Package: vaccine 1.3.1
vaccine: Statistical Tools for Immune Correlates Analysis of Vaccine Clinical Trial Data
Various semiparametric and nonparametric statistical tools for immune correlates analysis of vaccine clinical trial data. This includes calculation of summary statistics and estimation of risk, vaccine efficacy, controlled effects (controlled risk and controlled vaccine efficacy), and mediation effects (natural direct effect, natural indirect effect, proportion mediated). See Gilbert P, Fong Y, Kenny A, and Carone, M (2022) <doi:10.1093/biostatistics/kxac024> and Fay MP and Follmann DA (2023) <doi:10.48550/arXiv.2208.06465>.
Authors:
vaccine_1.3.1.tar.gz
vaccine_1.3.1.zip(r-4.7)vaccine_1.3.1.zip(r-4.6)vaccine_1.3.1.zip(r-4.5)
vaccine_1.3.1.tgz(r-4.6-any)vaccine_1.3.1.tgz(r-4.5-any)
vaccine_1.3.1.tar.gz(r-4.7-any)vaccine_1.3.1.tar.gz(r-4.6-any)
vaccine_1.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
vaccine/json (API)
NEWS
| # Install 'vaccine' in R: |
| install.packages('vaccine', repos = c('https://avi-kenny.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/avi-kenny/vaccine/issues
Pkgdown/docs site:https://avi-kenny.github.io
- hvtn505 - HVTN 505 Dataset
Last updated from:2ae23b123a. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 235 | ||
| source / vignettes | OK | 331 | ||
| linux-release-x86_64 | OK | 228 | ||
| macos-release-arm64 | OK | 260 | ||
| macos-oldrel-arm64 | OK | 215 | ||
| windows-devel | OK | 210 | ||
| windows-release | OK | 175 | ||
| windows-oldrel | OK | 187 | ||
| wasm-release | OK | 135 |
Exports:as_tablediagnosticsest_ceest_medest_overallload_dataparams_ce_coxparams_ce_npparams_med_npplot_cesummary_statstrim
Dependencies:abindassertthatbackportsbitopsbootbroomcarcarDatacaToolsChernoffDistclassclicodetoolscolorspacecorrplotcowplotcpp11cvAUCdata.tableDerivdigestdoBydplyre1071farverfdrtoolforeachforecastFormulafracdifffuturefuture.applygamgenericsggplot2ggpubrggrepelggsciggsignifglmnetglobalsgluegplotsgridExtragslgtablegtoolshal9001haldensifyinumIsoisobanditeratorsKernSmoothlabelinglatticelibcoinlifecyclelistenvlme4lmtestmagrittrMASSMatrixMatrixModelsmatrixStatsmboostmgcvmicrobenchmarkminqamodelrmvtnormnlmenloptrnnetnnlsnumDerivorigamiparallellypartykitpbkrtestpillarpkgconfigpolynomproxypurrrquadprogquantregR6rangerrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangROCRrpartRsolnprstatixS7scalesshapeSparseMstabsstringistringrSuperLearnersurvivalsurvMLtibbletidyrtidyselecttimeDatetruncnormurcautf8vctrsviridisLitewithrzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create table of estimates | as_table |
| Run diagnostics | diagnostics |
| Estimate controlled effect curves | est_ce |
| Estimate mediation effects | est_med |
| Estimate overall risk and vaccine efficacy | est_overall |
| HVTN 505 Dataset | hvtn505 |
| Load and format data object | load_data |
| Set parameters controlling Cox model estimation of controlled effect curves | params_ce_cox |
| Set parameters controlling nonparametric estimation of controlled effect curves | params_ce_np |
| Set parameters controlling nonparametric estimation of mediation effects | params_med_np |
| Plotting controlled effect curves | plot_ce |
| Calculate summary statistics | summary_stats |
| Trim data for plotting/reporting | trim |
