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# last modified 2015-05-14 by J. Fox
specify.model <- function(...){
.Deprecated("specifyModel", package="sem")
specifyModel(...)
}
specifyModel <- function(file="", text, exog.variances=FALSE, endog.variances=TRUE, covs, suffix="", quiet=FALSE){
add.variances <- function () {
if (!quiet) message("NOTE: it is generally simpler to use specifyEquations() or cfa()\n",
" see ?specifyEquations")
variables <- need.variance()
nvars <- length(variables)
if (nvars == 0) return(model)
message("NOTE: adding ", nvars, " variances to the model")
paths <- character(nvars)
par.names <- character(nvars)
for (i in 1:nvars) {
paths[i] <- paste(variables[i], "<->", variables[i])
par.names[i] <- paste("V[", variables[i], "]", sep = "")
}
model.2 <- cbind(c(model[, 1], paths), c(model[, 2], par.names),
c(model[, 3], rep(NA, length(paths))))
class(model.2) <- "semmod"
model.2
}
need.variance <- function () {
all.vars <- classifyVariables(model)
exo.vars <- all.vars$exogenous
end.vars <- all.vars$endogenous
variables <- logical(0)
for (paths in model[, 1]) {
vars <- strip.white(paths)
vars <- sub("-*>", "->", sub("<-*", "<-", vars))
vars <- sub("<->|<-", "->", vars)
vars <- strsplit(vars, "->")[[1]]
if (vars[1] != vars[2]) {
for (a.variable in vars) {
if (is.na(variables[a.variable])) variables[a.variable] <- TRUE
}
}
else {
variables[vars[1]] <- FALSE
}
}
if (!exog.variances && length(exo.vars) > 0) variables[exo.vars] <- FALSE
if (!endog.variances && length(end.vars) > 0) variables[end.vars] <- FALSE
names(variables)[variables]
}
model <- if (!missing(text)) scan(text=text, what=list(path="", par="", start=1, dump=""), sep=",",
strip.white=TRUE, comment.char="#", fill=TRUE, quiet=quiet)
else scan(file=file, what=list(path="", par="", start=1, dump=""), sep=",",
strip.white=TRUE, comment.char="#", fill=TRUE, quiet=quiet)
# dump permits comma at line end
model$path <- gsub("\\t", " ", model$path)
model$par[model$par == ""] <- NA
model <- cbind(model$path, model$par, model$start)
if (!(missing(covs))){
for (cov in covs){
vars <- strsplit(cov, "[ ,]+")[[1]]
nvar <- length(vars)
for (i in 1:nvar){
for (j in i:nvar){
row <- c(paste(vars[i], "<->", vars[j]),
if (i == j) paste("V[", vars[i], "]", sep="") else paste("C[", vars[i], ",", vars[j], "]", sep=""),
NA)
if (row[2] %in% model[,2]) next
model <- rbind(model, row)
}
}
}
}
model <- removeRedundantPaths(model, warn=FALSE)
result <- add.variances()
which.pars <- !is.na(result[, 2])
result[which.pars, 2] <- paste(result[which.pars, 2], suffix, sep="")
result
}
print.semmod <- function(x, ...){
path <- x[,1]
parameter <- x[,2]
parameter[is.na(parameter)] <- "<fixed>"
startvalue <- as.numeric(x[,3])
startvalue[is.na(startvalue)] <- " "
if (all(startvalue == " ")) print(data.frame(Path=path, Parameter=parameter),
right=FALSE)
else print(data.frame(Path=path, Parameter=parameter, StartValue=startvalue),
right=FALSE)
invisible(x)
}
classifyVariables <- function(model) {
variables <- logical(0)
for (paths in model[, 1]) {
vars <- strip.white(paths)
vars <- sub("-*>", "->", sub("<-*", "<-", vars))
if (grepl("<->", vars)){
vars <- strsplit(vars, "<->")[[1]]
if (is.na(variables[vars[1]])) variables[vars[1]] <- FALSE
if (is.na(variables[vars[2]])) variables[vars[2]] <- FALSE
}
else if (grepl("->", vars)){
vars <- strsplit(vars, "->")[[1]]
if (is.na(variables[vars[1]])) variables[vars[1]] <- FALSE
variables[vars[2]] <- TRUE
}
else if (grepl("<-", vars)){
vars <- strsplit(vars, "<-")[[1]]
if (is.na(variables[vars[2]])) variables[vars[2]] <- FALSE
variables[vars[1]] <- TRUE
}
else stop("incorrectly specified model")
}
list(endogenous=names(variables[variables]), exogenous=names(variables[!variables]))
}
strip.white <- function(x) gsub(' ', '', x)
removeRedundantPaths <- function(model, warn=TRUE){
paths <- model[, 1]
paths <- strip.white(paths)
paths <- sub("-*>", "->", sub("<-*", "<-", paths))
start <- regexpr("<->|<-|->", paths)
end <- start + attr(start, "match.length") - 1
arrows <- substr(paths, start, end)
vars <- matrix(unlist(strsplit(paths, "<->|<-|->")), ncol=2, byrow=TRUE)
for (i in 1:length(arrows)){
if (arrows[i] == "<-"){
arrows[i] <- "->"
vars[i, ] <- vars[i, 2:1]
}
}
vars <- cbind(vars, arrows)
dupl.paths <- duplicated(vars)
if (warn && any(dupl.paths)){
warning("the following duplicated paths were removed: ", paste(model[dupl.paths, 1], collapse=", "))
}
model <- model[!dupl.paths, , drop=FALSE]
class(model) <- "semmod"
model
}
specifyEquations <- function(file="", text, ...){
par.start <- function(coef, eq){
if (length(grep("\\(", coef)) == 0){
return(c(coef, "NA"))
}
par.start <- strsplit(coef, "\\(")[[1]]
if (length(par.start) != 2) stop("Parse error in equation: ", eq,
'\n Start values must be given in the form "parameter(value)".')
par <- par.start[[1]]
start <- par.start[[2]]
if (length(grep("\\)$", start)) == 0) stop("Parse error in equation: ", eq,
"\n Unbalanced parentheses.")
start <- sub("\\)", "", start)
return(c(par, start))
}
parseEquation <- function(eqn){
eq <- eqn
eqn <- gsub("\\s*", "", eqn)
eqn <- strsplit(eqn, "=")[[1]]
if (length(eqn) != 2) stop("Parse error in equation: ", eq,
"\n An equation must have a left- and right-hand side separated by =.")
lhs <- eqn[1]
rhs <- eqn[2]
if (length(grep("^[cC]\\(", lhs)) > 0){
if (length(grep("\\)$", lhs)) == 0) stop("Parse error in equation: ", eq,
"\n Unbalanced parentheses.")
lhs <- sub("[cC]\\(", "", lhs)
lhs <- sub("\\)", "", lhs)
variables <- strsplit(lhs, ",")[[1]]
if (length(variables) != 2) stop("Parse error in equation: ", eq,
"\n A covariance must be in the form C(var1, var2) = cov12")
if (not.number(rhs)){
par.start <- par.start(rhs, eq)
if (not.number(par.start[2]) && (par.start[2] != "NA"))
stop("Parse error in equation: ", eq,
"\n Start values must be numeric constants.")
ram <- paste(variables[1], " <-> ", variables[2], ", ", par.start[1], ", ", par.start[2], sep="")
}
else{
ram <- paste(variables[1], " <-> ", variables[2], ", NA, ", rhs, sep="")
}
}
else if (length(grep("^[vV]\\(", lhs)) > 0){
lhs <- sub("[vV]\\(", "", lhs)
if (length(grep("\\)$", lhs)) == 0) stop("Parse error in equation: ", eq,
"\n Unbalanced parentheses.")
lhs <- sub("\\)", "", lhs)
if (not.number(rhs)){
par.start <- par.start(rhs, eq)
if (not.number(par.start[2]) && (par.start[2] != "NA"))
stop("Parse error in equation: ", eq,
"\n Start values must be numeric constants.")
ram <- paste(lhs, " <-> ", lhs, ", ", par.start[1], ", ", par.start[2], sep="")
}
else{
ram <- paste(lhs, " <-> ", lhs, ", NA, ", rhs, sep="")
}
}
else{
terms <- strsplit(rhs, "\\+")[[1]]
terms <- strsplit(terms, "\\*")
ram <- character(length(terms))
for (term in 1:length(terms)){
trm <- terms[[term]]
if (length(trm) != 2) stop("Parse error in equation: ", eq,
'\n The term "', trm, '" is malformed.',
'\n Each term on the right-hand side of a structural equation must be of the form "parameter*variable".')
coef <- trm[1]
if (not.number(coef)){
par.start <- par.start(coef, eq)
if (not.number(par.start[2]) && (par.start[2] != "NA"))
stop("Parse error in equation: ", eq,
"\n Start values must be numeric constants.")
ram[term] <- paste(trm[2], " -> ", lhs, ", ", par.start[1], ", ", par.start[2], sep="")
}
else{
ram[term] <- paste(trm[2], " -> ", lhs, ", NA, ", coef, sep="")
}
}
}
ram
}
equations <- if (!missing(text)) scan(text=text, what="", sep=";", strip.white=TRUE, comment.char="#")
else scan(file=file, what="", sep=";", strip.white=TRUE, comment.char="#")
equations2 <- character(0)
eqn <- 0
skip <- FALSE
for(equation in equations){
eqn <- eqn + 1
if (skip){
skip <- FALSE
next
}
if (substring(equation, 1, 1) == "+"){
equations2[length(equations2)] <- paste(equations2[length(equations2)], equation)
}
else if (substring(equation, nchar(equation)) == "+"){
equations2 <- c(equations2, paste(equation, equations[eqn + 1]))
skip <- TRUE
}
else equations2 <- c(equations2, equation)
}
ram <- unlist(lapply(equations2, parseEquation))
specifyModel(text=ram, ..., quiet=TRUE)
}
# the following function (not exported) checks whether a text string can be converted into a number
not.number <- function(constant){
save <- options(warn = -1)
on.exit(save)
is.na(as.numeric(constant))
}
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