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Helper functions for Cox proportional hazards regression

Source: R/h_cox_regression.R
h_cox_regression.Rd

[Stable]

Helper functions used in fit_coxreg_univar() and fit_coxreg_multivar().

Usage 

h_coxreg_univar_formulas(variables, interaction = FALSE)

h_coxreg_multivar_formula(variables)

h_coxreg_univar_extract(effect, covar, data, mod, control = control_coxreg())

h_coxreg_multivar_extract(var, data, mod, control = control_coxreg())

Arguments

variables

(named list of string)
list of additional analysis variables.

interaction

(flag)
if TRUE, the model includes the interaction between the studied treatment and candidate covariate. Note that for univariate models without treatment arm, and multivariate models, no interaction can be used so that this needs to be FALSE.

effect

(string)
the treatment variable.

covar

(string)
the name of the covariate in the model.

data

(data.frame)
the dataset containing the variables to summarize.

mod

(coxph)
Cox regression model fitted by survival::coxph().

control

(list)
a list of controls as returned by control_coxreg().

var

(string)
single variable name that is passed by rtables when requested by a statistics function.

Value

  • h_coxreg_univar_formulas() returns a character vector coercible into formulas (e.g stats::as.formula()).

  • h_coxreg_multivar_formula() returns a string coercible into a formula (e.g stats::as.formula()).

  • h_coxreg_univar_extract() returns a data.frame with variables effect, term, term_label, level, n, hr, lcl, ucl, and pval.

  • h_coxreg_multivar_extract() returns a data.frame with variables pval, hr, lcl, ucl, level, n, term, and term_label.

Functions

  • h_coxreg_univar_formulas(): Helper for Cox regression formula. Creates a list of formulas. It is used internally by fit_coxreg_univar() for the comparison of univariate Cox regression models.

  • h_coxreg_multivar_formula(): Helper for multivariate Cox regression formula. Creates a formulas string. It is used internally by fit_coxreg_multivar() for the comparison of multivariate Cox regression models. Interactions will not be included in multivariate Cox regression model.

  • h_coxreg_univar_extract(): Utility function to help tabulate the result of a univariate Cox regression model.

  • h_coxreg_multivar_extract(): Tabulation of multivariate Cox regressions. Utility function to help tabulate the result of a multivariate Cox regression model for a treatment/covariate variable.

See also

cox_regression

Examples 

# `h_coxreg_univar_formulas`

## Simple formulas.
h_coxreg_univar_formulas(
  variables = list(
    time = "time", event = "status", arm = "armcd", covariates = c("X", "y")
  )
)
#>                                        ref 
#>     "survival::Surv(time, status) ~ armcd" 
#>                                          X 
#> "survival::Surv(time, status) ~ armcd + X" 
#>                                          y 
#> "survival::Surv(time, status) ~ armcd + y" 

## Addition of an optional strata.
h_coxreg_univar_formulas(
  variables = list(
    time = "time", event = "status", arm = "armcd", covariates = c("X", "y"),
    strata = "SITE"
  )
)
#>                                                       ref 
#>     "survival::Surv(time, status) ~ armcd + strata(SITE)" 
#>                                                         X 
#> "survival::Surv(time, status) ~ armcd + X + strata(SITE)" 
#>                                                         y 
#> "survival::Surv(time, status) ~ armcd + y + strata(SITE)" 

## Inclusion of the interaction term.
h_coxreg_univar_formulas(
  variables = list(
    time = "time", event = "status", arm = "armcd", covariates = c("X", "y"),
    strata = "SITE"
  ),
  interaction = TRUE
)
#>                                                       ref 
#>     "survival::Surv(time, status) ~ armcd + strata(SITE)" 
#>                                                         X 
#> "survival::Surv(time, status) ~ armcd * X + strata(SITE)" 
#>                                                         y 
#> "survival::Surv(time, status) ~ armcd * y + strata(SITE)" 

## Only covariates fitted in separate models.
h_coxreg_univar_formulas(
  variables = list(
    time = "time", event = "status", covariates = c("X", "y")
  )
)
#>                                      X                                      y 
#> "survival::Surv(time, status) ~ 1 + X" "survival::Surv(time, status) ~ 1 + y" 

# `h_coxreg_multivar_formula`

h_coxreg_multivar_formula(
  variables = list(
    time = "AVAL", event = "event", arm = "ARMCD", covariates = c("RACE", "AGE")
  )
)
#> [1] "survival::Surv(AVAL, event) ~ ARMCD + RACE + AGE"

# Addition of an optional strata.
h_coxreg_multivar_formula(
  variables = list(
    time = "AVAL", event = "event", arm = "ARMCD", covariates = c("RACE", "AGE"),
    strata = "SITE"
  )
)
#> [1] "survival::Surv(AVAL, event) ~ ARMCD + RACE + AGE + strata(SITE)"

# Example without treatment arm.
h_coxreg_multivar_formula(
  variables = list(
    time = "AVAL", event = "event", covariates = c("RACE", "AGE"),
    strata = "SITE"
  )
)
#> [1] "survival::Surv(AVAL, event) ~ 1 + RACE + AGE + strata(SITE)"

library(survival)

dta_simple <- data.frame(
  time = c(5, 5, 10, 10, 5, 5, 10, 10),
  status = c(0, 0, 1, 0, 0, 1, 1, 1),
  armcd = factor(LETTERS[c(1, 1, 1, 1, 2, 2, 2, 2)], levels = c("A", "B")),
  var1 = c(45, 55, 65, 75, 55, 65, 85, 75),
  var2 = c("F", "M", "F", "M", "F", "M", "F", "U")
)
mod <- coxph(Surv(time, status) ~ armcd + var1, data = dta_simple)
result <- h_coxreg_univar_extract(
  effect = "armcd", covar = "armcd", mod = mod, data = dta_simple
)
result
#>       effect  term       term_label level n       hr       lcl      ucl
#> 1 Treatment: armcd B vs control (A)     B 8 6.551448 0.4606904 93.16769
#>       pval
#> 1 0.165209

mod <- coxph(Surv(time, status) ~ armcd + var1, data = dta_simple)
result <- h_coxreg_multivar_extract(
  var = "var1", mod = mod, data = dta_simple
)
result
#>        pval        hr      lcl      ucl level n term term_label
#> 2 0.4456195 0.9423284 0.808931 1.097724  var1 8 var1       var1