R help - Dec 2013 - Polychoric Principal Component Analysis (pPCA)

I have data set with binary responses. I would like to
conduct polychoric principal component analysis (pPCA). I know there are several
packages used in PCA but I could not find one that directly estimate pPCA and
graph the individuals and variables maps. I will appreciate any help that expand
these reproducible scripts.
#How to conduct polychoric principal component analysis pPCA using 
#either of these packages
library(psych) 
library(FactoMineR)
library(nsprcomp)

#Bock and Liberman (1970) data set of 1000 observations of the LSAT
#from psych

data(bock)
responses <- table2df(bock.table[,2:6],count=bock.table[,7],
??????????????? labs= paste ("lsat6.",1:5,sep=""))
fix(responses) 
describe(responses)
#Estimate the polychoric correlation matrix to be used in 
#PCA using psych 
W <- polychoric(responses, smooth=TRUE,global=TRUE,polycor=F, 
??????????? ML = FALSE,??std.err=FALSE,progress=TRUE) 
#Regular PCA using stat, psych and FactoMiner, respectively
#There is no option for?including the matrix
princomp(responses, cor=TRUE) #What kind of correlation is used here?
?
principal(r = responses, nfactors = 3, rotate = "Promax")
principal(r = W, nfactors = 3, rotate = "Promax") #Do not work

PCA(responses, scale.unit=TRUE, ncp=3, graph=T) 
#How to conduct polychoric principal component analysis using either of #the
above package and producing individual and variable factor maps as #above

Peter Maclean
Department of Economics
UDSM

Peter,
I am not sure if anyone answered your question about doing biplots using
polychoric output and PCA.

The biplot.psych  example # 3 shows how to do this

library(psych)
> responses <- table2df(bock.table[,2:6],count=bock.table[,7],
>                 labs= paste ("lsat6.",1:5,sep="?))
> W <- polychoric(responses, smooth=TRUE,global=TRUE,polycor=F, 
>             ML = FALSE,  std.err=FALSE,progress=TRUE) 
#this returns an object with both the correlations and the difficulties

#get the object returned by principal  (see biplot.psych  example 3)

p3 <- principal(r = W$rho, nfactors = 3, rotate = "Promax") # works
if you actually give it the matrix

p3$scores <- factor.scores(responses,p3)   #find the scores from the response
data set with the p3 pca solution
 biplot.psych(p3)

Bill




On Dec 17, 2013, at 2:18 PM, Peter Maclean <pmaclean2011 at yahoo.com>
wrote:
> I have data set with binary responses. I would like to
> conduct polychoric principal component analysis (pPCA). I know there are
several packages used in PCA but I could not find one that directly estimate
pPCA and graph the individuals and variables maps. I will appreciate any help
that expand these reproducible scripts.
> #How to conduct polychoric principal component analysis pPCA using 
> #either of these packages
> library(psych) 
> library(FactoMineR)
> library(nsprcomp)
> 
> #Bock and Liberman (1970) data set of 1000 observations of the LSAT
> #from psych
> 
> data(bock)
> responses <- table2df(bock.table[,2:6],count=bock.table[,7],
>                 labs= paste ("lsat6.",1:5,sep=""))
> fix(responses) 
> describe(responses)
> #Estimate the polychoric correlation matrix to be used in 
> #PCA using psych 
> W <- polychoric(responses, smooth=TRUE,global=TRUE,polycor=F, 
>             ML = FALSE,  std.err=FALSE,progress=TRUE) 
> #Regular PCA using stat, psych and FactoMiner, respectively
> #There is no option for including the matrix
> princomp(responses, cor=TRUE) #What kind of correlation is used here?
>  
> principal(r = responses, nfactors = 3, rotate = "Promax")
> principal(r = W, nfactors = 3, rotate = "Promax") #Do not work
> 
> PCA(responses, scale.unit=TRUE, ncp=3, graph=T) 
> #How to conduct polychoric principal component analysis using either of
#the above package and producing individual and variable factor maps as #above
> 
> Peter Maclean
> Department of Economics
> UDSM
> 
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