Package: AMISforInfectiousDiseases 0.1.1
AMISforInfectiousDiseases: Implement the AMIS Algorithm for Infectious Disease Models
Implements the Adaptive Multiple Importance Sampling (AMIS) algorithm, as described by Retkute et al. (2021, <doi:10.1214/21-AOAS1486>), to estimate key epidemiological parameters by combining outputs from a geostatistical model of infectious diseases (such as prevalence, incidence, or relative risk) with a disease transmission model. Utilising the resulting posterior distributions, the package enables forward projections at the local level.
Authors:
AMISforInfectiousDiseases_0.1.1.tar.gz
AMISforInfectiousDiseases_0.1.1.zip(r-4.5)AMISforInfectiousDiseases_0.1.1.zip(r-4.4)AMISforInfectiousDiseases_0.1.1.zip(r-4.3)
AMISforInfectiousDiseases_0.1.1.tgz(r-4.4-x86_64)AMISforInfectiousDiseases_0.1.1.tgz(r-4.4-arm64)AMISforInfectiousDiseases_0.1.1.tgz(r-4.3-x86_64)AMISforInfectiousDiseases_0.1.1.tgz(r-4.3-arm64)
AMISforInfectiousDiseases_0.1.1.tar.gz(r-4.5-noble)AMISforInfectiousDiseases_0.1.1.tar.gz(r-4.4-noble)
AMISforInfectiousDiseases_0.1.1.tgz(r-4.4-emscripten)AMISforInfectiousDiseases_0.1.1.tgz(r-4.3-emscripten)
AMISforInfectiousDiseases.pdf |AMISforInfectiousDiseases.html✨
AMISforInfectiousDiseases/json (API)
| # Install 'AMISforInfectiousDiseases' in R: |
| install.packages('AMISforInfectiousDiseases', repos = c('https://drsimonspencer.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/drsimonspencer/amisforinfectiousdiseases-dev/issues
Last updated 11 days agofrom:53af1c09c2. Checks:9 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 21 2025 |
| R-4.5-win-x86_64 | OK | Jan 21 2025 |
| R-4.5-linux-x86_64 | OK | Jan 21 2025 |
| R-4.4-win-x86_64 | OK | Jan 21 2025 |
| R-4.4-mac-x86_64 | OK | Jan 21 2025 |
| R-4.4-mac-aarch64 | OK | Jan 21 2025 |
| R-4.3-win-x86_64 | OK | Jan 21 2025 |
| R-4.3-mac-x86_64 | OK | Jan 21 2025 |
| R-4.3-mac-aarch64 | OK | Jan 21 2025 |
Exports:amiscalculate_summariesdefault_amis_paramsplot_mixture_componentssample_parameters
Dependencies:backportsbase64encbitbit64bootbroombslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayondata.tabledigestdplyrevaluatefansifarverfastmapfontawesomeforcatsforeachforeignFormulafsgdatagenericsggplot2glmnetgluegridExtragtablegtoolshavenhighrHmischmshtmlTablehtmltoolshtmlwidgetsisobanditeratorsjomojquerylibjsonliteknitrlabelinglatticelifecyclelme4magrittrMASSMatrixmclustmemoisemgcvmicemimeminqamitmlmnormtmunsellnlmenloptrnnetnumDerivordinalpanpillarpkgconfigprettyunitsprogresspurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreformulasrlangrmarkdownrpartrstudioapisassscalesshapestringistringrsurvivaltibbletidyrtidyselecttinytextzdbucminfutf8vctrsviridisviridisLitevroomweightswithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Run the AMIS algorithm to fit a transmission model to a map | amis |
| Calculate summaries of weighted statistics | calculate_summaries |
| Produce list containing the default AMIS parameters | default_amis_params |
| Wrapper function for 'plot.Mclust()' | plot_mixture_components |
| Plot histogram or credible interval of weighted distributions given a model fitted by 'amis()' | plot.amis |
| Print method for object of class 'amis' | print.amis |
| Sample parameters from their weighted distributions given a model fitted by 'amis()' | sample_parameters |
| Summary method for object of class 'amis' | summary.amis |
