustean variance / covariance matrix.}
\usage{
\method{print}{procmod
.
varls}(x, ...)
\method{print}{procmod
_
varls}(x, ...)
}
\arguments{
\item{x}{a \code{procmod
.
varls}
\item{x}{a \code{procmod
_
varls}
object}
\item{...}{other parameters passed to other functions}
...
...
man/varls.Rd
View file @
6e42ea2c
...
...
@@ -30,7 +30,7 @@ belongsone of the folowing values: \code{"holm"},
The default is,set to \code{"holm"}.}
}
\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.
The following attribute is always added:
...
...
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