plsRglm (version 1.5.1)

plots.confints.bootpls: Plot bootstrap confidence intervals

Description

This function plots the confidence intervals derived using the function confints.bootpls from from a bootpls based object.

Usage

plots.confints.bootpls(
  ic_bootobject,
  indices = NULL,
  legendpos = "topleft",
  prednames = TRUE,
  articlestyle = TRUE,
  xaxisticks = TRUE,
  ltyIC = c(2, 4, 5, 1),
  colIC = c("darkgreen", "blue", "red", "black"),
  typeIC,
  las = par("las"),
  mar,
  mgp,
  ...
)

Value

NULL

Arguments

ic_bootobject

an object created with the confints.bootpls function.

indices

vector of indices of the variables to plot. Defaults to NULL: all the predictors will be used.

legendpos

position of the legend as in legend, defaults to "topleft"

prednames

do the original names of the predictors shall be plotted ? Defaults to TRUE: the names are plotted.

articlestyle

do the extra blank zones of the margin shall be removed from the plot ? Defaults to TRUE: the margins are removed.

xaxisticks

do ticks for the x axis shall be plotted ? Defaults to TRUE: the ticks are plotted.

ltyIC

lty as in plot

colIC

col as in plot

typeIC

type of CI to plot. Defaults to typeIC=c("Normal", "Basic", "Percentile", "BCa") if BCa intervals limits were computed and to typeIC=c("Normal", "Basic", "Percentile") otherwise.

las

numeric in 0,1,2,3; the style of axis labels. 0: always parallel to the axis [default], 1: always horizontal, 2: always perpendicular to the axis, 3: always vertical.

mar

A numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot. The default is c(5, 4, 4, 2) + 0.1.

mgp

The margin line (in mex units) for the axis title, axis labels and axis line. Note that mgp[1] affects title whereas mgp[2:3] affect axis. The default is c(3, 1, 0).

...

further options to pass to the plot function.

Author

Frédéric Bertrand

https://fbertran.github.io/homepage/

See Also

confints.bootpls

Examples

data(Cornell)
modpls <- plsR(Y~.,data=Cornell,3)

# Lazraq-Cleroux PLS (Y,X) bootstrap
set.seed(250)
Cornell.bootYX <- bootpls(modpls, R=250, verbose=FALSE)
temp.ci <- confints.bootpls(Cornell.bootYX,2:8)

plots.confints.bootpls(temp.ci)
plots.confints.bootpls(temp.ci,prednames=FALSE)
plots.confints.bootpls(temp.ci,prednames=FALSE,articlestyle=FALSE,
main="Bootstrap confidence intervals for the bj")
plots.confints.bootpls(temp.ci,indices=1:3,prednames=FALSE)
plots.confints.bootpls(temp.ci,c(2,4,6),"bottomright")
plots.confints.bootpls(temp.ci,c(2,4,6),articlestyle=FALSE,
main="Bootstrap confidence intervals for some of the bj")

temp.ci <- confints.bootpls(Cornell.bootYX,typeBCa=FALSE)
plots.confints.bootpls(temp.ci)
plots.confints.bootpls(temp.ci,2:8)
plots.confints.bootpls(temp.ci,prednames=FALSE)


# Bastien CSDA 2005 (Y,T) bootstrap
Cornell.boot <- bootpls(modpls, typeboot="fmodel_np", R=250, verbose=FALSE)
temp.ci <- confints.bootpls(Cornell.boot,2:8)

plots.confints.bootpls(temp.ci)
plots.confints.bootpls(temp.ci,prednames=FALSE)
plots.confints.bootpls(temp.ci,prednames=FALSE,articlestyle=FALSE,
main="Bootstrap confidence intervals for the bj")
plots.confints.bootpls(temp.ci,indices=1:3,prednames=FALSE)
plots.confints.bootpls(temp.ci,c(2,4,6),"bottomright")
plots.confints.bootpls(temp.ci,c(2,4,6),articlestyle=FALSE,
main="Bootstrap confidence intervals for some of the bj")

temp.ci <- confints.bootpls(Cornell.boot,typeBCa=FALSE)
plots.confints.bootpls(temp.ci)
plots.confints.bootpls(temp.ci,2:8)
plots.confints.bootpls(temp.ci,prednames=FALSE)


# \donttest{
data(aze_compl)
modplsglm <- plsRglm(y~.,data=aze_compl,3,modele="pls-glm-logistic")

# Lazraq-Cleroux PLS (Y,X) bootstrap
# should be run with R=1000 but takes much longer time
aze_compl.bootYX3 <- bootplsglm(modplsglm, typeboot="plsmodel", R=250, verbose=FALSE)
temp.ci <- confints.bootpls(aze_compl.bootYX3)

plots.confints.bootpls(temp.ci)
plots.confints.bootpls(temp.ci,prednames=FALSE)
plots.confints.bootpls(temp.ci,prednames=FALSE,articlestyle=FALSE,
main="Bootstrap confidence intervals for the bj")
plots.confints.bootpls(temp.ci,indices=1:33,prednames=FALSE)
plots.confints.bootpls(temp.ci,c(2,4,6),"bottomleft")
plots.confints.bootpls(temp.ci,c(2,4,6),articlestyle=FALSE,
main="Bootstrap confidence intervals for some of the bj")
plots.confints.bootpls(temp.ci,indices=1:34,prednames=FALSE)
plots.confints.bootpls(temp.ci,indices=1:33,prednames=FALSE,ltyIC=1,colIC=c(1,2))
 
temp.ci <- confints.bootpls(aze_compl.bootYX3,1:34,typeBCa=FALSE)
plots.confints.bootpls(temp.ci,indices=1:33,prednames=FALSE)


# Bastien CSDA 2005 (Y,T) Bootstrap
# much faster
aze_compl.bootYT3 <- bootplsglm(modplsglm, R=1000, verbose=FALSE)
temp.ci <- confints.bootpls(aze_compl.bootYT3)

plots.confints.bootpls(temp.ci)
plots.confints.bootpls(temp.ci,typeIC="Normal")
plots.confints.bootpls(temp.ci,typeIC=c("Normal","Basic"))
plots.confints.bootpls(temp.ci,typeIC="BCa",legendpos="bottomleft")
plots.confints.bootpls(temp.ci,prednames=FALSE)
plots.confints.bootpls(temp.ci,prednames=FALSE,articlestyle=FALSE,
main="Bootstrap confidence intervals for the bj")
plots.confints.bootpls(temp.ci,indices=1:33,prednames=FALSE)
plots.confints.bootpls(temp.ci,c(2,4,6),"bottomleft")
plots.confints.bootpls(temp.ci,c(2,4,6),articlestyle=FALSE,
main="Bootstrap confidence intervals for some of the bj")
plots.confints.bootpls(temp.ci,prednames=FALSE,ltyIC=c(2,1),colIC=c(1,2))
 
temp.ci <- confints.bootpls(aze_compl.bootYT3,1:33,typeBCa=FALSE)
plots.confints.bootpls(temp.ci,prednames=FALSE)
# }