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getMatrix <- function(x,name,diag=FALSE,symmetrical=FALSE,estimates)
{
# browser()
### Fix default naming:
x <- gsub("VAR (?=\\d)","VAR",x,perl=TRUE)
x <- gsub("ETA (?=\\d)","ETA",x,perl=TRUE)
x <- gsub("KSI (?=\\d)","KSI",x,perl=TRUE)
xorig <- x
# Make similar to readLines if length==1:
if (length(x)==1) x <- strsplit(x,split="\n")[[1]]
# Check if estimate matrix:
if (missing(estimates))
{
estimates <- any(grepl("\\(",x))
}
if (estimates)
{
# First append spaces to every line:
maxSpace <- max(nchar(x))
for (i in seq_along(x))
{
x[i] <- paste(x[i],paste(rep(" ",maxSpace - nchar(x[i])), collapse=""), sep = "")
}
# Loop over lines, check if one contains "- -" and the next a bracket, and fill in "- -" signs
for (i in which(grepl("- -",x[-length(x)]) & grepl("\\(",x[-1])))
{
emLocs <- gregexpr("- -",x[i])[[1]]
for (j in 1:length(emLocs))
{
substring(x[i+1],emLocs[j],emLocs[j]+2) <- "- -"
substring(x[i+2],emLocs[j],emLocs[j]+2) <- "- -"
# Check if CI is included (new LISREL verson) and add more:
if (grepl(";",x[i+1])){
substring(x[i+3],emLocs[j],emLocs[j]+2) <- "- -"
substring(x[i+4],emLocs[j],emLocs[j]+2) <- "- -"
substring(x[i+5],emLocs[j],emLocs[j]+2) <- "- -"
}
}
}
}
# Remove leading and trailing spaces:
x <- gsub("^\\s+","",x)
x <- gsub("\\s+$","",x)
# Remove empty lines:
x <- x[x!=""]
# Normalize spacing:
# x <- gsub("\\s+"," ",x)
# Make "- -" NA:
x <- gsub("- -","NA",x)
# Identify start of submatrices:
sub <- grep(name,x)
# Extract submatrices:
X <- list()
for (i in seq_along(sub))
{
if (i<length(sub))
{
X[[i]] <- x[(sub[i]+1):(sub[i+1]-1)]
} else {
X[[i]] <- x[(sub[i]+1):length(x)]
}
}
# Remove second line and note lines:
X <- lapply(X,'[',-2)
X <- lapply(X,function(x)x[!grepl("Note:",x,ignore.case=TRUE)])
## If estimate matrix, remove standard errors and t-values:
if (estimates)
{
# Detect if CI is added (also assume then p-value is added):
CIs <- sapply(X,function(xx)any(grepl(";$",xx)))
seLocs <- lapply(X,function(x)grep("\\(\\d*\\.?\\d*\\)",x))
Xse <- X
Xt <- X
for (i in 1:length(X))
{
if (CIs[i]){
# New behavior:
Xse[[i]][-seLocs[[i]]] <- gsub("^.+? ","",Xse[[i]][-seLocs[[i]]])
Xse[[i]][-seLocs[[i]]] <- gsub("[^ ]+","NA",Xse[[i]][-seLocs[[i]]])
Xse[[i]] <- Xse[[i]][-c(seLocs[[i]]-3,seLocs[[i]]-2,seLocs[[i]]-1,seLocs[[i]]+1,seLocs[[i]]+2)]
Xse[[i]] <- gsub("\\(|\\)","",Xse[[i]])
Xse[[i]] <- Xse[[i]][-1]
Xse[[i]] <- c(X[[i]][1],Xse[[i]])
Xt[[i]][-(seLocs[[i]]+1)] <- gsub("^.+? ","",Xt[[i]][-(seLocs[[i]]+1)])
Xt[[i]][-(seLocs[[i]]+1)] <- gsub("[^ ]+","NA",Xt[[i]][-(seLocs[[i]]+1)])
Xt[[i]] <- Xt[[i]][-c(seLocs[[i]]-3,seLocs[[i]]-2,seLocs[[i]]-1,seLocs[[i]],seLocs[[i]]+2)]
Xt[[i]] <- Xt[[i]][-1]
Xt[[i]] <- c(X[[i]][1],Xt[[i]])
X[[i]] <- X[[i]][-c(seLocs[[i]]-2,seLocs[[i]]-1,seLocs[[i]],seLocs[[i]]+1,seLocs[[i]]+2)]
} else {
# Old behavior:
Xse[[i]][-seLocs[[i]]] <- gsub("^.+? ","",Xse[[i]][-seLocs[[i]]])
Xse[[i]][-seLocs[[i]]] <- gsub("[^ ]+","NA",Xse[[i]][-seLocs[[i]]])
Xse[[i]] <- Xse[[i]][-c(seLocs[[i]]-1,seLocs[[i]]+1)]
Xse[[i]] <- gsub("\\(|\\)","",Xse[[i]])
Xse[[i]] <- Xse[[i]][-1]
Xse[[i]] <- c(X[[i]][1],Xse[[i]])
Xt[[i]][-(seLocs[[i]]+1)] <- gsub("^.+? ","",Xt[[i]][-(seLocs[[i]]+1)])
Xt[[i]][-(seLocs[[i]]+1)] <- gsub("[^ ]+","NA",Xt[[i]][-(seLocs[[i]]+1)])
Xt[[i]] <- Xt[[i]][-c(seLocs[[i]]-1,seLocs[[i]])]
Xt[[i]] <- Xt[[i]][-1]
Xt[[i]] <- c(X[[i]][1],Xt[[i]])
X[[i]] <- X[[i]][-c(seLocs[[i]],seLocs[[i]]+1)]
}
}
}
# Extract and remove rownames:
rowNames <- regmatches(X[[1]][-1],regexpr("^.+?(?= )",X[[1]][-1],perl=TRUE))
if (any(grepl("[a-z]",rowNames,ignore.case=TRUE))) X <- lapply(X,function(txt)c(txt[1],gsub("^.+? ","",txt[-1])))
# Combine:
X <- lapply(X,paste,collapse="\n")
# Read table:
Tabs <- lapply(X,function(txt)as.matrix(read.table(text=txt,header=TRUE,fill=TRUE,quote=NULL)))
if (estimates)
{
seTabs <- lapply(Xse,function(txt)as.matrix(read.table(text=txt,header=TRUE,fill=TRUE,quote=NULL)))
tTabs <- lapply(Xt,function(txt)as.matrix(read.table(text=txt,header=TRUE,fill=TRUE,quote=NULL)))
}
# Check if same number of rows, or append (triangle matrices):
if (length(unique(sapply(Tabs,nrow)))>1)
{
if (missing(symmetrical)) symmetrical <- TRUE
totR <- nrow(Tabs[[1]])
for (i in 2:length(Tabs))
{
Tabs[[i]] <- rbind(matrix(NA,totR-nrow(Tabs[[i]]),ncol(Tabs[[i]])),Tabs[[i]])
if (estimates)
{
seTabs[[i]] <- rbind(matrix(NA,totR-nrow(seTabs[[i]]),ncol(seTabs[[i]])),seTabs[[i]])
tTabs[[i]] <- rbind(matrix(NA,totR-nrow(tTabs[[i]]),ncol(tTabs[[i]])),tTabs[[i]])
# Xse[[i]] <- c(rep(paste(rep(NA,ncol(Tabs[[i]])),collapse=" "),totR-length(Xse[[i]])),Xse[[i]])
# Xt[[i]] <- c(rep(paste(rep(NA,ncol(Tabs[[i]])),collapse=" "),totR-length(Xt[[i]])),Xt[[i]])
}
}
}
# Combine:
Tab <- as.matrix(do.call(cbind,Tabs))
rownames(Tab) <- rowNames
if (!any(dim(Tab)==1)) diag <- FALSE
# Diagonalize:
if (diag)
{
nm <- colnames(Tab)
Tab <- diag(c(Tab),length(Tab),length(Tab))
rownames(Tab) <- colnames(Tab) <- nm
}
# Symmetrize:
if (symmetrical)
{
Tab[upper.tri(Tab)] <- t(Tab)[upper.tri(Tab)]
}
Tab[is.na(Tab)] <- 0
# Compute SE and t-value matrices if needed:
if (estimates)
{
# seTabs <- lapply(Xse,function(txt)as.matrix(read.table(text=txt,header=TRUE,fill=TRUE)))
seTab <- do.call(cbind,seTabs)
# tTabs <- lapply(Xt,function(txt)as.matrix(read.table(text=txt,header=TRUE,fill=TRUE)))
tTab <- do.call(cbind,tTabs)
# Diagonalize:
if (diag)
{
seTab <- diag(c(seTab),length(seTab),length(seTab))
tTab <- diag(c(tTab),length(tTab),length(tTab))
}
colnames(seTab) <- colnames(tTab) <- colnames(Tab)
rownames(seTab) <- rownames(tTab) <- rownames(Tab)
# Symmetrize:
if (symmetrical)
{
seTab[upper.tri(seTab)] <- t(seTab)[upper.tri(seTab)]
tTab[upper.tri(tTab)] <- t(tTab)[upper.tri(tTab)]
}
# Return list:
return(list(est=Tab,se=seTab,t=tTab))
}
# Return matrix:
return(Tab)
}
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