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# with contributions by Adam Kramer and Michael Friendly (originally by J. Fox)
# last modified 2020-04-20 by J. Fox
globalVariables("dot")
Greek <- read.table(system.file("etc/GreekLetters.txt", package="sem"), as.is=TRUE)
Subscripts <- read.table(system.file("etc/subscripts.txt", package="sem"), as.is=TRUE)
Superscripts <- read.table(system.file("etc/superscripts.txt", package="sem"), as.is=TRUE)
math <- function(text, html.only=FALSE, hat=FALSE){
if (length(text) > 1) {
result <- sapply(text, math, html=html.only, hat=hat)
names(result) <- names(text)
return(result)
}
# subscripts <- c("₀", "₁", "₂", "₃", "₄", "₅", "₆",
# "₇", "₈", "₉", "₋")
# superscripts <- c("⁰", "¹", "²", "³", "⁴", "⁵",
# "⁶", "⁷", "⁸", "⁹")
# names(subscripts) <- c(0:9, "-")
# names(superscripts) <- 0:9
subscripts <- Subscripts$hex
superscripts <- Superscripts$hex
names(subscripts) <- rownames(Subscripts)
names(superscripts) <- rownames(Superscripts)
hat <- if (hat) "̂" else ""
text <- gsub(" ", "", text)
symbol <- regexpr("^[a-zA-Z]+", text)
if (symbol != 1) stop("text does not start with an alphabetic symbol name")
symbol <- if (html.only) {
paste0("&", substring(text, 1, attr(symbol, "match.length")), ";")
}
else{
ss <- substring(text, 1, attr(symbol, "match.length"))
s <- Greek[ss, "decimal"]
if (is.na(s)) stop(ss, " is not a Greek letter")
s
}
subscript <- regexpr("_\\{", text)
subscript <- if (subscript >= 1){
subscript <- substring(text, subscript + 2)
endbrace <- regexpr("\\}", subscript)
if (endbrace < 1) stop("unmatched closing brace in ", text)
substring(subscript, 1, endbrace - 1)
}
else ""
if (subscript != ""){
subscript <- unlist(strsplit(subscript, split=""))
subscript <- subscripts[subscript]
if (any(is.na(subscript))) stop ("invalid subscript")
subscript <- paste(subscript, collapse="")
}
superscript <- regexpr("\\^\\{", text)
superscript <- if (superscript >= 1){
superscript <- substring(text, superscript + 2)
endbrace <- regexpr("\\}", superscript)
if (endbrace < 1) stop("unmatched closing brace in ", text)
substring(superscript, 1, endbrace - 1)
}
else ""
if (superscript != ""){
superscript <- unlist(strsplit(superscript, split=""))
superscript <- superscripts[superscript]
if (any(is.na(superscript))) stop ("invalid superscript")
superscript <- paste(superscript, collapse="")
}
paste0(symbol, hat, subscript, superscript)
}
path.diagram <- function(...) {
.Deprecated("pathDiagram", package = "sem")
pathDiagram(...)
}
pathDiagram <- function (model, ...)
{
UseMethod("pathDiagram")
}
pathDiagram.semmod <- function(model, obs.variables, ...) {
parse.path <-
function(path) {
path.1 <- gsub("-", "", gsub(" ","", path))
direction <- if (regexpr("<>", path.1) > 0)
2
else if (regexpr("<", path.1) > 0)
- 1
else if (regexpr(">", path.1) > 0)
1
else
stop(paste("ill-formed path:", path))
path.1 <- strsplit(path.1, "[<>]")[[1]]
list(first = path.1[1], second = path.1[length(path.1)], direction =
direction)
}
if ((!is.matrix(model)) |
ncol(model) != 3)
stop ("model argument must be a 3-column matrix")
startvalues <- as.numeric(model[,3])
par.names <- model[,2]
n.paths <- length(par.names)
heads <- from <- to <- rep(0, n.paths)
for (p in 1:n.paths) {
path <- parse.path(model[p,1])
heads[p] <- abs(path$direction)
to[p] <- path$second
from[p] <- path$first
if (path$direction == -1) {
to[p] <- path$first
from[p] <- path$second
}
}
ram <- matrix(0, p, 5)
all.vars <- unique(c(to, from))
latent.vars <- setdiff(all.vars, obs.variables)
vars <- c(obs.variables, latent.vars)
pars <- na.omit(unique(par.names))
ram[,1] <- heads
ram[,2] <- apply(outer(vars, to, "=="), 2, which)
ram[,3] <- apply(outer(vars, from, "=="), 2, which)
par.nos <- apply(outer(pars, par.names, "=="), 2, which)
if (length(par.nos) > 0)
ram[,4] <-
unlist(lapply(par.nos, function(x)
if (length(x) == 0)
0
else
x))
ram[,5] <- startvalues
colnames(ram) <-
c("heads", "to", "from", "parameter", "start value")
pars <- unique(na.omit(par.names))
coeff <- rep(0, length(pars))
names(coeff) <- pars
fake.sem <-
list(
ram = ram, n = length(obs.variables), var.names = vars, coeff = coeff,
semmod = model
)
class(fake.sem) <- "sem"
pathDiagram(fake.sem, ...)
}
pathDiagram.sem <-
function (model, file = "pathDiagram", style = c("ram", "traditional"),
output.type = c("html", "graphics", "dot"), graphics.fmt = "pdf", dot.options = NULL,
size = c(8, 8), node.font = c("Helvetica", 14),
edge.font = c("Helvetica", 10), digits = 2, rank.direction = c("LR", "TB"),
min.rank = NULL, max.rank = NULL, same.rank = NULL,
variables = model$var.names, var.labels, parameters, par.labels,
ignore.double = TRUE, ignore.self = FALSE, error.nodes = TRUE,
edge.labels = c("names", "values", "both"), edge.colors = c("black", "black"),
edge.weight = c("fixed", "proportional"),
node.colors = c("transparent", "transparent", "transparent"),
standardize = FALSE, ...) {
Dot <- function(..., semicolon = TRUE, newline = TRUE) {
cat(file = handle, paste0(..., if (semicolon)
";"
else
"",
if (newline)
"\n"
else
""))
}
style <- match.arg(style)
output.type <- match.arg(output.type)
edge.labels <- match.arg(edge.labels)
edge.weight <- match.arg(edge.weight)
rank.direction <- match.arg(rank.direction)
if (output.type == "html") {
handle <- textConnection("dot", "w")
}
else {
dot.file <- paste0(file, ".dot")
handle <- file(dot.file, "w")
if (output.type == "graphics")
graph.file <- paste0(file, ".", graphics.fmt)
}
on.exit(close(handle))
Dot("digraph \"", deparse(substitute(model)), "\" {", semicolon = FALSE)
Dot(" rankdir=", rank.direction)
Dot(" size=\"", size[1], ",", size[2], "\"")
Dot(
" node [fontname=\"", node.font[1],
"\" fontsize=", node.font[2], " fillcolor=\"", node.colors[1],
"\" shape=box style=filled]"
)
Dot(" edge [fontname=\"", edge.font[1],
"\" fontsize=", edge.font[2], "]")
Dot(" center=1")
if (!is.null(min.rank)) {
min.rank <- paste0("\"", min.rank, "\"")
min.rank <- gsub(",", "\" \"", gsub(" ", "", min.rank))
Dot(" {rank=min ", min.rank, "}", semicolon = FALSE)
}
if (!is.null(max.rank)) {
max.rank <- paste0("\"", max.rank, "\"")
max.rank <- gsub(",", "\" \"", gsub(" ", "", max.rank))
Dot(" {rank=max ", max.rank, "}", semicolon = FALSE)
}
if (!is.null(same.rank)) {
for (s in 1:length(same.rank)) {
same <- paste0("\"", same.rank[s], "\"")
same <- gsub(",", "\" \"", gsub(" ", "", same))
Dot(" {rank=same ", same, "}", semicolon = FALSE)
}
}
latent <- variables[-(1:model$n)]
for (lat in latent) {
Dot(" \"", lat, "\" [shape=ellipse]", semicolon = FALSE)
}
endogenous <- classifyVariables(model$semmod)$endogenous
endogenous <-
variables[apply(outer(endogenous, model$var.names, "=="), 1, which)]
if (style == "traditional") {
variables <- c(variables, paste0(endogenous, ".error"))
error.color <-
if (length(node.colors) < 3)
node.colors[1]
else
node.colors[3]
}
for (endog in endogenous) {
Dot(" \"", endog, "\" [fillcolor=\"", node.colors[2], "\"]", semicolon =
FALSE)
if (style == "traditional") {
if (error.nodes) Dot(
" \"", endog, ".error\" [shape=ellipse] [fillcolor=\"", error.color, "\"]",
semicolon = FALSE
)
else Dot(
" \"", endog,
".error\" [shape=ellipse width=0 height=0 fixedsize=true label=\"\"] [fillcolor=\"",
error.color, "\"]",
semicolon = FALSE
)
}
}
ram <- model$ram
if (missing(parameters)) {
par.names <- names(coef(model))
rownames(ram)[ram[, "parameter"] != 0] <-
par.names[ram[, "parameter"]]
rownames(ram)[ram[, "parameter"] == 0] <-
ram[ram[, "parameter"] == 0, "start value"]
parameters <- rownames(ram)
}
if (standardize)
ram[, 5] <- stdCoef(model)[, 2]
else
ram[names(model$coeff), 5] <- model$coeff
coefs <- ram[, 5] # handle equality constraints, if any
na.coefs <- is.na(coefs)
if (any(na.coefs)) {
for (coef in which(na.coefs)) {
ram[coef, 5] <-
(ram[ram[coef, 4] == ram[, 4], 5])[1] # paste in the estimate
}
}
values <- round(ram[, 5], digits)
heads <- ram[, 1]
to <- ram[, 2]
from <- ram[, 3]
if (!missing(par.labels)) {
check <- names(par.labels) %in% parameters
if (any(!check)) {
msg <- if (sum(!check) > 1)
paste(
"The following parameters do not appear in the model:", paste(names(par.labels)[!check], collapse =
", ")
)
else
paste("The following parameter does not appear in the model:", names(par.labels)[!check])
warning(msg)
par.labels <- par.labels[check]
}
names(parameters) <- parameters
parameters[names(par.labels)] <- par.labels
}
labels <- if (edge.labels == "names")
parameters
else if (edge.labels == "values")
values
else
paste(parameters, values, sep = "=")
colors <- ifelse(values > 0, edge.colors[1], edge.colors[2])
direction <- ifelse((heads == 2), " dir=both", "")
lineweight <- rep(1, nrow(ram))
if (edge.weight == "proportional") {
lineweight <- abs(values) / mean(values)
if (!standardize)
warning("proportional edge weights requested for an unstandardized model")
}
if (style == "ram") {
for (par in 1:nrow(ram)) {
if ((!ignore.double) || (heads[par] == 1)) {
if (ignore.self && to[par] == from[par]) next
Dot(
" \"", variables[from[par]],
"\" -> \"", variables[to[par]], "\" [label=\"",
labels[par], "\"", direction[par], " color=", colors[par],
" penwidth=", round(lineweight[par] + 0.001, 3), "]"
)
}
}
}
else
for (par in 1:nrow(ram)) {
# style == "traditional"
if (heads[par] == 1) {
Dot(
" \"", variables[from[par]],
"\" -> \"", variables[to[par]], "\" [label=\"",
labels[par], "\"", direction[par], " color=", colors[par],
" penwidth=", round(lineweight[par] + 0.001, 3), "]"
)
}
else if (variables[to[par]] %in% endogenous) {
if (variables[to[par]] == variables[from[par]]) {
# convert self-arrow to residual path
lab <- labels[par]
val <-
round(sqrt(values[par]), digits = digits)
lab <-
if (edge.labels == "names")
paste0("sqrt(", lab, ")")
else if (edge.labels == "values")
val
else
paste0("sqrt(", parameters[par], ")=", val)
Dot(
" \"", variables[to[par]], ".error\" -> \"",
variables[to[par]], "\" [color=", edge.colors[1], " label=\"", lab,
"\" penwidth=", round(sqrt(lineweight[par]) + 0.001, 3)," ]"
)
}
else{
# convert endogenous covariance to error covariance
Dot(
" \"", variables[to[par]], ".error\" -> \"",
variables[from[par]], ".error\" [dir=both label=\"", labels[par],
"\" color=", colors[par],
" penwidth=", round(lineweight[par] + 0.001, 3), "]"
)
}
}
else if (!ignore.double &&
(variables[to[par]] != variables[from[par]])) {
Dot(
" \"", variables[from[par]],
"\" -> \"", variables[to[par]], "\" [label=\"",
labels[par], "\"", direction[par], " color=", colors[par],
" penwidth=", round(lineweight[par] + 0.001, 3), "]"
)
}
}
if (!missing(var.labels)) {
check <- names(var.labels) %in% variables
if (any(!check)) {
msg <- if (sum(!check) > 1)
paste(
"The following variables do not appear in the model:", paste(names(var.labels)[!check], collapse =
", ")
)
else
paste("The following variable does not appear in the model:", names(var.labels)[!check])
warning(msg)
var.labels <- var.labels[check]
}
Dot(" // variable labels: ", semicolon = FALSE)
lines <-
paste0(' "', names(var.labels), '" [label="', var.labels, '"];\n')
Dot(paste(lines, collapse = ""), semicolon = FALSE, newline = FALSE)
}
Dot("}", semicolon = FALSE)
if (output.type == "graphics") {
cmd <-
paste0("dot -T", graphics.fmt, " -o ", graph.file, " -Gcharset=latin1 ",
dot.options, " ", dot.file)
cat("Running ", cmd, "\n")
result <- try(system(cmd))
}
if (output.type == "html" && requireNamespace("DiagrammeR")) {
print(DiagrammeR::DiagrammeR(dot, type = "grViz"))
}
result <-
if (output.type == "html")
dot
else
readLines(dot.file)
invisible(result)
}
|
