This package is considered a duplicate. The official version of this package is found at:https://drsimonspencer.r-universe.dev/AMISforInfectiousDiseases

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.tar.gz(r-4.7-arm64)AMISforInfectiousDiseases_0.1.0.tar.gz(r-4.6-arm64)AMISforInfectiousDiseases_0.1.0.tar.gz(r-4.7-x86_64)AMISforInfectiousDiseases_0.1.0.tar.gz(r-4.6-x86_64)
AMISforInfectiousDiseases_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
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:

cpp openmp

3.00 score 7 scripts 198 downloads 5 exports 109 dependencies

Last updated from:abcffec5d1. Checks:4 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	OK	236
source / vignettes	OK	320
linux-release-x86_64	OK	236
wasm-release	OK	201

Exports:amis calculate_summaries default_amis_params plot_mixture_components sample_parameters

Dependencies:backports base64enc bit bit64 boot broom bslib cachem checkmate cli clipr cluster codetools colorspace cpp11 crayon data.table digest dplyr evaluate farver fastmap fontawesome forcats foreach foreign Formula fs gdata generics ggplot2 glmnet glue gridExtra gtable gtools haven highr Hmisc hms htmlTable htmltools htmlwidgets isoband iterators jomo jquerylib jsonlite knitr labeling lattice lifecycle lme4 magrittr MASS Matrix mclust memoise mice mime minqa mitml mnormt nlme nloptr nnet numDeriv ordinal pan pillar pkgconfig prettyunits progress purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr reformulas rlang rmarkdown rpart rstudioapi S7 sass scales shape stringi stringr survival tibble tidyr tidyselect tinytex tzdb ucminf utf8 vctrs viridisLite vroom weights withr xfun yaml

Fitting Ascariasis data

Rendered fromascariasis.Rmdusingknitr::rmarkdownon Jun 01 2026.

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

Simulation study

Rendered fromsimulation_study.Rmdusingknitr::rmarkdownon Jun 01 2026.

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

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

Package: AMISforInfectiousDiseases 0.1.0

AMISforInfectiousDiseases: Implement the AMIS Algorithm for Infectious Disease Models

Fitting Ascariasis data

Simulation study

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)