The question | Terms and clocks | The data | The analysis plan | Step 1: build the cohort | Check the condition of delayed entry | Step 2: describe the cohort | Step 3: fit the ladder of models | How to read a hazard ratio per SD | Why the hazard ratios change between rows | Hazard ratios for death | Step 4: does the progression score add information? | Step 5: CAD risk by score group | Step 6: choose a design for the absolute risks | Step 7: predict absolute risk | Which horizons can be evaluated? | Absolute risk for a person | Risk across the score distribution | Step 8: internal validation | Apparent performance | One plan for all functions | Discrimination | Calibration: are the risks right? | Decision curves | Step 9: external validation | The export | The external cohort | Performance in the second biobank | The primary tests in the second biobank | Step 10: start follow-up at the T2D diagnosis | Step 11: deaths treated as censoring | Risk by score group | Absolute risk | Fine-Gray models | Step 12: answer the question | Reporting checklist | Limitations to report | References
This package is hidden from search results because it is not hosted in the universe of the upstream owner
bitbucket-bklamer. To fix this you can add URL: https://bklamer.r-universe.dev/prsladder to the package DESCRIPTION file. See also theR-universe documentation.Package: prsladder 2026.9.23
prsladder: Polygenic Risk Scores and Time to Disease Progression
Measures the association of one or more polygenic risk scores with time to a disease event among persons who have a first diagnosis. Fits a ladder of Cox proportional-hazards models over all subsets of the scores, compares nested models, predicts absolute risk at a horizon with delayed entry, and evaluates discrimination, calibration, and reclassification. With competing events, fits cause-specific hazard models and estimates the cumulative incidence. Draws risk curves with risk tables, hazard ratios across the ladder, and calibration and discrimination, and makes tables of risk by score group. Estimates standardized risk at score percentiles, risk ratios, case shares, and time lost by score group, and net benefit. Includes a simulator with known hazard ratios.
Authors:
prsladder_2026.9.23.tar.gz
prsladder_2026.9.23.zip(r-4.7-any)prsladder_2026.9.23.zip(r-4.6-any)prsladder_2026.9.23.zip(r-4.5-any)
prsladder_2026.9.23.tgz(r-4.6-any)prsladder_2026.9.23.tgz(r-4.5-any)
prsladder_2026.9.23.tar.gz(r-4.7-any)prsladder_2026.9.23.tar.gz(r-4.6-any)
prsladder_2026.9.23.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
prsladder/json (API)
| # Install 'prsladder' in R: |
| install.packages('prsladder', repos = c('https://bklamer.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://bitbucket.org/bklamer/prsladder
Last updated from:9ec3ca7166. Checks:5 ERROR, 4 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | ERROR | 293 | ||
| source / vignettes | OK | 238 | ||
| linux-release | ERROR | 289 | ||
| macos-release | ERROR | 362 | ||
| macos-oldrel | ERROR | 325 | ||
| windows-devel | ERROR | 496 | ||
| windows-release | OK | 494 | ||
| windows-oldrel | OK | 495 | ||
| wasm-release | OK | 93 |
Exports:assess_calibrationassess_discriminationassess_net_benefitassess_stabilityassess_thresholdsbootstrap_plancheck_designcheck_entrycompare_laddercumulative_riskdescribe_case_mixdescribe_cohortdescribe_riskexport_ladderfit_ladderhorizon_supportplot_calibrationplot_discriminationplot_gradientplot_ladderplot_net_benefitplot_riskplot_stackedpredict_riskprediction_dataprs_cohortsimulate_prs_datastandardized_risk
Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglatticelifecycleMatrixpatchworkR6rbibutilsRColorBrewerRdpackrlangS7scalessurvivalvctrsviridisLitewithr
