library(psych) # library for the 'principal()' function


TOMCAT <- read.table("cohesionMetricsFinal_Tomcat_tab.txt", header=TRUE, sep="\t"); # reading
TOMCAT2 <- TOMCAT[,c(1,2,3,4,5,6)] # eliminating the CC variable for this analysis (last column)
TOMCAT2 <- na.omit(TOMCAT2) # omiting N/A measures
TOMCAT_PCA <- principal(TOMCAT2, nfactors=4, rotate="varimax") # PCA function with varimax rotation
TOMCAT_PCA

RHINO <- read.table("cohesionMetricsFinal_Rhino_tab.txt", header=TRUE, sep="\t")
RHINO2 <- RHINO[,c(1,2,3,4,5,6)]
RHINO2 <- na.omit(RHINO2)
RHINO_PCA2 <- principal(RHINO2, nfactors=4, rotate="varimax")
RHINO_PCA2

JFREECHART<- read.table("cohesionMetricsFinal_JFreeChart_tab.txt", header=TRUE, sep="\t")
JFREECHART2 <- JFREECHART[,c(1,2,3,4,5,6)]
JFREECHART2 <- na.omit(JFREECHART2)
JFREECHART_PCA <- principal(JFREECHART2, nfactors=4, rotate="varimax")
JFREECHART_PCA

JEDIT <- read.table("cohesionMetricsFinal_jEdit_tab.txt", header=TRUE, sep="\t")
JEDIT2 <- JEDIT[,c(1,2,3,4,5,6)]
JEDIT2 <- na.omit(JEDIT2)
JEDIT_PCA <- principal(JEDIT2, nfactors=4, rotate="varimax")
JEDIT_PCA

FINDBUGS <- read.table("cohesionMetricsFinal_Findbugs_tab.txt", header=TRUE, sep="\t")
FINDBUGS2 <- FINDBUGS[,c(1,2,3,4,5,6)]
FINDBUGS2 <- na.omit(FINDBUGS2)
FINDBUGS_PCA <- principal(FINDBUGS2, nfactors=4, rotate="varimax")
FINDBUGS_PCA

FREECOL <- read.table("cohesionMetricsFinal_Freecol_tab.txt", header=TRUE, sep="\t")
FREECOL2 <- FREECOL[,c(1,2,3,4,5,6)]
FREECOL2 <- na.omit(FREECOL2)
FREECOL_PCA <- principal(FREECOL2, nfactors=4, rotate="varimax")
FREECOL_PCA