sstable.survcomp: Summarize results for a Cox survival model or restricted mean...

In oucru-biostats/C306: Collection of useful R codes for data analysis from the Biostatistics group at OUCRU

Summarize results for a Cox survival model or restricted mean survival time with the treatment arm as the main covariate

Description

A function to summarize results for a survival model with the treatment arm (variable "arm") as the main covariate

Usage

sstable.survcomp(
  model,
  data,
  add.risk = TRUE,
  time = Inf,
  reference.arm = c("B", "A"),
  compare.method = c("cox", "rmst", "cuminc"),
  compare.args = list(),
  add.prop.haz.test = TRUE,
  medsum = TRUE,
  p.compare = TRUE,
  digits = 2,
  pdigits = 3,
  pcutoff = 0.001,
  footer = NULL,
  flextable = TRUE,
  bg = "#F2EFEE"
)

Arguments

model	a formula which can be used to fit the survival model. This formula can include other covariates than arm BUT arm must be the first covariate in the model.
data	a data frame to fit the survival model.
add.risk	[TRUE] a logical value specifies whether the event probability ("absolute risk") at time "infinity" should be displayed.
time	[Inf] the truncation time, affecting the descriptive and the RMST model, set to Inf to perform analyses at maximum time available (minimax of the observed time across two arms in RMST model)
reference.arm	[B] reference arm, default to the second arm ("B"), change to "A" for base on the first arm
compare.method	[cox] a string, either "cox" for CoxPH model, "cuminc" for cumulative incidence, or "rmst" for restricted mean survival time. Note that if "cox" is specified and model is a mstate model, a Fine-Gray model is used. If CoxPH is preferred, used Surv(t, ev == 'event-of-interest') on the LHS.
add.prop.haz.test	[TRUE] (legacy, depricated), please move this to compare.args
medsum	[TRUE] a logical value, specifying whether median (IQR) of time to event should be described.
p.compare	[TRUE] a logical value, specifying whether we should report p-value for the main comparison
digits	[2] a number specifies number of significant digits for numeric statistics.
pdigits	[3] a number specifies number of significant digits for p value.
pcutoff	[0.001] a number specifies threshold value of p value to be displayed as "< pcutoff".
footer	a [NULL] vector of strings to be used as footnote of table.
flextable	[TRUE] a logical value specifies whether output will be a flextable-type table.
bg	[#F2EFEE] a character specifies color of the odd rows in the body of flextable-type table.
compare.args:	a list of additional args for compare.methods, For compare.method = 'cox', it is 'add.prop.haz.test' [TRUE]: a logical value specifies whether a test for proportional hazards should be added,, additional args are fed directly to 'survival::coxph'. only when model is a mstate model, 'cause', default to whatever the first cause. For compare.method = 'cuminc', args are fed to cumincglm 'type': [diff] a string, "diff" for difference in cumulative incidence, "ratio' for ratio of cumulative incidence, other optional args include: model.censoring, formula.censoring, ipcw.method. See cumincglm for more details. For compare.method = 'rmst', args are fed to rmeanglm , 'type': [diff] a string, "diff" for difference in RMST, "ratio' for ratio of RMST, "lost.diff" for difference in restricted mean time lost (RMTL, = -diff), and "lost.ratio" for ratio of RMTL other optional args include: model.censoring, formula.censoring, ipcw.method. See rmeanglm for more details.

Value

a flextable-type table or a list with values/headers/footers

Author(s)

This function was originally written by Marcel Wolbers. Lam Phung Khanh did some modification.

oucru-biostats/C306 documentation built on Sept. 1, 2024, 10:04 a.m.