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##' Read Mplus output files
##'
##' @title Read Mplus output
##' @param infile Mplus output file
##' @param coef Coefficients only
##' @param \dots additional arguments to lower level functions
##' @author Klaus K. Holst
##' @export
##' @seealso getSAS
`getMplus` <-
function(infile="template.out",coef=TRUE,...) {
if (coef) {
start <- "MODEL RESULTS"
end1 <- "R-SQUARE"
res0 <- findfileseg(infile,start)[-c(seq(5))]
res <- sapply(res0,function(x) { val <- strsplit(x," ")[[1]]; val[val!=""] })
res <- res[unlist(lapply(res, length))!=0]
coef.idx <- unlist(lapply(res, length))>3
lab.idx <- which(!coef.idx)
count <- 0
mycoef <- c()
myrownames <- c()
for (i in seq_along(res)) {
if (i %in% lab.idx) {
count <- count+1
} else {
val <- char2num(res[[i]][-1])
if (length(val)<5) val <- c(val,rep(0,5-length(val)))
mycoef <- rbind(mycoef, val)
myrownames <- c(myrownames,
paste(paste(res[[lab.idx[count]]],collapse=" "),res[[i]][1])
)
}
}
rownames(mycoef) <- myrownames
colnames(mycoef) <- c("Estimate","Std.Err","Z-value","Std","StdYX")
return(mycoef)
}
start <- "Estimate S.E. Est./S.E."
end1 <- "MODEL RESULTS"
## end2 <- "QUALITY OF NUMERICAL RESULTS"
res <- findfileseg(infile,start,end1);
cat(paste(res,"\n"))
res <- findfileseg(infile, "TESTS OF MODEL FIT", "Chi-Square Test of Model Fit for the Baseline Model")
cat(paste(res,"\n"))
}
`findfileseg` <-
function(infile, startstring, endstring,nlines) {
con <- file(infile, blocking = FALSE)
inp <- readLines(con)
close(con)
linestart <- 1; lineend <- length(inp)
mycmd1 <- paste0("grep -n \"",startstring,"\" ", infile); a1 <- system(mycmd1,intern=TRUE);
if (length(a1)>0)
linestart <- char2num(strsplit(a1,":")[[1]][1])
nn <- length(inp)
if (!missing(nlines)) nn <- linestart+nlines
if (missing(endstring)) {
for (i in seq(linestart,nn)) {
lineend <- i-1
if (inp[i]==inp[i-1]) break;
}
} else {
mycmd2 <- paste0("grep -n \"",endstring,"\" ", infile); a2 <- system(mycmd2,intern=TRUE);
if (length(a2)>0)
lineend <- char2num(strsplit(a2,":")[[1]][1])
}
res <- inp[linestart:lineend-1]
return(res)
}
##################################################
### Generate code and run mplus...
##################################################
`mplus` <-
function(file="template.mplus",wait=TRUE,intern=TRUE,...) {
if (!file.exists(file)) file <- paste0(file,".mplus")
if (!file.exists(file)) stop("File does not exist")
if (!exists("winecmd")) winecmd <- "wine"
if (!exists("mplus.directory")) mplus.directory <- ""
mycmd <- paste0(winecmd, " \"", mplus.directory, "mplus.exe\" ", file)
system(mycmd, wait=wait, intern=TRUE)
prefix <- strsplit(file, ".", fixed=TRUE)[[1]][1]
return(getMplus(paste0(prefix,".out"),coef=TRUE))
}
`toMplus.data.frame` <-
function(x, datafile="data.tab",
mplusfile="template.mplus",
na.string=".", model="!f1 by x1;",
analysis=NULL,
categorical=NULL,
group,
run=FALSE, techout=FALSE,missing=TRUE,...) {
write.table(x, file=datafile, sep="\t",
quote=FALSE, row.names=FALSE, col.names=FALSE, na=na.string)
varnames <- c()
ngroups <- ceiling(ncol(x)/4)
for (i in seq_len(ngroups)) {
newline <- c("\t",colnames(x)[((i-1)*4+1):min(ncol(x), (i*4))],"\n")
varnames <- c(varnames, newline)
}
zz <- file(mplusfile, "w") # open an output file connection
cat(file=zz, "TITLE: ...\n")
cat(file=zz, "!-----------------------------------------------------\n")
cat(file=zz,"DATA:\n\tFILE=\"", datafile, "\";\n")
cat(file=zz,"VARIABLE:\n\tNAMES ARE\n")
cat(file=zz, varnames, ";\n")
if (!missing(group)) {
groups <- unique(x[,group])
mygroupdef <- paste("(",paste(groups,groups,sep="=",collapse=","),")")
cat(file=zz, "GROUPING IS ", group, mygroupdef, ";\n", sep="")
} else {
cat(file=zz, "!GROUPING IS g (1=male, 2=female);\n")
}
cat(file=zz, "USEVARIABLES=\n", varnames,";\n")
if (!is.null(categorical))
cat(file=zz, paste("CATEGORICAL=",paste(categorical,collapse=" "),";\n"))
cat(file=zz, "MISSING=",na.string,";\n",sep="")
cat(file=zz, "!IDVARIABLE=?;\n")
cat(file=zz, "!DEFINE: define new variables here;\n")
cat(file=zz, "!SAVEDATA: save data and/or results;\n\n")
if (is.null(analysis)) {
cat(file=zz, "ANALYSIS: TYPE=MEANSTRUCTURE");
if (missing) cat(file=zz, " MISSING;\n")
else cat(file=zz,";\n")
cat(file=zz, "ESTIMATOR=ML;\n")
cat(file=zz, "INFORMATION=EXPECTED;\n")
cat(file=zz, "ITERATIONS=5000;\n")
cat(file=zz, "CONVERGENCE=0.00005;\n\n")
} else {
cat(file=zz,"ANALYSIS:\n")
cat(file=zz, analysis,"\n")
}
cat(file=zz, "!-----------------------------------------------------\n")
cat(file=zz, "MODEL:\n")
cat(file=zz, model,"\n")
cat(file=zz, "!-----------------------------------------------------\n")
if (!techout)
cat(file=zz, "OUTPUT: STANDARDIZED;\n")
else
cat(file=zz, "OUTPUT: MODINDICES(0); TECH1; TECH2; TECH5; STANDARDIZED;\n")
cat(file=zz, "!\tSAMPSTAT;RESIDUAL;CINTERVAL;MODINDICES(0);\n")
cat(file=zz, "!Other output options are:\n")
cat(file=zz, "!\tSTANDARDIZED; !Standardized coefficients\n")
cat(file=zz, "!\tH1SE; !Standard errors for the H1 model\n")
cat(file=zz, "!\tH1TECH3; !Estimated covar,corr matrices for par. estimates\n")
cat(file=zz, "!\tPATTERNS; !Summary of missing data patterns\n")
cat(file=zz, "!\tFSCOEFFICIENT; !Factor score coefficients and posterior covar matrix\n")
cat(file=zz, "!\tFSDERTERMINACY; !Factor score determinacy for each factor\n")
cat(file=zz, "!\tTECH1; !Parameter specifications and starting values\n")
cat(file=zz, "!\tTECH2 !Parameter derivatives;\n")
cat(file=zz, "!\tTECH3; !Covar and Corr matrices for estimates\n")
cat(file=zz, "!\tTECH4; !Estimated means and covar for the latent variables\n")
cat(file=zz, "!\tTECH5; !Optimization matrix\n")
cat(file=zz, "!\tTECH6; !Optimization for categorical variables\n")
cat(file=zz, "!\tTECH7; !output for type Mixture\n")
cat(file=zz, "!\tTECH8; !Output for type mixture\n")
cat(file=zz, "!\tTECH9; !Error messages for MC study\n")
cat(file=zz, "!\tMONTECARLO: File is\n")
close(zz)
if (run & exists("mplus")) {
res <- mplus(mplusfile)
outfile <- paste0(strsplit(mplusfile,".",fixed=TRUE)[[1]][1],".out")
getMplus(outfile)
return(res)
}
}
`toMplus.lvmfit` <-
function(x, model=NULL, data=model.frame(x), run=TRUE, categorical=NULL,##binary(Model(x)),
mplusfile="template.mplus", ...) {
mymodel <- ""
M <- index(x)$M
P <- index(x)$P
nn <- vars(x)
p <- length(nn)
lat.var <- latent(x)
lat.idx <- match(lat.var, vars(x))
for (i in seq_len(p)) {
for (j in seq_len(p)) {
if (M[i,j]!=0) {
var1 <- nn[i]; var2 <- nn[j];
if (i %in% lat.idx & !(j %in% lat.idx)) {## & !(j %in% lat.idx)) {
mymodel <- paste0(mymodel, "\n", var1, " by ", var2, ";")
} else {
mymodel <- paste0(mymodel, "\n", var2, " on ", var1, ";")
}
}
}
}
for (i in seq_len(p-1)) {
for (j in ((i+1):p)) {
if (P[i,j]!=0) {
var1 <- nn[i]; var2 <- nn[j];
mymodel <- paste0(mymodel, "\n", var1, " with ", var2, ";")
}
}
}
if (is.null(model))
model <- mymodel
mydata <- subset(as.data.frame(data), select=setdiff(nn,lat.var))
toMplus.data.frame(mydata,model=mymodel,run=run, mplusfile=mplusfile, ...)
}
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