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#factor analysis and sem diagrams
#based upon fa.graph with some ideas taken from the diagram and shape packages of Karline Soetaert
#version of September 20, 2009
#developed to replace Rgraphviz which is too much of a pain to install
#Rgraphviz uses a NEL (Node, Edge) represenation while diagram uses a complete linking matrix
#thus, I am trying to combine these two approaches
#modified 31/5/14 to allow for drawing factor extension derived omegas
#and again 7/2/18 to include omegaDirect output
"omega.diagram" <-
function(om.results,sl=TRUE,sort=TRUE,labels=NULL,flabels=NULL,cut=.2,gcut=.2,simple=TRUE,errors=FALSE,
digits=1,e.size=.1,rsize=.15,side=3,main=NULL,cex=NULL,color.lines=TRUE
,marg=c(.5,.5,1.5,.5),adj=2, ...) {
if(color.lines) { colors <- c("black","red")} else {colors <- c("black","black") }
Phi <- NULL #the default case
if(is.null(cex)) cex <- 1
old.par<- par(mar=marg) #give the window some narrower margins
on.exit(par(old.par)) #set them back
#Figure out what type of input we are drawing (done July 2, 2018)
#fixed for R 4.0.0 December 11, 2019
extend<- FALSE
#which kind of input are we drawing?
if(length(class(om.results)) > 1) {
omegaSem <- omegaDirect <- omega <- NULL #strange fix to R 4,0,0 compiler
names <- cs(matrix, extend, omegaSem, omegaDirect, omega)
value <- inherits(om.results,names,which=TRUE) # value <- class(x)[2]
if(any(value > 1) ) { result <- names[which(value > 0)]} else {result <- "other"}
} else {result <- "extend"} #just a raw matrix
if(result == "matrix") result <- "extend"
#dispatch to the right option
switch(result,
extend = {extend <- TRUE
#class(om.results)[2] <- "omega"
factors <- om.results
nvar <- num.var <- nrow(factors)
num.factors <- ncol(factors) -1
if(sort) {temp <- fa.sort(factors[,-1])
temp2 <- factors[,1,drop=FALSE] #added the drop option November 4, 2018
factors <- cbind(g=temp2[rownames(temp),1],temp)} #added column 1
},
omegaSem = {
#did we do an omegaSem or just an omegaFromSem?
if(is.null(om.results$omega.efa$cfa.loads)) {cfa.loads <- om.results$cfa.loads} else {cfa.loads <- om.results$omega.efa$cfa.loads}
# factors <- as.matrix(om.results$omega.efa$cfa.loads[,2:ncol(om.results$omega.efa$cfa.loads)])
class(cfa.loads) <- c("psych","omegaSem")
if(sort) cfa.loads <- fa.sort(cfa.loads)
factors <- as.matrix(cfa.loads)
gloading <- cfa.loads[,1,drop=FALSE]
nvar <- num.var <- nrow(gloading)
num.factors <- ncol(factors) -1
sl=TRUE
main <- "Omega from SEM"
},
omegaDirect = {factors <- om.results$loadings
nvar <- num.var <- nrow(factors)
num.factors <- ncol(factors) -1
if(sort) {temp <- fa.sort(factors[,-1])
temp2 <- factors[,1]
factors <- cbind(g=temp2[rownames(temp)],temp)} },
omega ={
if(extend) class(om.results) <- c("psych","omega")
if(sort) om.results <- fa.sort(om.results) #usually sort, but sometimes it is better not to do so
if (sl) {factors <- as.matrix(om.results$schmid$sl)
if(is.null(main)) {main <- "Omega with Schmid Leiman Transformation" }
} else {factors <- as.matrix(om.results$schmid$oblique)
if(is.null(main)) {main <- "Hierarchical (multilevel) Structure" }
}
gloading <- om.results$schmid$gloading
nvar <- num.var <- dim(factors)[1] #how many variables?
if (sl ) {num.factors <- dim(factors)[2] - 1 - (!extend) *3 } else {num.factors <- dim(factors)[2]
}
},
other ={warning("I am sorry, I don't know how to diagram this input")}
)
if(result !="other") {#skip to the end if we don' know what we are doing
#now draw the figure
e.size <- e.size * 10/ nvar #this is an arbitrary setting that seems to work
#first some basic setup parameters
vars <- paste("V",1:num.var,sep="")
# if (!is.null(labels)) {vars <- paste(labels)} else{vars <- rownames(factors) }
#patched to actually draw the labels! 8/21/22
if (!is.null(labels)) {rownames(factors) <- paste(labels)} else{vars <- rownames(factors) }
if(!is.null(flabels)) {fact <- flabels} else { if(sl) {fact <- c("g",paste("F",1:num.factors,"*",sep="")) } else {fact <- c(paste("F",1:num.factors,sep="")) } } # e.g. "g" "F'1" "F2" "F3"
colnames(factors)[1:length(fact)] <- fact
var.rect <- list()
arrows.list <- list()
fact.rect <- list()
max.len <- max(nchar(rownames(factors)))*rsize
cex <- min(cex,40/nvar)
xleft <- -max.len/2 #0#
xright <- nvar + 1 # or hard code to 3?
plot(0,type="n",xlim=c(xleft-max.len,xright+1),ylim=c(1,nvar+1),frame.plot=FALSE,axes=FALSE,ylab="",xlab="",main=main)
if (sl) {vloc <- (xright)/2
gloc <- xleft
grouploc <-xright
start <- 1
end <- num.factors+1} else {
vloc <- xleft
gloc <- xright
grouploc <- (xright)/2
start <- 0
end <- num.factors
}
for (v in 1:nvar) {
var.rect[[v]] <- dia.rect(vloc,nvar-v+1,rownames(factors)[v],xlim=c(0,nvar),ylim=c(0,nvar),cex=cex,draw=FALSE,...)
}
f.scale <- (nvar+ 1)/(num.factors+1)
f.shift <- nvar/num.factors
for (f in 1:num.factors) {
fact.rect[[f]] <- dia.ellipse(grouploc,(num.factors+1-f)*f.scale,colnames(factors)[f+start],xlim=c(0,nvar),ylim=c(0,nvar),e.size=e.size,draw=TRUE,...)
for (v in 1:nvar) {
if (abs(factors[v,f+start]) > cut) {d.arrow <- dia.arrow(from=fact.rect[[f]],to=var.rect[[v]]$right,col=colors[((sign(factors[v,f+start])<0) +1)],lty=((sign(factors[v,f+start])<0)+1),labels=round(factors[v,f+start],digits),adj=f %% adj +1,draw=FALSE)
if(!is.null(d.arrow) )arrows.list <- c(arrows.list,d.arrow) }
}
}
g.ellipse <- dia.ellipse(gloc,(num.var+1)/2,"g",xlim=c(0,nvar),ylim=c(0,nvar),e.size=e.size,...)
if(!sl) {
for (f in 1:num.factors) {
d.arrow <- dia.arrow(from=g.ellipse,to=fact.rect[[f]],col=colors[((sign(gloading[f])<0) +1)],lty=((sign(gloading[f])<0) +1),labels=round(gloading[f],digits),adj=f %% adj +1,draw=FALSE)
arrows.list <- c(arrows.list,d.arrow) }
} else {
for (i in 1:nvar) {
if(abs(factors[i,1]) > gcut) {
d.arrow <- dia.arrow(from=g.ellipse,to=var.rect[[i]]$left,col=colors[((sign(factors[i,1])<0) +1)],lty=((sign(factors[i,1])<0)+1),labels=round(factors[i,1],digits),adj=1,draw=FALSE)}
if(!is.null(d.arrow) ) arrows.list <- c(arrows.list,d.arrow)
}
}
if (errors) {for (v in 1:nvar) {
dia.self(location=var.rect[[v]],scale=.5,side=side) }
}
} #end of normal case
tv <- matrix(unlist(var.rect),nrow=nvar,byrow=TRUE)
all.rects.x <- tv[,5] #the center of the figure
all.rects.y <- tv[,2]
all.rects.names <- rownames(factors)
dia.rect(all.rects.x, all.rects.y,all.rects.names)
# multi.rect(var.rect,...)
#draw the factors not implemented
fv <- matrix(unlist(fact.rect),nrow=num.factors,byrow=TRUE)
all.rects.x <- fv[,5] #the center of the figure
all.rects.y <- fv[,6]
all.rects.names <- colnames(factors)[2:(num.factors+1)]
# dia.ellipse1(all.rects.x, all.rects.y,all.rects.names)
# now show all the loadings as arrows
# tv <- matrix(unlist(arrows.list),byrow=TRUE,ncol=20)
# cname<- colnames(tv)
# tv <- data.frame(tv)
# tv[,c(1:18,20)] <- nchar2numeric(tv[,c(1:18,20)])
# colnames(tv) <- cname
# text(tv[,1],tv[,2],tv[,3],cex=tv[,4])
# len1 <- as.numeric(tv[1,9])
# len2 <- as.numeric(tv[1,16])
# arrows(x0=tv[,5],y0=tv[,6],x1=tv[,7],y1=tv[,8],length=len1,angle=30,code=1,col=tv[,19],lty=tv[,20],...)
# arrows(x0=tv[,12],y0=tv[,13],x1=tv[,14],y1=tv[,15],length=len2,angle=30,code=2,col=tv[,19],lty=tv[,29],...)
#
multi.arrow(arrows.list,...)
}
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