finalfit (version 0.9.7)

extract_fit: Extract model output to dataframe

Description

Internal function, not usually called directly.

Internal function, not called directly.

Internal function, not called directly.

extract_fit.coxme = function(.data, explanatory_name="explanatory", estimate_name="HR", estimate_suffix = "", p_name = "p", confint_level = 0.95, ...) x=.data if(confint_type == "default") confint_type = "Wald" explanatory = names(coxme::fixef(x)) estimate = exp(coxme::fixef(x)) # confint = # p = L_confint_name = paste0("L", confint_level*100) U_confint_name = paste0("U", confint_level*100)

df.out = dplyr::tibble(explanatory, estimate, confint[,1], confint[,2], p) colnames(df.out) = c(explanatory_name, paste0(estimate_name, estimate_suffix), L_confint_name, U_confint_name, p_name)

if(confint_level != 0.95) df.out = df.out

df.out = data.frame(df.out) return(df.out)

Extract model output to dataframe

Usage

extract_fit(...)
# S3 method for glm
extract_fit(.data, explanatory_name = "explanatory",
  estimate_name = "OR", estimate_suffix = "", p_name = "p",
  exp = TRUE, confint_type = "profile", confint_level = 0.95, ...)
# S3 method for glmerMod
extract_fit(.data, explanatory_name = "explanatory",
  estimate_name = "OR", estimate_suffix = "", p_name = "p",
  exp = TRUE, confint_type = "Wald", confint_level = 0.95, ...)
# S3 method for lm
extract_fit(.data, explanatory_name = "explanatory",
  estimate_name = "Coefficient", estimate_suffix = "", p_name = "p",
  confint_level = 0.95, ...)
# S3 method for lmerMod
extract_fit(.data, explanatory_name = "explanatory",
  estimate_name = "OR", estimate_suffix = "", p_name = "p",
  confint_type = "Wald", confint_level = 0.95, ...)
# S3 method for coxph
extract_fit(.data, explanatory_name = "explanatory",
  estimate_name = "HR", estimate_suffix = "", p_name = "p", ...)
# S3 method for crr
extract_fit(.data, explanatory_name = "explanatory",
  estimate_name = "HR", estimate_suffix = "", p_name = "p", ...)
# S3 method for stanfit
extract_fit(.data, explanatory_name = "explanatory",
  estimate_name = "OR", estimate_suffix = "", p_name = "p",
  digits = c(2, 2, 3), X, ...)

Arguments

...

Other arguments.

.data

Model output.

explanatory_name

Name for this column in output.

estimate_name

Name for this column in output.

estimate_suffix

Appeneded to estimate name.

p_name

Name given to p-value estimate

confint_type

One of c("profile", "default") for GLM models or c("profile", "Wald", "boot") for glmer/lmer models. Not implemented for lm, coxph or coxphlist.

confint_level

The confidence level required.

X

Design matrix from Stan modelling procedure.