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-4.5-noble)AMISforInfectiousDiseases_0.1.0.tar.gz(r-4.4-noble)
AMISforInfectiousDiseases_0.1.0.tgz(r-4.4-emscripten)AMISforInfectiousDiseases_0.1.0.tgz(r-4.3-emscripten)
AMISforInfectiousDiseases.pdf |AMISforInfectiousDiseases.html✨
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

cpp openmp

3.00 score 4 scripts 5 exports 112 dependencies

Last updated 9 days agofrom:abcffec5d1. Checks:2 OK. Indexed: no.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 20 2025
R-4.5-linux-x86_64	OK	Jan 20 2025

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 fansi 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 mgcv mice mime minqa mitml mnormt munsell 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 sass scales shape stringi stringr survival tibble tidyr tidyselect tinytex tzdb ucminf utf8 vctrs viridis viridisLite vroom weights withr xfun yaml

Fitting Ascariasis data

Rendered fromascariasis.Rmdusingknitr::rmarkdownon Jan 20 2025.

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

Simulation study

Rendered fromsimulation_study.Rmdusingknitr::rmarkdownon Jan 20 2025.

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)