Package: AMISforInfectiousDiseases 0.1.0

Simon Spencer

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:Evandro Konzen [aut], Renata Retkute [aut], Raiha Browning [aut], Thilbault Lestang [aut], Simon Spencer [aut, cre], University of Warwick [cph], Oxford Research Software Engineering [cph]

AMISforInfectiousDiseases_0.1.0.tar.gz
AMISforInfectiousDiseases_0.1.0.zip(r-4.7-x86_64)AMISforInfectiousDiseases_0.1.0.zip(r-4.7-arm64)AMISforInfectiousDiseases_0.1.0.zip(r-4.6-x86_64)AMISforInfectiousDiseases_0.1.0.zip(r-4.6-arm64)
AMISforInfectiousDiseases_0.1.0.tar.gz(r-4.7-arm64)AMISforInfectiousDiseases_0.1.0.tar.gz(r-4.7-x86_64)AMISforInfectiousDiseases_0.1.0.tar.gz(r-4.6-arm64)AMISforInfectiousDiseases_0.1.0.tar.gz(r-4.6-x86_64)
AMISforInfectiousDiseases_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
AMISforInfectiousDiseases/json (API)

# Install 'AMISforInfectiousDiseases' in R:
install.packages('AMISforInfectiousDiseases', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/drsimonspencer/amisforinfectiousdiseases-dev/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

cppopenmp

3.00 score 7 scripts 313 downloads 5 exports 109 dependencies

Last updated from:abcffec5d1. Checks:10 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK229
linux-devel-x86_64OK226
source / vignettesOK362
linux-release-arm64OK211
linux-release-x86_64OK182
windows-devel-arm64OK372
windows-devel-x86_64OK263
windows-release-arm64OK282
windows-release-x86_64OK241
wasm-releaseOK174

Exports:amiscalculate_summariesdefault_amis_paramsplot_mixture_componentssample_parameters

Dependencies:backportsbase64encbitbit64bootbroombslibcachemcheckmateclicliprclustercodetoolscolorspacecpp11crayondata.tabledigestdplyrevaluatefarverfastmapfontawesomeforcatsforeachforeignFormulafsgdatagenericsggplot2glmnetgluegridExtragtablegtoolshavenhighrHmischmshtmlTablehtmltoolshtmlwidgetsisobanditeratorsjomojquerylibjsonliteknitrlabelinglatticelifecyclelme4magrittrMASSMatrixmclustmemoisemicemimeminqamitmlmnormtnlmenloptrnnetnumDerivordinalpanpillarpkgconfigprettyunitsprogresspurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreformulasrlangrmarkdownrpartrstudioapiS7sassscalesshapestringistringrsurvivaltibbletidyrtidyselecttinytextzdbucminfutf8vctrsviridisLitevroomweightswithrxfunyaml

Fitting Ascariasis data
Loading packages | Prevalence map | Model | Priors | Running AMIS | Analysing AMIS outputs | References
Rendered fromascariasis.Rmdusingknitr::rmarkdown

Last update: 2025-01-20
Started: 2025-01-20

Simulation study
Data generating process | Loading packages | Generating spatially-varying mean number of worms | Generating map samples for multiple time points | Choosing the transmission model function | Choosing the prior distributions and AMIS control parameters | Running AMIS | Looking at posterior distribution of parameters | Introducing intervention
Rendered fromsimulation_study.Rmdusingknitr::rmarkdown

Last update: 2025-01-20
Started: 2025-01-20