nicecoxph: Lisa's Cox Proportional Hazards Regression Table Reporting...

In lisaerein/nicesurv: This package creates a nice summary tables and plots for survival analysis

Lisa's Cox Proportional Hazards Regression Table Reporting Function

Description

This function creates a nice looking table of regression results for a coxph model. Input either a coxph object or dataframe, event variable, time variable, vector of covariates, and type of analysis (univariate or multiple regression). The function returns a dataframe of formatted regression results and prints the results table using kable or htmlTable.

Usage

nicecoxph(
  fit = NA,
  df = NA,
  covs = NA,
  ttevent = "ttevent",
  event = "event",
  ttentry = NA,
  weightvar = NA,
  cluster = NA,
  strata = NA,
  frailty = NA,
  regtype = "uni",
  type2 = FALSE,
  type3 = FALSE,
  phtest = FALSE,
  labels = NA,
  estname = NA,
  refcat = FALSE,
  est.dec = 2,
  ci.dec = 2,
  pval.dec = 3,
  color = "#EEEEEE",
  kable = TRUE,
  htmlTable = FALSE,
  title = "",
  footer = TRUE
)

Arguments

fit	coxph model object [fit or df/event/ttevent/covs are REQUIRED].
df	Dataframe [fit or df/event/ttevent/covs are REQUIRED].
covs	Character. Vector of covariates to include in model [fit or df/event/ttevent/covs are REQUIRED].
ttevent	Character. Name of time to event variable [fit or df/event/ttevent/covs are REQUIRED].
event	Character. Name of event variable [fit or df/event/ttevent/covs are REQUIRED].
ttentry	Character. Name of entry time variable for left truncated data. Default is NA (no delayed entry).
weightvar	Character. Name of weighting variable. Default is NA (no weights).
cluster	Character. Name of cluster variable. Default is NA (no clustering).
strata	Character. Vector of names of strata variable(s). Default is NA (no strata).
frailty	Character. Name of frailty variable. Default is NA (no random effect).
regtype	Logical. Should the covariates be run separately ("uni") or together in a multiple regression model ("multi") [REQUIRED if no fit].
type2	Logical. If TRUE, type II p-values will be added to the table. Default is FALSE.
type3	Logical, If TRUE, type III p-values will be added to the table. Default is FALSE.
phtest	Logical. If TRUE, a test for proportional hazards (via cox.zph) will be included in the footnote. Default is FALSE.
labels	Character. Vector of labels for covariates. Default is NA (use variable names).
estname	Character. Label for estimate. Default = NA: "HR" for univariate and "aHR" for multiple regression.
refcat	Logical. If TRUE the table will create a separate line for the reference category. Default is FALSE.
est.dec	Numeric. Number of decimal places for estimates. Default is 2.
ci.dec	Numeric. Number of decimal places for confidence interval. Default is 2.
pval.dec	Numeric. Number of decimal places for pvalues. Must be an integer from 1 to 4. Default is 3.
color	Character. Color to use for htmlTable striping. Default is "#EEEEEE" (light grey). Use "white" for no striping.
kable	Logical. Indicator to use kable to display table. Default = TRUE.
htmlTable	Logical. Indicator to use htmlTable package to display table instead of kable Default = FALSE.
title	Character. Optional title above table. Default is "".
footer	Logical. If TRUE, table will include a footnote with model details, nobs, R2. Default is TRUE.

lisaerein/nicesurv documentation built on Dec. 9, 2024, 12:17 a.m.