PSP-methods {ePCR}

PSP-methods

Description

PSP-methods

print.PSP: Print general information of PSPs contents to the terminal

plot.PSP: By default the mean CV surface in terms of alpha/lambda is plotted using hamlet-package's hmap-function

coef.PSP: Default PSP coef-function extracts only the optimum parameters, not whole lambda-range

predict.PSP: Predict for a novel patient from current PSP

PSP.KM: Kaplan-Meier with division at a given cutoff point within [0,1]

PSP.PCA: Principal Component Plot of a single PSP, showing 2 principal axes with a colouring if strata have been indicated; newx can also be plotted in relation to fitting data

PSP.BOX: Boxplot of a single variable in a PSP in respect to strata, for outlier detection and observing variable distributions

PSP.CSP: Cumulative survival probabilities

PSP.NA: Nelson-Aalen with time-to-event prediction at point t = F^-1(0.5)

Usage

## S4 method for signature 'PSP'
print(x, ...)

plot(x, y, ...)

## S4 method for signature 'PSP'
plot(x, y, bias = 0.1, ...)

## S4 method for signature 'PSP'
coef(object)

## S4 method for signature 'PSP'
predict(object, type = "response", newx, verb = 0)

PSP.KM(object, ...)

## S4 method for signature 'PSP'
PSP.KM(object, cutoff = 0.5)

PSP.PCA(object, ...)

## S4 method for signature 'PSP'
PSP.PCA(
  object,
  newx,
  expanded = TRUE,
  type = "all",
  shuffle = TRUE,
  z = TRUE,
  cex = 1,
  col = c("aquamarine", "coral", "royalblue", "black"),
  pch = 16
)

PSP.BOX(object, ...)

## S4 method for signature 'PSP'
PSP.BOX(object, newx, var = colnames(object@x)[1], expanded = FALSE)

PSP.CSP(object, ...)

## S4 method for signature 'PSP'
PSP.CSP(object, newx, t = seq(from = 1, to = 36 * 30.5, by = 1), plot = FALSE)

PSP.NA(object, ...)

## S4 method for signature 'PSP'
PSP.NA(object, newx, plot = TRUE)

Arguments

x

Generic x

...

Additional custom parameters passed on

y

Generic y

bias

Bias for skewing the color in heatmap key plotting

object

PSP-object

type

Types of variables to include; recognizes (int)eger, (bin)ary and (num)eric

newx

New data matrix

verb

Level of verbosity

cutoff

Cutoff point for division

expanded

Should data matrix expansion through interactions be included

shuffle

Shuffle plotting order

z

Should data centering and scaling should be conducted

cex

Zooming multiplier

col

Vector of color numbers or names to use for strata

pch

Point type to use (refer to par-function pch-parameter)

var

Name of variable to plot

t

Sequence of time points to evaluate cumulative survival probabilities at

plot

Plot the corresponding functionality

Note

Please refer to the PSP-class examples for applying these PSP-methods