Package: bhm 1.19
bhm: Biomarker Threshold Models
Contains tools to fit both predictive and prognostic biomarker effects using biomarker threshold models and continuous threshold models. Evaluate the treatment effect, biomarker effect and treatment-biomarker interaction using probability index measurement. Test for treatment-biomarker interaction using residual bootstrap method.
Authors:
bhm_1.19.tar.gz
bhm_1.19.zip(r-4.5)bhm_1.19.zip(r-4.4)bhm_1.19.zip(r-4.3)
bhm_1.19.tgz(r-4.4-any)bhm_1.19.tgz(r-4.3-any)
bhm_1.19.tar.gz(r-4.5-noble)bhm_1.19.tar.gz(r-4.4-noble)
bhm_1.19.tgz(r-4.4-emscripten)bhm_1.19.tgz(r-4.3-emscripten)
bhm.pdf |bhm.html✨
bhm/json (API)
| # Install 'bhm' in R: |
| install.packages('bhm', repos = c('https://statapps.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/statapps/bhm/issues
- data - Dataset
Last updated 1 months agofrom:4c990823a3. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 14 2024 |
| R-4.5-win | WARNING | Sep 14 2024 |
| R-4.5-linux | WARNING | Sep 14 2024 |
| R-4.4-win | WARNING | Sep 14 2024 |
| R-4.4-mac | WARNING | Sep 14 2024 |
| R-4.3-win | WARNING | Sep 14 2024 |
| R-4.3-mac | WARNING | Sep 14 2024 |
Exports:bhmbhm.defaultbhm.formulabhmControlbhmFitbhmGibbsbrmbrm.defaultbrm.formulacoxScoreHessdpicexpgendat.glmgendat.survggkmglmpLRTglmpLRT.defaultglmpLRT.formulahpicexpHpicexpllmllm.defaultllm.formulamplmpl.formulamplFitmultiRootnumHessiannumJacobiannumScorepicfitpicregpIndexpIndex.defaultpIndex.formulapIndexControlpIndexFitpIndexLocalpIndexThresholdplot.bhmplot.brmplot.glmpLRTplot.llmplot.pIndexplot.resbootplot.residuals.brmplot.rmscbppicexpprint.bhmprint.brmprint.glmpLRTprint.llmprint.mplprint.picregprint.pIndexprint.resbootprint.rmscbprint.summary.bhmprint.summary.brmprolikFitqpicexpresbootresboot.defaultresboot.formularesiduals.brmrmscbrmscb.defaultrmscb.formularmsControlrpicexpsummary.bhmsummary.brmsummary.glmpLRTsummary.picregsummary.rmscbthm.fitthm.likx.cdf
Dependencies:clicodacolorspacefansifarverggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalessurvivaltibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| An R package for the biomarker threshold models | bhm-package bhm-doc |
| Fitting Biomarker Threshold Models | bhm bhm.default bhm.formula bhmFit bhmGibbs prolikFit summary.bhm thm.fit thm.lik x.cdf |
| Auxiliary function for bhm fitting | bhmControl prolikControl |
| Fitting Biomarker Continuous Threshold Models | brm brm.default brm.formula residuals.brm summary.brm |
| dataset | data gendat.glm gendat.surv |
| Creates a Kaplan-Meier plot with at risk tables below | ggkm |
| Penalized likelihood ratio test for the generalized linear models. | glmpLRT glmpLRT.default glmpLRT.formula plot.glmpLRT print.glmpLRT summary.glmpLRT |
| Fit an L-shape linear model | llm llm.default llm.formula plot.llm print.llm |
| Joint models for clustered data with binary and survival outcomes. | mpl mpl.formula mplFit |
| m-Dimensional Root (Zero) Finding | multiRoot |
| Calculate Hessian or Information Matrix | numHessian |
| Calculate the Score / Jacobian Function | numJacobian numScore |
| Probability Index for Survival Time Difference | pIndex pIndex.default pIndex.formula pIndexFit pIndexLocal pIndexThreshold |
| Auxiliary function for pIndex fitting | pIndexControl |
| Plot a fitted biomarker threhold model | plot.bhm plot.brm plot.pIndex plot.resboot plot.residuals.brm |
| print a fitted object or a summary of fitted object | print.bhm print.brm print.mpl print.picreg print.pIndex print.resboot print.summary.bhm print.summary.brm |
| Rresidual Bootstrap Test (RBT) for treatment-biomarker interaction | resboot resboot.default resboot.formula |
| Fitting Restricted Mean Survival Time Models with a Continuous Biomarker | plot.rmscb print.rmscb rmscb rmscb.default rmscb.formula rmsControl summary.rmscb |
| The Piecewise Exponential Distribution | dpicexp Hpicexp hpicexp picfit picreg ppicexp qpicexp rpicexp summary.picreg |
