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#
# Copyright 2007-2019 by the individuals mentioned in the source code history
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
########################################################################
#RUNMX
#R function by Matthew C Keller & Mike Neale
#Many thanks to Eric Schmitt, Steve Boker, Gary Xie, and Sara Medland
# 5/30/2007
##' Run an classic mx script
##'
##' For this to work, classic mx must be installed, and callable from the command line.
##'
##' @param mx.filename Name of file containing the mx script.
##' @param output.directory Where to write mxo output from the script
##' @return processed matrix output.
##' @examples
#' \dontrun{
##' output = imxOriginalMx(mx.filename = "power1.mx", "~/Desktop")
##' }
imxOriginalMx <- function(mx.filename, output.directory) {
original.directory <- getwd()
result <- tryCatch(originalMxHelper(mx.filename, output.directory),
finally=setwd(original.directory))
return(result)
}
originalMxHelper <- function(mx.filename, output.directory) {
if (is.na(file.info(mx.filename)$size)) {
stop(paste("Cannot find the file named", mx.filename))
}
############
#Grab the mx.filename, place "!@front" at the top, and write it back out to the working directory
mx.bottom <- suppressWarnings(readLines(mx.filename))
paths <- strsplit(mx.filename, '[/\\]')[[1]]
mx.filename <- paths[[length(paths)]]
mx.tot <- c("!@front",mx.bottom)
mxfile <- paste(output.directory, "/", mx.filename, sep="")
write(mx.tot,file=mxfile)
mxo.filename <- paste(gsub(".mx","",mx.filename),".mxo",sep="")
############
setwd(output.directory)
############
#Run MX file
if (.Platform$OS.type == "windows") {
command <- substitute(system(paste("mx", x, y)), list(x = mx.filename, y = mxo.filename))
eval(command)
}
if (.Platform$OS.type == "unix") {
command <- substitute(system(paste("mx < ", x, "> ", y)), list(x = mx.filename, y = mxo.filename))
eval(command)
}
############
############
#Read in the MXO file
mxo <- suppressWarnings(readLines(mxo.filename))
#Check for Mx Errors
if (length(grep("Error: file not found",mxo)) != 0) {
stop(paste("It appears that Mx cannot find the datafile it needs.",
"Make sure the datafile(s) are placed in your working directory"))
}
if (length(grep("!@error",mxo)) != 0) {
stop(paste("Your Mx script did not complete running for some reason. Check over",
"your *.mxo file to diagnose the problem and try, try again."))
}
#Find the start of the fit functions
if (length(grep("!@machine; GROUP_FIT",mxo)) != 0) { #grepping for how windows seems to write the .mxo file
fits <- grep("!@machine; GROUP_FIT",mxo)
} else {
machines <- grep("!@machine;",mxo) #grepping for how unix seems to write the .mxo file
grpfits <- grep("GROUP_FIT",mxo)
tots <- c(machines,grpfits)
tots <- tots[order(tots)]
fits <- tots[c(FALSE,diff(tots)==1)]
}
#Find the start of the matrices
if (length(grep("!@machine; SPECS",mxo)) != 0) { #grepping for how windows seems to write the .mxo file
mats <- grep("!@machine; SPECS",mxo)
} else {
machines <- grep("!@machine;",mxo) #grepping for how unix seems to write the .mxo file
grpspecs <- grep("SPECS",mxo)
tots <- c(machines,grpspecs)
tots <- tots[order(tots)]
mats <- tots[c(FALSE,diff(tots)==1)]
}
############
############
#Number of jobs, starts & ends
number.jobs <- length(grep("!@SUBJOB",mxo))+1
x.starts <- mats
x.ends <- fits[(1:number.jobs)*2]
y.starts <- fits[((1:number.jobs)*2)-1]
y.ends <- mats
#Start the list
matrices <- list()
#Outer Loop - looping through different jobs
for (k in 1:number.jobs){
x <- mxo[x.starts[k]:x.ends[k]] #x = matrices
y <- mxo[y.starts[k]:y.ends[k]] #y = fit functions
j <- 0
ms <- grep("VALUE",x)
me <- grep("^ ;",x)
me <- me[seq(2,length(me),by=2)]
#Remove the parts of "x" that break matrix elements into 100 element
#chunks & recreate "x" s.t. matrices are contiguous
to.remove.ends <- (as.numeric(x[ms+4])*as.numeric(x[ms+5])) - as.numeric(x[ms+6]) > 100
start.remove <- (ms+108)*to.remove.ends
start.remove <- start.remove[start.remove>0]
end.remove <- (ms+116)*to.remove.ends
end.remove <- end.remove[end.remove>0]
if (length(start.remove)>0) {
removes <- vector()
for (u in 1:length(start.remove)) {
removes <- c(removes,start.remove[u]:end.remove[u])
}
x <- x[-removes]
}
#Find starts and ends of new matrix "x"
mat.starts <- grep("VALUE",x)
mat.ends <- grep("^ ;",x)
mat.ends <- mat.ends[seq(2,length(mat.ends),by=2)]
############
############
#Finding the fit function information if "User defined function value" is in the mxo file
if (length(grep("User defined function value =",y)) != 0) {
User.fit <- as.numeric(strsplit(y[grep("User defined function value =",y)],"=")[[1]][2])
DF <- as.numeric(strsplit(y[grep("Degrees of freedom",y)],">")[[1]][17])
#Attaching fit functions onto the matrices list
cat(paste("matrices$User.fit.",k, " <- ",User.fit,sep=""),file="temp");eval(parse(file="temp"))
cat(paste("matrices$DF.",k, " <- ",DF,sep=""),file="temp");eval(parse(file="temp"))
}
############
# XXX CODE SO BROKEN. Sometimes log-likelihood appears but not the other statistics
############
#Finding the fit function information if "log-likelihood" is in the mxo file
# if (length(grep("-2 times log-likelihood of data >",y)) != 0) {
# LL <- as.numeric(strsplit(y[grep("-2 times log-likelihood of data >",y)],">")[[1]][4])
# DF <- as.numeric(strsplit(y[grep("Degrees of freedom >",y)],">")[[1]][17])
# AIC <- as.numeric(strsplit(y[grep("Akaike's Information Criterion >",y)],">")[[1]][5])
# BIC <- as.numeric(strsplit(y[grep("Bayesian Information Criterion >",y)],">")[[1]][5])
# Adj.BIC <- as.numeric(strsplit(y[grep("Sample size Adjusted BIC >",y)],">")[[1]][5])
# DIC <- as.numeric(strsplit(y[grep("Deviance Information Criterion >",y)],">")[[1]][5])
#Attaching fit functions onto the matrices list
# cat(paste("matrices$LL.",k, " <- ",LL,sep=""),file="temp");eval(parse(file="temp"))
# cat(paste("matrices$DF.",k, " <- ",DF,sep=""),file="temp");eval(parse(file="temp"))
# cat(paste("matrices$AIC.",k, " <- ",AIC,sep=""),file="temp");eval(parse(file="temp"))
# cat(paste("matrices$BIC.",k, " <- ",BIC,sep=""),file="temp");eval(parse(file="temp"))
# cat(paste("matrices$Adj.BIC.",k, " <- ",Adj.BIC,sep=""),file="temp");eval(parse(file="temp"))
# cat(paste("matrices$DIC.",k, " <- ",DIC,sep=""),file="temp");eval(parse(file="temp"))
# }
############
############
#Inner Loop - looping through different matrices within groups
for (i in mat.starts) {
j <- j+1
Grp <- as.numeric(x[(mat.starts[j]+1)])
Mat <- substr(x[(mat.starts[j]+2)],2,2)
Type <- as.numeric(x[(mat.starts[j]+3)])
Dims <- as.numeric(x[(mat.starts[j]+4):(mat.starts[j]+5)])
num.elements <- as.numeric(x[mat.starts[j]+7])
if (length(start.remove)>0 & as.numeric(x[mat.starts[j]+7])==100 & (Dims[1]*Dims[2])> 100) {
num.elements <- Dims[1]*Dims[2]
}
if (Type !=1 & Type !=2 & Type !=3 & Type !=4 & Type != 11) {
elements <- as.numeric(x[(mat.starts[j]+8):(mat.starts[j]+7+num.elements)])
}
#Calculated, Constructed, or Full Matrices
if (Type <= -1|Type==9){
cat(paste(Mat,Grp,".",k," <- matrix(elements,nrow=Dims[1],ncol=Dims[2],byrow=TRUE)",sep=""),file="temp")
}
#Zero Matrix
if (Type==1) {
cat(paste(Mat,Grp,".",k," <- matrix(0,nrow=Dims[1],ncol=Dims[2])",sep=""),file="temp")
}
#Identity Matrix
if (Type==2) {
cat(paste(Mat,Grp,".",k," <- diag(Dims[1])",sep=""),file="temp")
}
#Identity-Zero Matrix
if (Type==3) {
ident <- diag(Dims[1])
zeros <- matrix(0,nrow=Dims[1],ncol=(Dims[2]-Dims[1]))
cat(paste(Mat,Grp,".",k," <- cbind(ident,zeros)",sep=""),file="temp")
}
#Zero-Identity Matrix
if (Type==4) {
ident <- diag(Dims[1])
zeros <- matrix(0,nrow=Dims[1],ncol=(Dims[2]-Dims[1]))
cat(paste(Mat,Grp,".",k," <- cbind(zeros,ident)",sep=""),file="temp")
}
#Diagonal Matrix
if (Type==5) {
cat(paste(Mat,Grp,".",k," <- diag(elements)",sep=""),file="temp")
}
#Subdiagonal Matrix
if (Type==6){
tempmat <- matrix(0,nrow=Dims[1],ncol=Dims[2])
tempmat[upper.tri(tempmat)] <- elements
tempmat <- t(tempmat)
cat(paste(Mat,Grp,".",k," <- tempmat",sep=""),file="temp")
}
#Standardized Matrix
if (Type==7) {
tempmat <- matrix(1,nrow=Dims[1],ncol=Dims[2])
tempmat[upper.tri(tempmat)] <- elements
tempmat[lower.tri(tempmat)] <- elements
tempmat <- t(tempmat)
cat(paste(Mat,Grp,".",k," <- tempmat",sep=""),file="temp")
}
#Symmetric Matrix
if (Type==8) {
tempmat <- matrix(0,nrow=Dims[1],ncol=Dims[2])
tempmat[upper.tri(tempmat,diag=TRUE)] <- elements
tempmat <- t(tempmat)
tempmat[upper.tri(tempmat)] <- tempmat[lower.tri(tempmat)]
cat(paste(Mat,Grp,".",k," <- tempmat",sep=""),file="temp")
}
#Lower Matrix
if (Type==10){
tempmat <- matrix(0,nrow=Dims[1],ncol=Dims[2])
tempmat[upper.tri(tempmat,diag=TRUE)] <- elements
tempmat <- t(tempmat)
cat(paste(Mat,Grp,".",k," <- tempmat",sep=""),file="temp")
}
#Unit Matrix
if (Type==11) {
cat(paste(Mat,Grp,".",k," <- matrix(1,nrow=Dims[1],ncol=Dims[2])",sep=""),file="temp")
}
#Make the new matrix & latch it onto the "matrices" list eval(parse(file="temp"))
cat(paste("matrices$",Mat,Grp,".",k, " <- ",Mat,Grp,".",k,sep=""),file="temp")
eval(parse(file="temp"))
############
} # Inner loop - matrices
} # Outer loop - jobs
return(matrices)
}
########################################################################
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