I'm putting together some tables with results from a series of Cox Proportional Hazards Models. I'd like to exponentiate the coefficients so the tables display the Hazard Ratios rather than the raw beta values. Does anyone know of a way to do this with huxtable? It's my preferred package for building regression tables. I've done some googling and can't find a solution.
You can use the tidy_args
argument to huxreg:
library(huxtable)
library(survival)
test1 <- list(time=c(4,3,1,1,2,2,3),
status=c(1,1,1,0,1,1,0),
x=c(0,2,1,1,1,0,0),
sex=c(0,0,0,0,1,1,1))
mod <- coxph(Surv(time, status) ~ x + strata(sex), test1)
huxreg(mod)
─────────────────────────────────────────────────
(1)
─────────────────────────
x 0.802
(0.822)
─────────────────────────
N 5.000
R2 0.144
logLik -3.328
AIC 8.655
─────────────────────────────────────────────────
*** p < 0.001; ** p < 0.01; * p < 0.05.
Column names: names, model1
huxreg(mod, tidy_args = list(exponentiate = TRUE))
─────────────────────────────────────────────────
(1)
─────────────────────────
x 2.231
(0.822)
─────────────────────────
N 5.000
R2 0.144
logLik -3.328
AIC 8.655
─────────────────────────────────────────────────
*** p < 0.001; ** p < 0.01; * p < 0.05.
Column names: names, model1
tidy(mod, exponentiate = TRUE)
appears to exponentiate the coefficients but not the standard errors, which is presumably a bug in broom
and worth reporting? Confidence intervals appear correct, though, so you can do:
huxreg(mod, tidy_args = list(exponentiate = TRUE),
error_format = "[{conf.low}-{conf.high}]", ci_level = 0.95)
─────────────────────────────────────────────────
(1)
─────────────────────────
x 2.231
[0.445-11.180]
─────────────────────────
N 5.000
R2 0.144
logLik -3.328
AIC 8.655
─────────────────────────────────────────────────
*** p < 0.001; ** p < 0.01; * p < 0.05.
Column names: names, model1