Tidy a flexsurv model object

Tidy summarizes information about the components of the model into a tidy data frame.

Usage

# S3 method for flexsurvreg
tidy(
  x,
  conf.int = FALSE,
  conf.level = 0.95,
  pars = "all",
  transform = "none",
  ...
)

Arguments

x

Output from flexsurvreg or flexsurvspline, representing a fitted survival model object.

conf.int

Logical. Should confidence intervals be returned? Default is FALSE.

conf.level

The confidence level to use for the confidence interval if conf.int = TRUE. Default is 0.95.

pars

One of "all", "baseline", or "coefs" for all parameters, baseline distribution parameters, or covariate effects (i.e. regression betas), respectively. Default is "all".

transform

Character vector of transformations to apply to requested pars. Default is "none", which returns pars as-is.

Users can specify one or both types of transformations:

• "baseline.real" which transforms the baseline distribution parameters to the real number line used for estimation.

• "coefs.exp" which exponentiates the covariate effects.

See Details for a more complete explanation.

...

Not currently used.

Value

A tibble containing the columns: term, estimate, std.error, statistic, p.value, conf.low, and conf.high, by default.

statistic and p.value are only provided for covariate effects (NA for baseline distribution parameters). These are computed as Wald-type test statistics with p-values from a standard normal distribution.

Details

flexsurvreg models estimate two types of coefficients, baseline distribution parameters, and covariate effects which act on the baseline distribution. By design, flexsurvreg returns distribution parameters on the same scale as is found in the relevant d/p/q/r functions. Covariate effects are returned on the log-scale, which represents either log-time ratios (accelerated failure time models) or log-hazard ratios for proportional hazard models. By default, tidy() will return baseline distribution parameters on their natural scale and covariate effects on the log-scale.

To transform the baseline distribution parameters to the real-value number line (the scale used for estimation), pass the character argument "baseline.real" to transform. To get time ratios or hazard ratios, pass "coefs.exp" to transform. These transformations may be done together by submitting both arguments as a character vector.

Examples

fitg <- flexsurvreg(formula = Surv(futime, fustat) ~ age, data = ovarian, dist = "gengamma")
tidy(fitg)
#> # A tibble: 4 × 5
#>   term  estimate std.error statistic   p.value
#>   <chr>    <dbl>     <dbl>     <dbl>     <dbl>
#> 1 mu     11.7       1.66       NA    NA       
#> 2 sigma   0.751     0.244      NA    NA       
#> 3 Q       0.295     0.912      NA    NA       
#> 4 age    -0.0875    0.0250     -3.50  0.000467
tidy(fitg, pars = "coefs", transform = "coefs.exp")
#> # A tibble: 1 × 5
#>   term  estimate std.error statistic  p.value
#>   <chr>    <dbl>     <dbl>     <dbl>    <dbl>
#> 1 age      0.916      1.03     -3.50 0.000467