README.md

In martinparies/PCAOS: PCA.OS

PCAOS

PCAOS package allows to perform Single and MultiBlock exploratory analysis of datasets composed of variables with different natures.

How do you install an use the latest version of PCAOS available on GitHub?

if (!require("devtools")) install.packages("devtools")
library(devtools)
install_github("martinparies/PCA.OS")
library(PCA.OS)
help(PCA.OS)

1. Single block data

data("antibiotic")
help(antibiotic)

1.1 Setting nature of each variable

#Manually
level.scale <- rep(NA,ncol(antibiotic)) #Setting level.scale argument
level.scale[c(3,4)] <- "num"
level.scale[c(6:14)] <- "nom"
level.scale[c(1,15)] <- "ord"

#Or using nature.variables()
level.scale <- rep(NA,ncol(antibiotic))
res.nature <- nature.variables(antibiotic)
level.scale [res.nature$p.numeric] <- "num"
level.scale [res.nature$p.quali] <- "nom"
#Warning; the ordinal nature of variables can not be detected automaticaly.
level.scale[c(1,15)] <- "ord"

1.2 Choice of number of component

help(choice.component)
res.choice <- choice.component(antibiotic,level.scale)
res.choice

1.3 Single block exploratory analysis : PCAOS

help(PCAOS)
res.PCAOS <- PCAOS(
  data = antibiotic,
  level.scale = level.scale,
  nb.comp = 2)

1.4 Plots

help(plot.PCAOS)
#Individuals
plot.PCAOS(
  x = res.PCAOS,
  choice = "ind",
  coloring.indiv = antibiotic$Atb.conso,
  size.legend = 12,
  size.label = 4
)

# Variables
plot.PCAOS(x = res.PCAOS,choice = "all.var")

2. Multiblock data

data('antibiotic')
antb.uses <- antibiotic[,c('Atb.conso','Atb.Sys')]
health <- antibiotic[,c('Age','Loss')]
vet.practices <- antibiotic[,c(6:15)]
antibiotic.MB <- data.frame(antb.uses,health,vet.practices)

2.1 Defining the blocks

blocks.name =  c("antibiotic.uses","Health.of.turkeys","Veterinary.practices")
blocks <- c(2,2,10)

2.2 Level of scaling

level.scale.MB <- rep(NA,ncol(antibiotic.MB))
res.nature <- nature.variables(antibiotic.MB)
level.scale.MB [res.nature$p.numeric] <- "num"
level.scale.MB [res.nature$p.quali] <- "nom"
#Warning; the ordinal nature of variables can not be detected automaticaly.
level.scale.MB[c(1,14)] <- "ord"

2.3 Choice of number of component

help(choice.component.MB)
res.choice.MB <- choice.component.MB(antibiotic.MB,level.scale.MB, blocks , blocks.name, block.scaling = 'inertia')
res.choice.MB

2.4 Multiblock exploratory analysis : MBPCAOS

res.MBPCAOS <- MBPCAOS(data = antibiotic.MB,
                       level.scale = level.scale.MB,
                       blocks = blocks,
                       blocks.name = blocks.name,
                       nb.comp = 3)

2.5 Blocks graph

plot.MBPCAOS(res.MBPCAOS,choice = 'blocks')

martinparies/PCAOS documentation built on March 15, 2023, 7:19 a.m.