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# Function to extract parameters into model matrices:
# Object is semPlotModel or can be created:
# # Inner functions:
# getRAMmodel <- function(object)
# {
#
# # Parameters:
# Nvar <- nrow(object@Vars)
# Nman <- sum(object@Vars$manifest)
# Names <- object@Vars$name
#
# # Empty matrices:
# A <- S <- matrix(0,Nvar,Nvar)
# F <- cbind(diag(1,Nman),matrix(0,Nman,Nvar-Nman))
# F[,order(object@Vars$manifest,decreasing=TRUE)] <- F
# rownames(A) <- colnames(A) <- rownames(S) <- colnames(S) <- colnames(F) <- Names
# rownames(F) <- Names[object@Vars$manifest]
#
# # Fill matrices:
# for (i in seq_len(nrow(object@Pars)))
# {
# if (object@Pars$edge[i]=="<->")
# {
# S[which(Names==object@Pars$lhs[i])[1],which(Names==object@Pars$rhs[i])[1]] <-
# S[which(Names==object@Pars$rhs[i])[1],which(Names==object@Pars$lhs[i])[1]] <- object@Pars$est[i]
# }
# if (object@Pars$edge[i]%in%c("->","~>"))
# {
# A[which(Names==object@Pars$rhs[i])[1],which(Names==object@Pars$lhs[i])[1]] <- object@Pars$est[i]
# }
# }
#
# Res <- list(A=A,S=S,F=F)
# class(Res) <- "RAM"
# return(Res)
# }
modelMatrices <- function(object,model="ram", endoOnly = FALSE)
{
# Check if input is combination of models:
call <- paste(deparse(substitute(object)), collapse = "")
if (grepl("\\+",call))
{
args <- unlist(strsplit(call,split="\\+"))
obs <- lapply(args,function(x)semPlotModel(eval(parse(text=x))))
object <- obs[[1]]
for (i in 2:length(obs)) object <- object + obs[[i]]
}
if (!"semPlotModel"%in%class(object)) object <- semPlotModel(object)
stopifnot("semPlotModel"%in%class(object))
### SETUP ###
Model <- list()
class(Model) <- "semMatrixModel"
# Define exogeneity:
if (endoOnly)
{
object@Vars$exogenous <- FALSE
} else {
if (any(is.na(object@Vars$exogenous)))
{
object <- defExo(object)
}
}
### RAM MODEL ###
if (grepl("ram",model,ignore.case=TRUE))
{
# Extract names:
man <- object@Vars$name[object@Vars$manifest]
lat <- object@Vars$name[!object@Vars$manifest]
all <- object@Vars$name
# Extract matrices:
Model[['A']] <- Pars2Matrix(object@Pars, c("->","~>"), all, all)
Model[['S']] <- Pars2Matrix(object@Pars, "<->", all, all)
Model[['F']] <- FilterMatrix(object@Pars, object@Vars)
return(Model)
}
### LISREL MODEL ###:
if (grepl("lis",model,ignore.case=TRUE))
{
# Extract names:
manExo <- object@Vars$name[object@Vars$manifest & object@Vars$exogenous]
manEndo <- object@Vars$name[object@Vars$manifest & !object@Vars$exogenous]
latExo <- object@Vars$name[!object@Vars$manifest & object@Vars$exogenous]
latEndo <- object@Vars$name[!object@Vars$manifest & !object@Vars$exogenous]
# If any manifest var is used in regression, create dummy latents:
if (any(object@Pars$lhs[object@Pars$edge%in%c("->","~>")] %in% c(manExo,manEndo)))
{
message("Latent dummy variables added to include manifest regressions")
# Identify variables:
manRegs <- c(manExo,manEndo)[c(manExo,manEndo)%in%object@Pars$lhs[object@Pars$edge%in%c("->","~>")]]
newVars <- object@Vars[object@Vars$name %in% manRegs,]
newVars$manifest <- FALSE
newVars$name <- paste0(newVars$name,"@L@")
object@Vars <- rbind(object@Vars,newVars)
# Change regressions to latents:
object@Pars$lhs[object@Pars$lhs %in% manRegs & object@Pars$edge%in%c("->","~>")] <- paste0(object@Pars$lhs[object@Pars$lhs %in% manRegs & object@Pars$edge%in%c("->","~>")],"@L@")
manVarResids <- which(object@Pars$lhs %in% manRegs & object@Pars$rhs %in% manRegs & object@Pars$edge=="<->")
object@Pars$lhs[manVarResids] <- paste0(object@Pars$lhs[manVarResids],"@L@")
object@Pars$rhs[manVarResids] <- paste0(object@Pars$rhs[manVarResids],"@L@")
# Add factor loadings:
for (g in unique(object@Pars$group))
{
parLocs <- nrow(object@Pars)+seq_along(manRegs)
object@Pars[parLocs,"lhs"] <- paste0(manRegs,"@L@")
object@Pars[parLocs,"rhs"] <- manRegs
object@Pars[parLocs,"label"] <- ""
object@Pars[parLocs,"est"] <- 1
object@Pars[parLocs,"std"] <- NA
object@Pars[parLocs,"group"] <- g
object@Pars[parLocs,"fixed"] <- TRUE
object@Pars[parLocs,"par"] <- 0
}
# Extract names:
manExo <- object@Vars$name[object@Vars$manifest & object@Vars$exogenous]
manEndo <- object@Vars$name[object@Vars$manifest & !object@Vars$exogenous]
latExo <- object@Vars$name[!object@Vars$manifest & object@Vars$exogenous]
latEndo <- object@Vars$name[!object@Vars$manifest & !object@Vars$exogenous]
}
# Extract matrices:
Model[['LY']] <- Pars2Matrix(object@Pars, c("->","~>"), manEndo, latEndo)
Model[['TE']] <- Pars2Matrix(object@Pars, "<->", manEndo, manEndo)
Model[['PS']] <- Pars2Matrix(object@Pars, "<->", latEndo, latEndo)
Model[['BE']] <- Pars2Matrix(object@Pars, c("->","~>"), latEndo, latEndo)
Model[['LX']] <- Pars2Matrix(object@Pars, c("->","~>"), manExo, latExo)
Model[['TD']] <- Pars2Matrix(object@Pars, "<->", manExo, manExo)
Model[['PH']] <- Pars2Matrix(object@Pars, "<->", latExo, latExo)
Model[['GA']] <- Pars2Matrix(object@Pars, c("->","~>"), latEndo, latExo)
Model[['TY']] <- Pars2Matrix(object@Pars, "int", manEndo, "1")
Model[['TX']] <- Pars2Matrix(object@Pars, "int", manExo, "1")
Model[['AL']] <- Pars2Matrix(object@Pars, "int", latEndo, "1")
Model[['KA']] <- Pars2Matrix(object@Pars, "int", latExo, "1")
return(Model)
}
### Mplus MODEL ###:
if (grepl("mplus",model,ignore.case=TRUE))
{
# Extract names (exo only if manifest has outgoing cons. error if in and outgoing):
man <- object@Vars$name[object@Vars$manifest]
lat <- object@Vars$name[!object@Vars$manifest]
# Control input:
if (any(sapply(man, function(m) any((object@Pars$lhs==m & object@Pars$edge %in% c("->","~>")) & (object@Pars$rhs==m & object@Pars$edge %in% c("->","~>")))))) stop("Manifest variable found with both incoming and outgoing edge. This is not yet supported in modelMatrices.")
if (any(object@Pars$rhs %in% man & object@Pars$lhs %in% lat & object@Pars$edge == "~>"))
{
warning("Can not place regression (ON) from latent to manifest in a model matrix. Interpreted as factor loading (BY).")
object@Pars$edge[object@Pars$rhs %in% man & object@Pars$lhs %in% lat & object@Pars$edge == "~>"] <- "->"
}
trueExo <- sapply(man, function(m) any((object@Pars$lhs==m & object@Pars$edge %in% c("->","~>")) & !(object@Pars$rhs==m & object@Pars$edge %in% c("->","~>"))))
manEndo <- man[!trueExo]
manExo <- man[trueExo]
## Extract matrices:
# BY matrices:
Model[['Nu']] <- Pars2Matrix(object@Pars, "int", manEndo, "1")
Model[['Lambda']] <- Pars2Matrix(object@Pars, c("->","~>"), manEndo, lat)
Model[['Theta']] <- Pars2Matrix(object@Pars, "<->", manEndo, manEndo)
# ON matrices:
Model[['Kappa']] <- Pars2Matrix(object@Pars, c("->","~>"), manEndo, manExo)
Model[['Alpha']] <- Pars2Matrix(object@Pars, "int", lat, "1")
Model[['Beta']] <- Pars2Matrix(object@Pars, c("->","~>"), lat, lat)
Model[['Gamma']] <- Pars2Matrix(object@Pars, c("->","~>"), lat, manExo)
Model[['Psi']] <- Pars2Matrix(object@Pars, "<->", lat, lat)
return(Model)
}
else stop(paste("Model",model,"is not supported."))
}
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