screeArchetypal: Screeplot of archetypal individuals

In Anthropometry: Statistical Methods for Anthropometric Data

Screeplot of archetypal individuals

Description

This function allows us to represent in the same plot the screeplot of the archetypes and the both cand_ns, cand_alpha and cand_beta archetypoids.

Usage

screeArchetypal(numArch,rss_lass_def,rss_step_ns,rss_step_alpha,rss_step_beta,
                ylim,main,xlab,ylab,col=c("red","blue","green3"),axis2,seq,leg)

Arguments

numArch	Number of archetypal observations (archetypes and archetypoids).
rss_lass_def	Vector of the residual sum of squares (rss) associated with each archetype from 1 to numArch.
rss_step_ns	Vector of the residual sum of squares (rss) associated with each cand_ns archetypoid from 1 to numArch.
rss_step_alpha	Vector of the residual sum of squares (rss) associated with each cand_alpha archetypoid from 1 to numArch.
rss_step_beta	Vector of the residual sum of squares (rss) associated with each cand_beta archetypoid from 1 to numArch.
ylim	The y limits of the plot.
main	Title of the plot.
xlab	A title for the x axis.
ylab	A title for the y axis.
col	Color vector for the screeplots of the archetypoids. Default is c("red","blue","green3").
axis2	A logical value. If TRUE, the y axis can be customized to have spaced tick-marks by means of the following argument seq.
seq	Vector sequence with the values of the tick-marks to be drawn in the y axis.
leg	If TRUE, a legend is shown.

Value

A device with the desired plot.

Author(s)

Guillermo Vinue

References

Vinue, G., Epifanio, I., and Alemany, S., (2015). Archetypoids: a new approach to define representative archetypal data, Computational Statistics and Data Analysis 87, 102–115.

Cutler, A., and Breiman, L., (1994). Archetypal Analysis, Technometrics 36, 338–347.

Epifanio, I., Vinue, G., and Alemany, S., (2013). Archetypal analysis: contributions for estimating boundary cases in multivariate accommodation problem, Computers & Industrial Engineering 64, 757–765.

Eugster, M. J., and Leisch, F., (2009). From Spider-Man to Hero - Archetypal Analysis in R, Journal of Statistical Software 30, 1–23, doi: 10.18637/jss.v030.i08.

Eugster, M. J. A., (2012). Performance profiles based on archetypal athletes, International Journal of Performance Analysis in Sport 12, 166–187.

See Also

archetypoids, stepArchetypoids

Examples

## Not run: 
#COCKPIT DESIGN PROBLEM:
#The following R code allows us to obtain a similar plot regarding Figure 5 
#of the paper Vinue et al. (2015).
USAFSurvey_First25 <- USAFSurvey[1:25, ]
#Variable selection:
variabl_sel <- c(48, 40, 39, 33, 34, 36)
#Changing to inches: 
USAFSurvey_First25_inch <- USAFSurvey_First25[,variabl_sel] / (10 * 2.54)

#Data preprocessing:
USAFSurvey_preproc <- preprocessing(USAFSurvey_First25_inch, TRUE, 0.95, TRUE)

#For reproducing results, seed for randomness:
#suppressWarnings(RNGversion("3.5.0"))
#set.seed(2010) 
#Run archetype algorithm repeatedly from 1 to numArch archetypes:
#This is a toy example. In other situation, choose numArch=10 and numRep=20.
numArch <- 2 ; numRep <- 2
lass <- stepArchetypesRawData(data = USAFSurvey_preproc$data, 
                          numArch=1:numArch, numRep = numRep, 
                          verbose = FALSE)
#To understand the warning messages, see the vignette of the
#archetypes package.                            
  
rss_lass <- matrix(0, nrow = numArch, ncol = numRep)
for(i in 1:numArch){
  for(j in 1:numRep){
    rss_lass[i,j] <- lass[[i]][[j]]$rss
  }
}
(rss_lass_def <- apply(rss_lass, 1, min, na.rm = TRUE))

#Run archetypoids algorithm repeatedly from 1 to numArch archetypes:
for(numArchoid in 1:numArch){
  temp <-  stepArchetypoids(numArchoid, nearest = "cand_ns", 
                            USAFSurvey_preproc$data, lass)
  filename <- paste("res_ns", numArchoid, sep = "")
  assign(filename,temp)
  save(list = c(filename), file = paste(filename, ".RData", sep = "")) 
}   

#Run archetypoids algorithm repeatedly from 1 to numArch archetypes:
for(numArchoid in 1:numArch){
  temp <-  stepArchetypoids(numArchoid, nearest = "cand_alpha", 
                            USAFSurvey_preproc$data, lass)
  filename <- paste("res_alpha", numArchoid, sep = "")
  assign(filename,temp)
  save(list = c(filename), file = paste(filename, ".RData", sep = "")) 
}  

#Run archetypoids algorithm repeatedly from 1 to numArch archetypes:
for(numArchoid in 1:numArch){
  temp <-  stepArchetypoids(numArchoid, nearest = "cand_beta", 
                            USAFSurvey_preproc$data, lass)
  filename <- paste("res_beta", numArchoid, sep = "")
  assign(filename,temp)
  save(list = c(filename), file = paste(filename, ".RData", sep = "")) 
}  

#Numerical and graphical results:
#Cand_ns:
for(i in 1:numArch){
  load(paste("res_ns", i, ".RData", sep = ""))
}
rss_step <- c()
for (i in 1:numArch){
  rss_step[i] <- get(paste("res_ns", i, sep = ""))[[2]]
}
(rss_step_ns <- as.numeric(rss_step))

#Cand_alpha:
for(i in 1:numArch){
  load(paste("res_alpha", i, ".RData", sep = ""))
}
rss_step_which <- c()
for (i in 1:numArch){
  rss_step_which[i] <- get(paste("res_alpha", i, sep = ""))[[2]]
}
(rss_step_alpha <- as.numeric(rss_step_which))

#Cand_beta:
for(i in 1:numArch){
  load(paste("res_beta", i, ".RData", sep = ""))
}
rss_step_which <- c()
for (i in 1:numArch){
  rss_step_which[i] <- get(paste("res_beta", i, sep = ""))[[2]]
}
(rss_step_beta <- as.numeric(rss_step_which))

forYlim <- c(rss_lass_def, rss_step_ns, rss_step_alpha, rss_step_beta)
range(forYlim)
#[1] 0.06387125 0.27395811

#main <- "Aircraft pilots archetypes and archetypoids" 
xlab <- "Archetypes/Archetypoids"
ylab <- "RSS"
screeArchetypal(numArch, rss_lass_def, rss_step_ns, rss_step_alpha, rss_step_beta, 
                c(0,0.5), main = "", xlab, ylab, col = c("red","blue","green3"), 
                TRUE, seq(0,0.5,0.1), FALSE)
#rm(res_ns1.RData)
#rm(res_ns2.RData)
#rm(res_alpha1.RData)
#rm(res_alpha2.RData)
#rm(res_beta1.RData)
#rm(res_beta2.RData)

## End(Not run)

Anthropometry documentation built on March 7, 2023, 6:58 p.m.