Usage
kaps.control(pre.pt = list(), scope = list(), rho = 0, V = 5, ncl = 1, lower.limit = 0, upper.limit = 100, shortcut = TRUE, N.perm = 9999, N.boot = 200, alpha = 0.05, splits = c("logrank", "exact"), correct = c("Adj.Bf", "Bf", "None"), p.adjust.methods = c("none", "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr"))
Arguments
pre.pt
list parameter that treats pre-specified split candidates. Use the option as list(var = split points), i.e., x = 1:100
scope
list parameter that treats pre-determined split range. Use the option as list(var = ranges), i.e., x = c(1,100)
rho
scalar parameter that controls the type of logrank test. See survdiff. V
numeric parameter that determines the number of folds in the cross-validation subgroup selection.
ncl
integer parameter that determines the number of cores to improve computing power
lower.limit
numeric parameter that treats pre-determined overall lower bound. Default is 0.
upper.limit
numeric parameter that treats pre-determined overall upper bound. Default is 100.
shortcut
logical parameter. If shortcut = TRUE, we skip the off-diagonal matrix in pairwise-comparison to reduce computational cost. The default value is TRUE.
N.perm
numeric parameter that gives the number of permutation samples used in the kaps algorithm. The default value is 9999.
N.boot
numeric parameter that gives the number of Bootstrap samples used in the bootstrap and permuting kaps algorithm. The default value is 200.
alpha
numeric parameter that provides a significant level in the process of Bootstrap and permuting algorithm.
splits
character parameter that detemines the kind of pairwise test. Default is logrank test. At this stage, the option exact is not working.
correct
character parameter to select the criteria for the multiple comparison in the simple permuting kaps algorithm.
p.adjust.methods
character parameter to select the criteria for the multiple comparison.