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## PGLS.R (2022-06-22)
## Phylogenetic Generalized Least Squares
## Copyright 2004-2021 Julien Dutheil, and 2006-2017 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
corBrownian <- function(value = 1, phy, form = ~1)
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
attr(value, "formula") <- form
attr(value, "fixed") <- TRUE
attr(value, "tree") <- phy
class(value) <- c("corBrownian", "corPhyl", "corStruct")
value
}
corMartins <- function(value, phy, form = ~1, fixed = FALSE)
{
if (length(value) > 1)
stop("only one parameter is allowed")
if (value < 0) stop("the parameter alpha must be positive")
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
attr(value, "formula") <- form
attr(value, "fixed") <- fixed
attr(value, "tree") <- phy
class(value) <- c("corMartins", "corPhyl", "corStruct")
value
}
corGrafen <- function(value, phy, form = ~1, fixed = FALSE)
{
if (length(value) > 1)
stop("only one parameter is allowed")
if (value < 0) stop("parameter rho must be positive")
value <- log(value) # Optimization under constraint, use exponential transform.
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
attr(value, "formula") <- form
attr(value, "fixed") <- fixed
attr(value, "tree") <- phy
class(value) <- c("corGrafen", "corPhyl", "corStruct")
value
}
Initialize.corPhyl <- function(object, data, ...)
{
## The same as in Initialize corStruct:
form <- formula(object)
if (getCovariateFormula(object) == ~1) {
warning("No covariate specified, species will be taken as ordered in the data frame. To avoid this message, specify a covariate containing the species names with the 'form' argument.")
}
## Obtaining the group information, if any
if (is.null(getGroupsFormula(form))) {
attr(object, "Dim") <- Dim(object, as.factor(rep(1, nrow(data))))
} else { # no groups
attr(object, "groups") <- getGroups(object, form, data = data)
attr(object, "Dim") <- Dim(object, attr(object, "groups"))
}
## Obtaining the covariate(s)
attr(object, "covariate") <- getCovariate(object, data = data)
object
}
corMatrix.corBrownian <-
function(object, covariate = getCovariate(object), corr = TRUE, ...)
{
if (!("corBrownian" %in% class(object)))
stop('object is not of class "corBrownian"')
if (data.class(covariate) == "list") {
as.list(lapply(covariate, function(el) corMatrix(object, covariate = el)))
} else {
tree <- attr(object, "tree")
mat <- vcv.phylo(tree, corr = corr)
if (formula(object) == ~1) return(mat) # added by EP (2022-06-22)
covariate <- as.character(covariate)
mat[covariate, covariate]
}
}
corMatrix.corMartins <-
function(object, covariate = getCovariate(object), corr = TRUE, ...)
{
if (!("corMartins" %in% class(object)))
stop('object is not of class "corMartins"')
if (data.class(covariate) == "list") {
as.list(lapply(covariate, function(el) corMatrix(object, covariate = el)))
} else {
tree <- attr(object, "tree")
dist <- cophenetic.phylo(tree)
mat <- exp(-object[1] * dist)
if (corr) mat <- cov2cor(mat)
if (formula(object) == ~1) return(mat) # added by EP (2022-06-22)
covariate <- as.character(covariate)
mat[covariate, covariate]
}
}
corMatrix.corGrafen <-
function(object, covariate = getCovariate(object), corr = TRUE, ...)
{
if (!("corGrafen" %in% class(object)))
stop('object is not of class "corGrafen"')
if (data.class(covariate) == "list") {
as.list(lapply(covariate, function(el) corMatrix(object, covariate = el)))
} else {
tree <- compute.brlen(attr(object, "tree"),
method = "Grafen", power = exp(object[1]))
mat <- vcv.phylo(tree, corr = corr)
if (formula(object) == ~1) return(mat) # added by EP (2022-06-22)
covariate <- as.character(covariate)
mat[covariate, covariate]
}
}
coef.corBrownian <- function(object, unconstrained = TRUE, ...)
{
if (!("corBrownian" %in% class(object)))
stop('object is not of class "corBrownian"')
numeric(0)
}
coef.corMartins <- function(object, unconstrained = TRUE, ...)
{
if (!("corMartins" %in% class(object)))
stop('object is not of class "corMartins"')
if (unconstrained) {
if (attr(object, "fixed")) {
return(numeric(0))
} else {
return(as.vector(object))
}
}
aux <- as.vector(object)
names(aux) <- "alpha"
aux
}
coef.corGrafen <- function(object, unconstrained = TRUE, ...)
{
if (!("corGrafen" %in% class(object)))
stop('object is not of class "corGrafen"')
if (unconstrained) {
if (attr(object, "fixed")) {
return(numeric(0))
} else {
return(as.vector(object))
}
}
aux <- exp(as.vector(object))
names(aux) <- "rho"
aux
}
## changed by EP (2006-10-12):
compute.brlen <- function(phy, method = "Grafen", power = 1, ...)
{
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
Ntip <- length(phy$tip.label)
Nnode <- phy$Nnode
Nedge <- dim(phy$edge)[1]
if (is.numeric(method)) {
phy$edge.length <- rep(method, length.out = Nedge)
return(phy)
}
if (is.function(method)) {
phy$edge.length <- method(Nedge, ...)
return(phy)
}
if (is.character(method)) { # == "Grafen"
tr <- reorder(phy, "postorder")
xx <- .C(node_depth, as.integer(Ntip),
as.integer(tr$edge[, 1]), as.integer(tr$edge[, 2]),
as.integer(Nedge), double(Ntip + Nnode), 1L)[[5]] - 1
m <- Ntip - 1
phy$edge.length <-
(xx[phy$edge[, 1]]/m)^power - (xx[phy$edge[, 2]]/m)^power
return(phy)
}
}
## by EP:
corPagel <- function(value, phy, form = ~1, fixed = FALSE)
{
if (value < 0 || value > 1)
stop("the value of lambda must be between 0 and 1.")
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
attr(value, "formula") <- form
attr(value, "fixed") <- fixed
attr(value, "tree") <- phy
class(value) <- c("corPagel", "corPhyl", "corStruct")
value
}
corMatrix.corPagel <-
function(object, covariate = getCovariate(object), corr = TRUE, ...)
{
if (!("corPagel" %in% class(object)))
stop('object is not of class "corPagel"')
if (data.class(covariate) == "list") {
as.list(lapply(covariate, function(el) corMatrix(object, covariate = el)))
} else {
mat <- vcv.phylo(attr(object, "tree"), corr = corr)
tmp <- diag(mat)
mat <- object[1]*mat
diag(mat) <- tmp
if (formula(object) == ~1) return(mat) # added by EP (2022-06-22)
covariate <- as.character(covariate)
mat[covariate, covariate]
}
}
coef.corPagel <- function(object, unconstrained = TRUE, ...)
{
if (unconstrained) {
if (attr(object, "fixed")) return(numeric(0))
else return(object[1])
}
aux <- object[1]
names(aux) <- "lambda"
aux
}
corBlomberg <- function(value, phy, form = ~1, fixed = FALSE)
{
if (value <= 0)
stop("the value of g must be greater than 0.")
if (!inherits(phy, "phylo"))
stop('object "phy" is not of class "phylo"')
attr(value, "formula") <- form
attr(value, "fixed") <- fixed
attr(value, "tree") <- phy
class(value) <- c("corBlomberg", "corPhyl", "corStruct")
value
}
corMatrix.corBlomberg <-
function(object, covariate = getCovariate(object), corr = TRUE, ...)
{
if (object[1] <= 0)
stop("the optimization has reached a value <= 0 for parameter 'g':
probably need to set 'fixed = TRUE' in corBlomberg().")
if (data.class(covariate) == "list") {
as.list(lapply(covariate, function(el) corMatrix(object, covariate = el)))
} else {
phy <- attr(object, "tree")
d <- (dist.nodes(phy)[length(phy$tip.label) + 1, ])^(1/object[1])
phy$edge.length <- d[phy$edge[, 2]] - d[phy$edge[, 1]]
mat <- vcv.phylo(phy, corr = corr)
if (formula(object) == ~1) return(mat) # added by EP (2022-06-22)
covariate <- as.character(covariate)
mat[covariate, covariate]
}
}
coef.corBlomberg <- function(object, unconstrained = TRUE, ...)
{
if (unconstrained) {
if (attr(object, "fixed")) return(numeric(0))
else return(object[1])
}
aux <- object[1]
names(aux) <- "g"
aux
}
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