Introduction | Installation | Methods | Overview of available approaches | Which method should I use? | Literature and implementation status | Using ltRISK | Load the package | Data preparation | Example datasets | Data-frame and tidyverse-style interface | Rate modeling and confidence intervals | PMAJ rate modeling | Why interpolate age-specific rates? | Confidence intervals | Sampling assumptions and interpretation | Gamma confidence intervals | Delta-method confidence intervals | Method 1: DevCan method | Method 2: Wun method | Method 3: AMP method | Method 4: Traditional cumulative risk | Conclusion | References
Package: ltRISK 0.1.0
ltRISK: Estimate Lifetime and Age-Conditional Risk of Developing or Dying from Cancer
Estimates lifetime and age-conditional risks of developing or dying from cancer using population-based cancer registry data. Four established approaches for lifetime risk estimation are implemented: the DevCan method developed by the Surveillance, Epidemiology, and End Results (SEER) Program, the Wun method, the Adjusted for Multiple Primary Cancers (AMP) method, and a cumulative risk approach with a predefined upper age limit. The package provides a unified interface through the calc_ltr() function, which supports both gamma-based and delta-method confidence intervals, as well as the piecewise mid-age group joinpoint (PMAJ) model for age-specific rate modeling.
Authors:
ltRISK_0.1.0.tar.gz
ltRISK_0.1.0.zip(r-4.7-any)ltRISK_0.1.0.zip(r-4.6-any)ltRISK_0.1.0.zip(r-4.5-any)
ltRISK_0.1.0.tgz(r-4.6-any)ltRISK_0.1.0.tgz(r-4.5-any)
ltRISK_0.1.0.tar.gz(r-4.7-any)ltRISK_0.1.0.tar.gz(r-4.6-any)
ltRISK_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ltRISK/json (API)
| # Install 'ltRISK' in R: |
| install.packages('ltRISK', repos = c('https://gigu003.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gigu003/ltrisk/issues
Datasets:
- GCO_Today_2022 - GCO_Today_2022
- seer_example_data - Example Cancer Data from SEER
Last updated from:765db198c2. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 139 | ||
| source / vignettes | OK | 179 | ||
| linux-release | OK | 179 | ||
| macos-release | OK | 144 | ||
| macos-oldrel | OK | 178 | ||
| windows-devel | OK | 79 | ||
| windows-release | OK | 82 | ||
| windows-oldrel | OK | 78 | ||
| wasm-release | OK | 104 |
Exports:ampcalc_ltrcalc_ltr_dfclear_ltr_cachecumulativedevcanformat_risk_ciget_riskltr_cache_infopairwise_ztestpmajtrend_testwunztest
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute probabilities used for estimation of lifetime risk | amp |
| Estimate disease risk and its confidence interval | calc_ltr |
| Estimate disease risk from a data frame | calc_ltr_df |
| Manage ltRISK in-memory caches | clear_ltr_cache ltr_cache_info |
| Calculate cumulative rate and risk. | cumulative |
| Compute probabilities used for estimation of lifetime risk | devcan |
| Format risk estimates with 95% confidence intervals | format_risk_ci |
| GCO_Today_2022 | GCO_Today_2022 |
| Calculate the risk value for a specific age range | get_risk get_risk.amp get_risk.cumu get_risk.devcan get_risk.wun |
| Pairwise Z tests for risk differences among groups | pairwise_ztest |
| Smooth a Single Rate Using Piecewise Mid-Age Group Joinpoint (PMAJ) Method | pmaj |
| Example Cancer Data from SEER | seer_example_data |
| Test linear trend in risk across ordered groups | trend_test |
| Compute probabilities used for estimation of lifetime risk | wun |
| Test the difference in risk between two groups | ztest ztest.data.frame |