The goal of {riskybiz} is to provide both a formula framework for creating competing risks regression objects and also output useful components such as model.frame that the original {cmprsk} package does not provide.
Installation
The {riskybiz} package was written as a wrapper/enhancer to the {cmprsk} package.
To install the development version of {riskybiz}
Example
The standard cmprsk::crr() function has specific input requirements.
library(riskybiz)
#> Loading required package: cmprsk
#> Loading required package: survival
#>
#> Attaching package: 'riskybiz'
#> The following object is masked from 'package:cmprsk':
#>
#> crr
trial <- na.omit(trial)
#original crr
covars <- model.matrix(~ age + factor(trt) + factor(grade), trial)[,-1]
ftime1 <- trial$ttdeath
fstatus1 <- trial$death_cr
mod_orig <- crr(ftime=ftime1,
fstatus = fstatus1,
cov1 = covars)Output of model does not contain elements like model.frame since the function does not take a data.frame as input.
summary(mod_orig)
#> Competing Risks Regression
#>
#> Call:
#> cmprsk::crr(ftime = ..1, fstatus = ..2, cov1 = ..3)
#>
#> coef exp(coef) se(coef) z p-value
#> age 5.27e-05 1.000 0.00599 0.0088 0.99
#> factor(trt)Placebo -1.15e-01 0.892 0.17919 -0.6404 0.52
#> factor(grade)II -1.01e-01 0.904 0.23149 -0.4368 0.66
#> factor(grade)III 2.96e-01 1.345 0.20284 1.4606 0.14
#>
#> exp(coef) exp(-coef) 2.5% 97.5%
#> age 1.000 1.000 0.988 1.01
#> factor(trt)Placebo 0.892 1.122 0.628 1.27
#> factor(grade)II 0.904 1.106 0.574 1.42
#> factor(grade)III 1.345 0.744 0.904 2.00
#>
#> Num. cases = 173
#> Pseudo Log-likelihood = -434
#> Pseudo likelihood ratio test = 2.87 on 4 df,Using our wrapper function riskybiz::crr() allows for inputting an intuitive formula and data, which allows for downstream functions.
# using new wrapper function, accepts data and formula
mod_new <- crr(Surv(ttdeath, death_cr) ~ age + trt + grade, trial)
#> Warning in Surv(ttdeath, death_cr): Invalid status value, converted to NA
head(model.frame(mod_new))
#> Surv(ttdeath, death_cr) age trt grade
#> 1 24.00+ 23 Placebo II
#> 2 24.00+ 9 Drug I
#> 3 24.00 31 Placebo II
#> 6 15.64+ 39 Drug I
#> 10 10.53+ 34 Drug I
#> 11 24.00+ 42 Drug III
tidy(mod_new)
#> # A tibble: 4 x 7
#> term estimate std.error statistic p.value conf.low conf.high
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 age 0.0000527 0.00599 0.00880 0.99 -0.0117 0.0118
#> 2 trtPlacebo -0.115 0.179 -0.640 0.52 -0.466 0.236
#> 3 gradeII -0.101 0.231 -0.437 0.66 -0.555 0.353
#> 4 gradeIII 0.296 0.203 1.46 0.14 -0.101 0.694Contributing
Please note that the {riskybiz} project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms. A big thank you to all contributors!
@ddsjoberg, and @margarethannum
