PSP-methods: 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 PSP
print(x, ...)
plot(x, y, ...)
# S4 method for PSP
plot(x, y, bias = 0.1, ...)
# S4 method for PSP
coef(object)
# S4 method for PSP
predict(object, type = "response", newx, verb = 0)
PSP.KM(object, ...)
# S4 method for PSP
PSP.KM(object, cutoff = 0.5)
PSP.PCA(object, ...)
# S4 method for 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 PSP
PSP.BOX(object, newx, var = colnames(object@x)[1], expanded = FALSE)
PSP.CSP(object, ...)
# S4 method for PSP
PSP.CSP(object, newx, t = seq(from = 1, to = 36 * 30.5, by = 1), plot = FALSE)
PSP.NA(object, ...)
# S4 method for 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