Package: pmcalibration 0.1.1
pmcalibration: Calibration Curves for Clinical Prediction Models
Fit calibrations curves for clinical prediction models and calculate several associated metrics (Eavg, E50, E90, Emax). Ideally predicted probabilities from a prediction model should align with observed probabilities. Calibration curves relate predicted probabilities (or a transformation thereof) to observed outcomes via a flexible non-linear smoothing function. 'pmcalibration' allows users to choose between several smoothers (regression splines, generalized additive models/GAMs, lowess, loess). Both binary and time-to-event outcomes are supported. See Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>; Austin and Steyerberg (2019) <doi:10.1002/sim.8281>; Austin et al. (2020) <doi:10.1002/sim.8570>.
Authors:
pmcalibration_0.1.1.tar.gz
pmcalibration_0.1.1.zip(r-4.5)pmcalibration_0.1.1.zip(r-4.4)pmcalibration_0.1.1.zip(r-4.3)
pmcalibration_0.1.1.tgz(r-4.4-any)pmcalibration_0.1.1.tgz(r-4.3-any)
pmcalibration_0.1.1.tar.gz(r-4.5-noble)pmcalibration_0.1.1.tar.gz(r-4.4-noble)
pmcalibration_0.1.1.tgz(r-4.4-emscripten)pmcalibration_0.1.1.tgz(r-4.3-emscripten)
pmcalibration.pdf |pmcalibration.html✨
pmcalibration/json (API)
NEWS
| # Install 'pmcalibration' in R: |
| install.packages('pmcalibration', repos = c('https://stephenrho.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/stephenrho/pmcalibration/issues
Last updated 8 months agofrom:442db43bf2. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 11 2024 |
| R-4.5-win | OK | Oct 11 2024 |
| R-4.5-linux | OK | Oct 11 2024 |
| R-4.4-win | OK | Oct 11 2024 |
| R-4.4-mac | OK | Oct 11 2024 |
| R-4.3-win | NOTE | Oct 11 2024 |
| R-4.3-mac | NOTE | Oct 11 2024 |
Exports:bootcal_metricsgam_calget_ccglm_calinvlogitloess_callogistic_callogitlowess_calpmcalibrationpredict_lowessreg_spline_Xrun_bootssim_datsimb
Dependencies:backportsbase64encbslibcachemcheckmatechkcliclustercolorspacedata.tabledigestevaluatefansifarverfastmapfontawesomeforeignFormulafsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmennetpbapplypillarpkgconfigR6rappdirsRColorBrewerrlangrmarkdownrpartrstudioapisassscalesstringistringrsurvivaltibbletinytexutf8vctrsviridisviridisLitewithrxfunyaml
External validation using pmcalibration
Rendered fromexternal-validation.Rmdusingknitr::rmarkdownon Oct 11 2024.Last update: 2023-09-05
Started: 2023-08-16
Internal validation using pmcalibration
Rendered frominternal-validation.Rmdusingknitr::rmarkdownon Oct 11 2024.Last update: 2024-03-13
Started: 2023-08-16
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate calibration metrics from calibration curve | cal_metrics |
| Extract plot data from 'pmcalibration' object | get_cc |
| Run logistic calibration | logistic_cal |
| Plot a calibration curve ('pmcalibration' object) | plot.pmcalibration |
| Create a calibration curve | pmcalibration |
| Print a 'logistic_cal' object | print.logistic_cal |
| Print a logistic_cal summary | print.logistic_calsummary |
| print a pmcalibration object | print.pmcalibration |
| Print summary of pmcalibration object | print.pmcalibrationsummary |
| Simulate a binary outcome with either a quadratic relationship or interaction | sim_dat |
| Summarize a logistic_cal object | summary.logistic_cal |
| Summarize a pmcalibration object | summary.pmcalibration |
