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

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

Samuel Leung