calibrationbands

An R package to assess calibration of binary outcome predictions. Authored by Timo Dimitriadis (Heidelberg University), Alexander Henzi (University of Bern), and Marius Puke (University of Hohenheim).

Installation

calibrationband is available on The Comprehensive R Archive Network (CRAN).

install.packages("calibrationband")

Development version

The most current version is available from GitHub.

# install.packages("devtools")
devtools::install_github("marius-cp/calibrationband")

Example

library(calibrationband)
library(dplyr)
set.seed(123)
s=.8
n=10000
x <- runif(n)
p <- function(x,s){p = 1/(1+((1/x*(1-x))^(s+1)));return(p)}
dat <- tibble::tibble(pr=x, s=s, cep = p(pr,s), y=rbinom(n,1,cep))%>% dplyr::arrange(pr)

cb <- calibration_bands(x=dat$pr, y=dat$y,alpha=0.05, method = "round", digits = 3)
print(cb) # prints autoplot and summary, see also autoplot(.) and summary(.)

#> 
#>  Areas of misscalibration (ordered by length). In addition there are 2 more. 
#> # A tibble: 5 × 2
#>    min_x  max_x
#>    <dbl>  <dbl>
#> 1 0.0396 0.299 
#> 2 0.693  0.951 
#> 3 0.0389 0.0393
#> # … with 2 more rows

Use ggplot2:autolayer to customize the plot.

autoplot(cb,approx.equi=500, cut.bands = F,p_isoreg = NA,p_ribbon = NA,p_diag = NA)+
  ggplot2::autolayer(
    cb,
    cut.bands = F,
    p_diag = list(low = "green", high = "red", guide = "none", limits=c(0,1)),
    p_isoreg = list(linetype = "dashed"),
    p_ribbon = list(alpha = .1, fill = "red", colour = "purple")
                     )