Nothing
"fa.multi" <-
function(r,nfactors=3,nfact2=1,n.obs = NA,n.iter=1,rotate="oblimin",scores="regression", residuals=FALSE,SMC=TRUE,covar=FALSE,missing=FALSE,impute="median", min.err = .001,max.iter=50,symmetric=TRUE,warnings=TRUE,fm="minres",alpha=.1, p =.05,oblique.scores=FALSE,np.obs=NULL,use="pairwise",cor="cor",...) {
cl <- match.call()
if(nfactors < 2) stop("number of lower level factors must be at least 2")
f1 <- fa(r=r,nfactors=nfactors,n.obs=n.obs,rotate=rotate,scores=scores,residuals=residuals,SMC = SMC,covar=covar,missing=missing,impute=impute,min.err=min.err,max.iter=max.iter,symmetric=symmetric,warnings=warnings,fm=fm,alpha=alpha,oblique.scores=oblique.scores,np.obs=np.obs,use=use,cor=cor, ...=...) #call fa with the appropriate parameters
f2 <- fa(f1$Phi,nfactors=nfact2,rotate=rotate,fm=fm)
result <- list(f1=f1,f2=f2)
class(result) <- c("psych","fa.multi")
return(result)
}
#based upon the omegaDiagram function
#revised 7/23/23 to properly put in labels for first and second stratum
"fa.multi.diagram" <- function(multi.results,sort=TRUE,labels=NULL,flabels=NULL,f2labels=NULL,cut=.2,gcut=.2,simple=TRUE,errors=FALSE,
digits=1,e.size=.1,rsize=.15,side=3,main=NULL,cex=NULL,color.lines=TRUE
,marg=c(.5,.5,1.5,.5),adj=2, ...) {
if(color.lines) { colors <- c("black","red")} else {colors <- c("black","black") }
Phi <- NULL #the default case
if(is.null(cex)) cex <- 1
old.par<- par(mar=marg) #give the window some narrower margins
on.exit(par(old.par)) #set them back
if(sort) multi.results$f1 <- fa.sort(multi.results$f1)
factors <- as.matrix(multi.results$f1$loadings)
if(is.null(main)) {main <- "Hierarchical (multilevel) Structure" }
gloading <- multi.results$f2$loading
nvar <- num.var <- dim(factors)[1] #how many variables?
num.factors <- dim(factors)[2]
num.2level <- dim(gloading)[2]
e.size <- e.size * 10/ nvar #this is an arbitrary setting that seems to work
#first some basic setup parameters
vars <- paste("V",1:num.var,sep="")
if (!is.null(labels)) {vars <- paste(labels)} else{vars <- rownames(factors) }
if(!is.null(flabels)) {fact <- flabels} else { fact <- paste0("F",1:num.factors,sep="") } # e.g. "F'1" "F2" "F3"
rownames(factors)<- vars
colnames(factors)[1:length(fact)] <- fact
if(!is.null(f2labels)) {fact2<- f2labels} else { fact2 <- paste0("g",1:num.2level,sep="")}
colnames(gloading) <- fact2
colnames(multi.results$f2$loadings) <- fact2
arrows.list <- list()
var.rect <- list()
fact.rect <- list()
max.len <- max(nchar(rownames(factors)))*rsize
cex <- min(cex,40/nvar)
xleft <- -max.len/2 #0#
xright <- nvar + 1 # or hard code to 3?
plot(0,type="n",xlim=c(xleft-max.len,xright+1),ylim=c(1,nvar+1),frame.plot=FALSE,axes=FALSE,ylab="",xlab="",main=main)
vloc <- xleft
gloc <- xright
grouploc <- (xright)/2
start <- 0
end <- num.factors
for (v in 1:nvar) {
var.rect[[v]] <- dia.rect(vloc,nvar-v+1,rownames(factors)[v],xlim=c(0,nvar),ylim=c(0,nvar),cex=cex,draw=FALSE,...)
}
f.scale <- (nvar+ 1)/(num.factors+1)
f.shift <- nvar/num.factors
for (f in 1:num.factors) {
fact.rect[[f]] <- dia.ellipse(grouploc,(num.factors+1-f)*f.scale,colnames(factors)[f+start],xlim=c(0,nvar),ylim=c(0,nvar),e.size=e.size,draw=FALSE,...)
for (v in 1:nvar) {
if (abs(factors[v,f+start]) > cut) {arrows.list <- c(arrows.list,
dia.arrow(from=fact.rect[[f]],to=var.rect[[v]]$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) )
}
}
}
g.ellipse <- list()
f.2scale <- (num.var+1)/(num.2level +1)
for(g in 1:num.2level) {
g.ellipse[[g] ]<- dia.ellipse(gloc,(num.2level+1-g)*f.2scale,colnames(gloading)[g],xlim=c(0,nvar),ylim=c(0,nvar),e.size=e.size,draw=FALSE,...)
for (f in 1:num.factors) {
if (abs(gloading[f,g]) > cut) { arrows.list <- c(arrows.list, dia.arrow(from=g.ellipse[[g]],to=fact.rect[[f]],col=colors[((sign(gloading[f,g])<0) +1)],lty=((sign(gloading[f,g])<0) +1),labels=round(gloading[f,g],digits),adj=f %% adj +1,draw=FALSE) )
}}
}
if (errors) {for (v in 1:nvar) {
dia.self(location=var.rect[[v]],scale=.5,side=side) }
}
##now draw everything at once
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,...)
fv <- matrix(unlist(fact.rect),nrow=num.factors,byrow=TRUE)
fv2 <- matrix(unlist(g.ellipse), byrow=TRUE,nrow=num.2level)
fv <- rbind(fv,fv2)
all.rects.x <- fv[,5] #the center of the figure
all.rects.y <- fv[,2]
all.rects.names <- c(colnames(factors),colnames(multi.results$f2$loadings))
dia.multi.ellipse(all.rects.x,all.rects.y, all.rects.names)
# tv2 <- matrix(unlist(g.ellipse), byrow=TRUE,nrow=num.2level))
#
# # now show all the loadings as arrows
# tv <- matrix(unlist(arrows.list),byrow=TRUE,nrow=num.factors)
# 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])
# dia.arrow(x0=tv[,5],y0=tv[,6],x1=tv[,7],y1=tv[,8],length=len1,angle=30,code=1,col=tv[,19],lty=tv[,20],...)
# dia.arrow(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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