Author: Marie Chavent
Date: 2017-10-20

# Supplementary Observations, Variables or Groups

#### Marie Chavent

#### 2017-10-20

    library(PCAmixdata)

# Supplementary variables and groups

## In PCAmix

    data(wine)
    X.quanti <- splitmix(wine)$X.quanti[,1:5]
    X.quali <- splitmix(wine)$X.quali[,1,drop=FALSE]
    X.quanti.sup <-splitmix(wine)$X.quanti[,28:29]
    X.quali.sup <-splitmix(wine)$X.quali[,2,drop=FALSE]
    pca<-PCAmix(X.quanti,X.quali,ndim=4,graph=FALSE)
    pca2 <- supvar(pca,X.quanti.sup,X.quali.sup)
    plot(pca2,choice="levels")

    plot(pca2,choice="cor")

    plot(pca2,choice="sqload")

## In MFAmix

    data(wine)
    X.quanti <- splitmix(wine)$X.quanti[,1:5]
    X.quali <- splitmix(wine)$X.quali[,1,drop=FALSE]
    X.quanti.sup <- splitmix(wine)$X.quanti[,28:29]
    X.quali.sup <- splitmix(wine)$X.quali[,2,drop=FALSE]
    data <- cbind(X.quanti,X.quali)
    data.sup <- cbind(X.quanti.sup,X.quali.sup)

    groups <-c(1,2,2,3,3,1)
    name.groups <- c("G1","G2","G3")
    mfa <- MFAmix(data,groups,name.groups,ndim=4,rename.level=TRUE,graph=FALSE)

    groups.sup <- c(1,1,2)
    name.groups.sup <- c("Gsup1","Gsup2")
    mfa.sup <- supvar(mfa,data.sup,groups.sup,name.groups.sup,rename.level=TRUE)
    plot(mfa.sup,choice="sqload",coloring.var="groups")

    plot(mfa.sup,choice="axes",coloring.var="groups")

    plot(mfa.sup,choice="groups",coloring.var="groups")

    plot(mfa.sup,choice="levels",coloring.var="groups")

    plot(mfa.sup,choice="levels")

    plot(mfa.sup,choice="cor",coloring.var = "groups")

Case of a single group

    #devtools::install_github("chavent/PCAmixdata")
    library(PCAmixdata)
    data(wine)
    X.quanti <- splitmix(wine)$X.quanti[,1:5]
    X.quali <- splitmix(wine)$X.quali[,1,drop=FALSE]
    X.quali.sup <- splitmix(wine)$X.quali[,2,drop=FALSE]
    data <- cbind(X.quanti,X.quali)

    groups <-c(1,1,1,2,2,2)
    name.groups <- c("G1","G2")
    mfa <- MFAmix(data,groups,name.groups,ndim=4,rename.level=TRUE,graph=FALSE)

    groups.sup <- c(1)
    name.groups.sup <- "Gsup1"
    mfa.sup <- supvar(mfa,X.quali.sup,groups.sup,name.groups.sup,rename.level=TRUE)
    plot(mfa.sup,choice="levels",coloring.var = "groups")

    groups.sup <- c(1,1,2)
    name.groups.sup <- c("Gsup1","Gsup2")
    mfa.sup <- supvar(mfa,data.sup,groups.sup,name.groups.sup,rename.level=TRUE)
    plot(mfa.sup,choice="sqload",coloring.var="groups")

    plot(mfa.sup,choice="axes",coloring.var="groups")

    plot(mfa.sup,choice="groups",coloring.var="groups")

    plot(mfa.sup,choice="levels",coloring.var="groups")

    plot(mfa.sup,choice="levels")

    plot(mfa.sup,choice="cor",coloring.var = "groups")

# New observations.

## In PCAmix

    data(wine)
    X.quanti <- splitmix(wine)$X.quanti[,1:5]
    X.quali <- splitmix(wine)$X.quali
    n <- nrow(wine)
    sub <- sample(1:n,10)
    pca<-PCAmix(X.quanti[sub,],X.quali[sub,],ndim=4,graph=FALSE)
    pred <- predict(pca,X.quanti[-sub,],X.quali[-sub,])
    plot(pca,axes=c(1,2))
    points(pred[,c(1,2)],col=2,pch=16)
    text(pred[,c(1,2)], labels = rownames(X.quanti[-sub,1:5]), col=2,pos=3)

## In MFAmix

    data(gironde)
    groups <- c(rep(1,9),rep(2,5),rep(3,9),rep(4,4))
    name.groups <- c("employment","housing","services","environment")
    dat<-cbind(gironde$employment,gironde$housing,
                    gironde$services,gironde$environment)
    n <- nrow(dat)
    set.seed(10)
    sub <- sample(1:n,520)
    res<-MFAmix(data=dat[sub,],groups=groups,name.groups=name.groups, rename.level=TRUE, ndim=3,graph=FALSE)
    pred<-predict(res,data=dat[-sub,],groups=class.var,name.groups=names)
    plot(res,choice="ind",cex=0.6,lim.cos2.plot=0.7)
    points(pred[1:5,c(1,2)],col=2,pch=16,cex=0.6)
    text(pred[1:5,c(1,2)], labels = rownames(dat[-sub,])[1:5],
         col=2,pos=3,cex=0.6)