Phase 1: Preparing pathogen data | Phase 2: Configuring the model | Method | Smoothing parameters | Dispersion parameters | Pathogen noise | Day of week effect | Worked example | Output | Phase 3: Fitting | Checking convergence | Phase 4: Deriving epidemiological quantities | Additional worked example: COVID-19
Package: EpiStrainDynamics 0.1.0
Saras Windecker
EpiStrainDynamics: Infer temporal trends of multiple pathogens
'EpiStrainDynamics' is a statistical framework developed for inferring temporal trends of multiple pathogens from routinely collected surveillance data.
Authors:
EpiStrainDynamics_0.1.0.tar.gz
EpiStrainDynamics_0.1.0.zip(r-4.7-x86_64)EpiStrainDynamics_0.1.0.zip(r-4.6-x86_64)EpiStrainDynamics_0.1.0.zip(r-4.5-x86_64)
EpiStrainDynamics_0.1.0.tgz(r-4.6-x86_64)EpiStrainDynamics_0.1.0.tgz(r-4.6-arm64)EpiStrainDynamics_0.1.0.tgz(r-4.5-x86_64)EpiStrainDynamics_0.1.0.tgz(r-4.5-arm64)
EpiStrainDynamics_0.1.0.tar.gz(r-4.7-arm64)EpiStrainDynamics_0.1.0.tar.gz(r-4.7-x86_64)EpiStrainDynamics_0.1.0.tar.gz(r-4.6-arm64)EpiStrainDynamics_0.1.0.tar.gz(r-4.6-x86_64)
EpiStrainDynamics_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
EpiStrainDynamics/json (API)
| # Install 'EpiStrainDynamics' in R: |
| install.packages('EpiStrainDynamics', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org')) |
Reviews:rOpenSci Software Review #763
Bug tracker:https://github.com/ropensci/epistraindynamics/issues
Datasets:
Last updated from:11ce158cfe (on main). Checks:13 OK, 1 ERROR, 2 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 618 | ||
| linux-devel-x86_64 | OK | 809 | ||
| pkgdown docs | ERROR | 3738 | ||
| source / vignettes | OK | 867 | ||
| linux-release-arm64 | OK | 612 | ||
| linux-release-x86_64 | OK | 746 | ||
| macos-release-arm64 | OK | 774 | ||
| macos-release-x86_64 | OK | 1019 | ||
| macos-oldrel-arm64 | OK | 851 | ||
| macos-oldrel-x86_64 | OK | 898 | ||
| windows-devel-arm64 | FAIL | 188 | ||
| windows-devel-x86_64 | OK | 776 | ||
| windows-release-arm64 | FAIL | 174 | ||
| windows-release-x86_64 | OK | 753 | ||
| windows-oldrel-x86_64 | OK | 779 | ||
| wasm-release | OK | 316 |
Exports:construct_modeldiagnose_modeldispersion_structurefit_modelgrowth_rateincidencemultiplep_splineproportionrandom_walkRtsinglesmoothing_structuresubtyped
Dependencies:abindanytimeaskpassbackportsbase64encbayesplotBHbitbit64bslibcachemcallrcheckmateclassclicliprclockcodetoolscolorspacecpp11crayoncrosstalkcurldata.tabledescdiagramdigestdistributionaldplyrevaluatefarverfastmapfontawesomeforcatsforecastfracdifffsfurrrfuturefuture.applygenericsggplot2ggridgesglobalsgluegowergridExtragtablehardhathighrhmshtmltoolshtmlwidgetshttrinlineipredisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelavalazyevallifecyclelistenvlmtestloolubridatemagrittrMASSMatrixmatrixStatsmemoisemimenlmennetnumDerivopensslotelpadrparallellypillarpkgbuildpkgconfigplotlyplyrposteriorprettyunitsprocessxprodlimprogressprogressrpromisespspurrrquadprogquantmodQuickJSRR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRcppRollreadrrecipesreshape2rlangrmarkdownrpartrsamplerstanrstantoolsS7sassscalesshapeslidersparsevctrsSQUAREMStanHeadersstringistringrsurvivalsystensorAtibbletidyrtidyselecttimechangetimeDatetimetktinytextseriestsfeaturestsibbleTTRtzdburcautf8vctrsviridisviridisLitevroomwarpwithrxfunxtsyamlzoo
