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##' dr_extract generic
##'
##' @title dr_extract
##' @rdname dr-extract
##' @param result DrResult object
##' @return a list that contains components to construct a 'DrResult' object.
##' @export
##' @author Guangchuang Yu
dr_extract <- function(result) UseMethod("dr_extract")
##' @method dr_extract Rtsne
dr_extract.Rtsne <- function(result) {
## Rtsne::Rtsne
drdata <- as.data.frame(result$Y)
eigenvalue <- NULL
stress <- NULL
list(drdata = drdata, eigenvalue = eigenvalue, stress = stress)
}
##' @method dr_extract prcomp
dr_extract.prcomp <- function(result) {
## stats::prcomp
drdata <- as.data.frame(result$x)
eigenvalue <- result$sdev
stress <- NULL
list(drdata = drdata, eigenvalue = eigenvalue, stress = stress)
}
##' @method dr_extract ape
dr_extract.ape <- function(result) {
## ape::pcoa
drdata <- as.data.frame(result$vectors)
stress <- NULL
eigenvalue <- as.numeric(result$values$Eigenvalues)
list(drdata = drdata, eigenvalue = eigenvalue, stress = stress)
}
##' @method dr_extract smacof
dr_extract.smacof <- function(result) {
## smacof::mds
drdata <- as.data.frame(result$conf)
eigenvalue <- NULL
stress <- result$stress
stress <- format(stress, digits=4)
list(drdata = drdata, eigenvalue = eigenvalue, stress = stress)
}
##' @method dr_extract ecodist
dr_extract.ecodist <- function(result) {
## ecodist::pco
drdata <- as.data.frame(result$vectors)
stress <- NULL
eigenvalue <- as.numeric(result$values)
list(drdata = drdata, eigenvalue = eigenvalue, stress = stress)
}
##' @method dr_extract ade4
dr_extract.ade4 <- function(result) {
## ade4::dudi.pco
drdata <- as.data.frame(result$tab)
stress <- NULL
eigenvalue <- as.numeric(result$eig)
list(drdata = drdata, eigenvalue = eigenvalue, stress = stress)
}
##' @method dr_extract uwot
##' @author Lang Zhou
dr_extract.uwot <- function(result) {
## uwot::umap
## uwot::tumap
## uwot::lvish
drdata <- as.data.frame(result)
eigenvalue <- stress <- NULL
list(drdata = drdata, eigenvalue = eigenvalue, stress = stress)
}
##' @method dr_extract default
dr_extract.default <- function(result) {
drdata <- eigenvalue <- stress <- NULL
if ("points" %in% names(result)) {
drdata <- as.data.frame(result$points)
}
if ("eig" %in% names(result)) {
eigenvalue <- as.numeric(result$eig)
}
if ("stress" %in% names(result)) {
stress <- result$stress
stress <- format(stress, digits=4)
}
list(drdata = drdata, eigenvalue = eigenvalue, stress = stress)
}
## vegan::metaMDS
## no eigenvalue
##' @method dr_extract monoMDS
dr_extract.monoMDS <- dr_extract.default
## MASS::sammon
##' @method dr_extract MASS
dr_extract.MASS <- dr_extract.monoMDS
## vegan::wcmdscale
## no stress
##' @method dr_extract wcmdscale
dr_extract.wcmdscale <- dr_extract.default
## labdsv::pco
##' @method dr_extract labdsv
dr_extract.labdsv <- dr_extract.wcmdscale
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