Nothing
#Exactly the function 'getfam' included in the package 'geeM',
#authored by Lee S. McDaniel and Nick Henderson
#under the GPL-2 license.
getfam <- function(family){
if(is.character(family)){
family <- get(family, mode = "function", envir = parent.frame(2))
}
if(is.function(family)){
family <- family()
LinkFun <- family$linkfun
InvLink <- family$linkinv
VarFun <- family$variance
InvLinkDeriv <- family$mu.eta
FunList <- list("LinkFun" = LinkFun, "VarFun" = VarFun, "InvLink" = InvLink, "InvLinkDeriv" = InvLinkDeriv)
}else if(is.list(family) && !is.null(family$family)){
LinkFun <- family$linkfun
InvLink <- family$linkinv
VarFun <- family$variance
InvLinkDeriv <- family$mu.eta
FunList <- list("LinkFun" = LinkFun, "VarFun" = VarFun, "InvLink" = InvLink, "InvLinkDeriv" = InvLinkDeriv)
}else if(is.list(family)){
if(length(match(names(family), c("LinkFun", "VarFun", "InvLink", "InvLinkDeriv"))) == 4){
LinkFun <- family$LinkFun
InvLink <- family$InvLink
VarFun <- family$VarFun
InvLinkDeriv <- family$InvLinkDeriv
}else{
LinkFun <- family[[1]]
VarFun <- family[[2]]
InvLink <- family[[3]]
InvLinkDeriv <- family[[4]]
}
FunList <- list("LinkFun" = LinkFun, "VarFun" = VarFun, "InvLink" = InvLink, "InvLinkDeriv" = InvLinkDeriv)
return(FunList)
}else{
stop("problem with family argument: should be string, family object, or list of functions")
}
}
#Exactly the function 'getBlockDiag' included in the package 'geeM',
#authored by Lee S. McDaniel and Nick Henderson
#under the GPL-2 license.
### Get a block diagonal matrix. Each block has dimension corresponding to
### each cluster size. By default, each block is just a matrix filled with ones.
getBlockDiag <- function(len, xvec=NULL){
K <- length(len)
if(is.null(xvec)){
xvec <- rep.int(1, sum(len^2))
}
row.vec <- col.vec <- vector("numeric", sum(len^2))
add.vec <- cumsum(len) - len
index <- c(0, (cumsum(len^2) -len^2)[2:K], sum(len^2))
for(i in 1:K){
row.vec[(index[i] + 1):(index[i+1])] <- rep.int( (1:len[i]) + add.vec[i], len[i])
col.vec[(index[i] + 1):(index[i+1])] <- rep( (1:len[i]) + add.vec[i], each=len[i])
}
BlockDiag <- sparseMatrix(i = row.vec, j = col.vec, x = xvec)
return(list(BDiag = as(BlockDiag, "symmetricMatrix"), row.vec =row.vec, col.vec=col.vec))
}
#Exactly the function 'checkFixedMat' included in the package 'geeM',
#authored by Lee S. McDaniel and Nick Henderson
#under the GPL-2 license.
### Check some conditions on the FIXED correlation structure.
checkFixedMat <- function(corr.mat, len){
if(is.null(corr.mat)){
stop("corr.mat must be specified if using fixed correlation structure")
}
if(dim(corr.mat)[1] < max(len)){
stop("Dimensions of corr.mat must be at least as large as largest cluster")
}
if(!isSymmetric(corr.mat)){
stop("corr.mat must be symmetric")
}
if(determinant(corr.mat, logarithm=T)$modulus == -Inf){
stop("supplied correlation matrix is not invertible.")
}
return(corr.mat[1:max(len), 1:max(len)])
}
#' Fit CRTgeeDR object.
#'
#' Fit CRTgeeDR object to a dataset
#'
#' @param object CRTgeeDR object
#' @param ... ignored
#' @aliases fitted.CRTgeeDR fitted
#' @method fitted CRTgeeDR
#' @export
### fitted function for CRTgeeDR object
fitted.CRTgeeDR <- function(object, ...){
InvLink <- object$FunList$InvLink
return(InvLink(object$eta))
}
#' Predict CRTgeeDR object.
#'
#' Predict CRTgeeDR object to a dataset
#'
#' @param object CRTgeeDR object
#' @param newdata dataframe, new dataset to which the CRTgeeDRneed to be used for prediction
#' @param ... ignored
#' @method predict CRTgeeDR
#' @aliases predict.CRTgeeDR predict
#' @export
predict.CRTgeeDR <- function(object, newdata = NULL,...){
coefs <- object$beta
if(is.null(newdata)){
return(as.vector(object$X %*% object$beta))
}else{
if(dim(newdata)[2] != length(coefs)){warning("New observations must have the same number of rows as coefficients in the model")}
return(as.vector(newdata %*% object$beta))
}
}
cleandata<-function(dat,type,nameY,cc,formula,print=TRUE){
na.inds <- NULL
if(any(is.na(dat))){
na.inds <- which(is.na(dat), arr.ind=T)
}
if(sum(c(which(colnames(dat)%in%all.vars(formula[-2])))%in%na.inds[,2])!=0){
if(type=="marginal model"){
if(print)warning(paste("It exists missing data for covariates in the ",type," model \n -> Weights for these observation are set to 0",sep=""))
}else{
if(print)warning(paste("It exists missing data for covariates in the ",type," model \n -> Single imputation had been used for computation",sep=""))
}
}
if(!is.null(na.inds)){
if(cc){
#### If missing set to median value (No problem for outcome but carefull with covariates)
dat$weights[unique(na.inds[,1])] <- 0
for(i in unique(na.inds[,2])){
if(is.factor(dat[,i])){
dat[na.inds[,1], i] <- levels(dat[,i])[1]
}else{
dat[na.inds[,1], i] <- median(dat[,i], na.rm=T)
}
}
}else{
for(i in unique(na.inds[,2][!na.inds[,2] %in% which(colnames(dat)==nameY)])){
if(is.factor(dat[,i])){
dat[na.inds[,1], i] <- levels(dat[,i])[1]
}else{
dat[na.inds[,1], i] <- median(dat[,i], na.rm=T)
}
}
}
}
return(dat)
}
#Exactly the function 'cormax.ind' included in the package 'geesmv',
#authored by Ming Wang
#under the GPL-2 license.
cormax.ind <-
function(n){
matrix<-matrix(0,nrow=n,ncol=n)
diag(matrix)<-rep(1,n)
return(matrix)
}
#Exactly the function 'cormax.ar1' included in the package 'geesmv',
#authored by Ming Wang
#under the GPL-2 license.
cormax.ar1 <-
function(n, alpha){
n.max<- max(n)
cor.max<- diag(1,n.max)
lowertri<- rep(0,0)
for(j in (n.max-1):1){
lowertri<- c(lowertri,1:j)
}
cor.max[lower.tri(cor.max)]<- alpha^lowertri
cor.max[upper.tri(cor.max)]<- alpha^lowertri[length(lowertri):1]
return(cor.max)
}
#Exactly the function 'cormax.exch' included in the package 'geesmv',
#authored by Ming Wang
#under the GPL-2 license.
cormax.exch <-
function(n, alpha){
n.max<- n
cor.max<- diag(1,n.max)
cor.max[lower.tri(cor.max)]<- rep(alpha,n.max*(n.max-1)/2)
cor.max[upper.tri(cor.max)]<- rep(alpha,n.max*(n.max-1)/2)
return(cor.max)
}
#Exactly the function 'cluster.size' included in the package 'geesmv',
#authored by Ming Wang
#under the GPL-2 license.
cluster.size <-
function(id){
clid<- unique(id)
m<- length(unique(id))
n<- rep(0,m)
autotime<- rep(0,0)
for(i in 1:m){
n[i]<- length(which(id==clid[i]))
autotime<- c(autotime,1:n[i])
}
id<- rep(1:m,n)
return(list(m=m,n=n,id=id,autotime=autotime))
}
#Exactly the function 'vec' included in the package 'fBasics',
#authored by Rmetrics Core Team
#under the GPL-2 license.
vec <-
function(x)
{
t(t(as.vector(x)))
}
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