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### defineCategoricalLink.R ---
#----------------------------------------------------------------------
## author: Brice Ozenne
## created: okt 26 2017 (16:35)
## Version:
## last-updated: aug 6 2018 (15:32)
## By: Brice Ozenne
## Update #: 156
#----------------------------------------------------------------------
##
### Commentary:
##
### Change Log:
#----------------------------------------------------------------------
##
### Code:
## * documentation - defineCategoricalLink
#' @title Identify Categorical Links in LVM
#' @description Identify categorical links in latent variable models.
#' @name defineCategoricalLink
#'
#' @param object a \code{lvm} model.
#' @param link [character] the links to be analyzed. If \code{NULL}, all the coefficients from the lvm model are used instead.
#' @param data [data.frame] the dataset that will be used to fit the model. If \code{NULL}, a simulated data will be generated from the model.
#'
#' @return a \code{data.frame} with a description of each link in rows. \cr
#' The column factitious identify the links that will be replaced with other links
#' (e.g. "Y1~X1" becomes "Y1~X1b" and "Y1~X1c"). \cr
#'
#' @examples
#' \dontrun{
#' defineCategoricalLink <- lavaSearch2:::defineCategoricalLink
#' defineCategoricalLink.lvm <- lavaSearch2:::defineCategoricalLink.lvm
#'
#' ## linear model
#' m <- lvm(Y1~X1+X2,Y2~X1+X3)
#' categorical(m, K = 3) <- "X1"
#' try(defineCategoricalLink(m)) # error
#'
#' categorical(m, K = 3, labels = 1:3) <- "X1"
#' defineCategoricalLink(m)
#' defineCategoricalLink(m, "Y~X1")
#' defineCategoricalLink(m, "X1:0|1")
#' defineCategoricalLink(m, "X1:1|2")
#' defineCategoricalLink(m, c("X1:0|1", "X1:1|2"))
#' defineCategoricalLink(m, c("Y~X1","Y~X2"))
#' defineCategoricalLink(m, c("Y~X2","Y~X1"))
#'
#' ## latent variable model
#' m <- lvm()
#' regression(m) <- c(y1,y2,y3)~u
#' regression(m) <- u~x1+x2
#' latent(m) <- ~u
#' covariance(m) <- y1~y2
#' categorical(m, labels = as.character(1:3)) <- "X1"
#'
#' defineCategoricalLink(m)
#'}
#'
#' @concept setter
#' @keywords internal
`defineCategoricalLink` <-
function(object, link, data) UseMethod("defineCategoricalLink")
## * defineCategoricalLink.lvm
#' @rdname defineCategoricalLink
defineCategoricalLink.lvm <- function(object, link = NULL, data = NULL){
### ** normalize arguments
if(is.null(link)){
link <- stats::coef(object)
}
if(is.null(data)){
data <- lava::sim(object, 1e2)
}
### ** identify the type of regression variable (continuous or categorical)
index.cat <- which(link %in% unlist(object$attributes$ordinalparname))
index.Ncat <- setdiff(1:length(link), index.cat)
link.Ncat <- setdiff(link[index.Ncat], names(object$attributes$ordinalparname))
### ** caracterize links involving categorical variables
if(length(index.cat)>0){
link.cat <- link[index.cat]
xCAT <- lava_categorical2dummy(object, data)$x
## *** find exogenous variable
X.name.cat <- sapply(link.cat, function(iL){
test <- unlist(lapply(object$attributes$ordinalparname, function(vec.coef){iL %in% vec.coef}))
return(names(object$attributes$ordinalparname)[test])
})
UX.name.cat <- unique(X.name.cat)
## *** find the level of the exogenous variable
X.level.cat <- unlist(lapply(UX.name.cat, function(iL){
if(iL %in% names(xCAT$attributes$labels)){
labels <- xCAT$attributes$labels[[iL]]
index.label <- which(object$attributes$ordinalparname[[iL]] %in% link.cat)
return(labels[1+index.label])
}else {
stop("Categorical variables must have labels. Specify argument \'labels\' when calling categorical. \n")
}
}))
## *** find endogenous variable
M.link <- xCAT$M[paste0(X.name.cat,X.level.cat),,drop = FALSE]
M.link <- cbind(M.link, as.numeric(rowSums(M.link)==0))
convertion.back <- stats::setNames(X.name.cat,paste0(X.name.cat,X.level.cat))
indexLink <- which(M.link==1, arr.ind = TRUE)
Y.name.allcat <- colnames(M.link)[indexLink[,"col"]]
X.name.allcat <- as.character(convertion.back[rownames(M.link)][indexLink[,"row"]])
## *** characterize all links
Xcat.name.allcat <- rownames(M.link)[indexLink[,"row"]]
X.level.allcat <- as.character(X.level.cat[indexLink[,"row"]])
external.link.allcat <- link[index.cat[indexLink[,"row"]]]
original.link.allcat <- paste0(Y.name.allcat, lava.options()$symbol[1], X.name.allcat)
original.link.allcat[Y.name.allcat == ""] <- gsub("~","",original.link.allcat[Y.name.allcat == ""])
cat.link.allcat <- paste0(Y.name.allcat, lava.options()$symbol[1], Xcat.name.allcat)
cat.link.allcat[Y.name.allcat == ""] <- gsub("~","",cat.link.allcat[Y.name.allcat == ""])
df.cat <- data.frame(link = cat.link.allcat,
endogenous = Y.name.allcat,
exogenous = X.name.allcat,
type = "categorical",
factitious = FALSE,
level = X.level.allcat,
originalLink = original.link.allcat,
externalLink = external.link.allcat,
stringsAsFactors = FALSE)
}else{
df.cat <- NULL
}
### ** caracterize links involving continuous variables
if(length(index.Ncat)>0){
var.tempo <- initVarLinks(link.Ncat)
Y.name.Ncat <- var.tempo$var1
X.name.Ncat <- var.tempo$var2
test.factitious <- X.name.Ncat %in% names(object$attributes$ordinalparname)
df.Ncat <- data.frame(link = link.Ncat,
endogenous = Y.name.Ncat,
exogenous = X.name.Ncat,
type = "continuous",
factitious = test.factitious,
level = NA,
originalLink = link.Ncat,
externalLink = NA,
stringsAsFactors = FALSE)
}else{
df.Ncat <- NULL
}
### ** export
out <- rbind(df.Ncat,df.cat)
return(out)
}
#----------------------------------------------------------------------
### defineCategoricalLink.R ends here
|
