doInteractionCox: Do interaction test with cox model likelihood ratio test only...

In TalhoukLab/biostatUtil: Utility Functions Used in Biostatistics Projects

Do interaction test with cox model likelihood ratio test only - two terms only

Description

Only a LRT can be performed (2015-08-12). TODO: add penalized LRT?

Usage

doInteractionCox(
  input.d,
  var.names,
  var.descriptions,
  show.var.detail = FALSE,
  show.group.name.for.bin.var = FALSE,
  var.ref.groups = NULL,
  var.names.surv.time = c("os.yrs", "dss.yrs", "rfs.yrs"),
  var.names.surv.status = c("os.sts", "dss.sts", "rfs.sts"),
  event.codes.surv = c("os.event", "dss.event", "rfs.event"),
  surv.descriptions = c("OS", "DSS", "PFS"),
  missing.codes = c("N/A", "", "Unk"),
  use.firth = 1,
  firth.caption = FIRTH.CAPTION,
  round.digits.p.value = 4,
  round.small = FALSE,
  scientific = FALSE,
  caption = NA,
  html.table.border = 0,
  banded.rows = FALSE,
  css.class.name.odd = "odd",
  css.class.name.even = "even",
  split.table = 300,
  ...
)

Arguments

input.d	The data.frame containing the data
var.names	variables to include as predictors
var.descriptions	vector of strings to describe the variables as they are to appear in the table
show.var.detail	logical. If TRUE, details such as categories and the reference group for categorical variables are shown.
show.group.name.for.bin.var	logical. If TRUE, the non-reference group name is shown beside the hazard ratio for dichotomized variables.
var.ref.groups	a vector of reference groups. If NULL, assume all variables are binary/continuous. If an item in the vector is NA, assume that particular marker is binary or continuous (i.e., treat it as a numeric variable)
var.names.surv.time	variable names of survival time
var.names.surv.status	variable names of survival status
event.codes.surv	event coding of survival status variable
surv.descriptions	names abbreviated survival endpoints in returned output
missing.codes	character strings of missing values used in input.d
use.firth	percentage of censored cases before using Firth's method for Cox regression. If use.firth = 1 (default), Firth is never used and if use.firth = -1 Firth is always used.
firth.caption	subscript in html table output indicating Firth was used
round.digits.p.value	number of digits for p-value
round.small	if TRUE, uses small number rounding via round_small() for p-values
scientific	if TRUE, uses scientific notation when rounding
caption	caption for returned object
html.table.border	the border type to use for html tables
banded.rows	logical. If TRUE, rows have alternating shading colour
css.class.name.odd	Used to set the row colour for odd rows
css.class.name.even	Used to set the row colour for even rows
split.table	number of characters per row before splitting the table. Applies to the pandoc table output.
...	additional arguments to pander::pandoc.table.return()

Value

A list with the following elements

Note

the order of variable names in var.names dictates when will the term added in stepwise likelihood ratio test of nested models i.e. given var.names = c("A", "B", "C"), likelihood ratio test of nested model will be:

A A + B A + B + C

Author(s)

Samuel Leung

TalhoukLab/biostatUtil documentation built on April 14, 2025, 4:15 a.m.