Package: threemc 0.1.45

Patrick OToole

threemc: (Matt's) Multi-Level Model of Male Circumcision in Sub-Saharan Africa

Functions and datasets to support, and extend to other Sub-Saharan African countries, Thomas, M. et. al., 2021, A multi-level model for estimating region-age-time-type specific male circumcision coverage from household survey and health system data in South Africa, <arxiv:2108.091422>.

Authors:Matthew Thomas [aut], Jeffrey Imai-Eaton [aut], Patrick O'Toole [cre], Imperial College of Science, Technology and Medicine [cph]

threemc_0.1.45.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
threemc/json (API)

# Install 'threemc' in R:

install.packages('threemc', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrc-ide/threemc/issues

Datasets:

datapack_psnu_area_level - PSNU Area Levels for SSA
demo_areas - Malawi shapefiles
demo_populations - Malawi populations
demo_survey_circumcision - Malawi surveys
esa_wca_regions - WCA - ESA key for Sub-Saharan African countries

On CRAN:

2.38 score 16 scripts 19 exports 74 dependencies

Last updated from:e10f54bd54 (on master). Checks:11 WARNING, 1 ERROR, 1 FAIL. Indexed: yes.

Target	Result	Time
linux-devel-arm64	WARNING	1190
linux-devel-x86_64	WARNING	1140
source / vignettes	ERROR	1994
linux-release-arm64	WARNING	1147
linux-release-x86_64	WARNING	1133
macos-release-arm64	WARNING	579
macos-release-x86_64	WARNING	1077
macos-oldrel-arm64	WARNING	708
macos-oldrel-x86_64	WARNING	1448
windows-devel	WARNING	2397
windows-release	WARNING	1493
windows-oldrel	WARNING	2432
wasm-release	FAIL	172

Exports:compare_predictions compute_quantiles create_dirs_r create_shell_dataset find_circ_type minimise_fit_obj normalise_weights_kish prepare_survey_data read_circ_data reassign_survey_level spread_areas survey_points_dmppt2_convert_convention threemc_aggregate threemc_empirical_rates threemc_fit_model threemc_initial_pars threemc_ppc threemc_ppc2 threemc_prepare_model_data

Dependencies:abind backports boot checkmate class classInt cli cpp11 data.table DBI deldir distributional dplyr e1071 evaluate farver generics ggplot2 glue gtable highr isoband KernSmooth knitr labeling lattice lifecycle loo magrittr MASS Matrix matrixStats mgcv mvtnorm nlme numDeriv pillar pkgconfig posterior proxy purrr R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppArmadillo RcppEigen rlang s2 S7 scales scoringRules scoringutils sf sp spData spdep stringi stringr tensorA tibble tidyr tidyselect TMB units utf8 vctrs viridisLite withr wk xfun yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Calculate Quantiles for Rates and Cumulative Hazard	compute_quantiles
Recursively Create Missing Directories	create_dirs_r
Create Shell Dataset for Estimating Empirical Circumcision Rate	create_shell_dataset
PSNU Area Levels for SSA	datapack_psnu_area_level
Malawi shapefiles	demo_areas
Malawi populations	demo_populations
Malawi surveys	demo_survey_circumcision
WCA - ESA key for Sub-Saharan African countries	esa_wca_regions
Minimise Fit Object Size	minimise_fit_obj
Prepare Survey Data	prepare_survey_data
Function to read in Circumcision Data	read_circ_data
Create data frame of all ages within provided age group. Convert survey coverage points & dmppt2 data to match convention of aggregated results.	survey_points_dmppt2_convert_convention
Produce Population Weighted Aggregated Samples for All Area Levels	threemc_aggregate
Use model shell dataset to estimate empirical circumcision rates	threemc_empirical_rates
Produce TMB model fit with sample, or re-sample from existing optimised model fit.	threemc_fit_model
Initialise 'thremec' (hyper)parameters.	threemc_initial_pars
Posterior Predictive Distribution and checks on OOS survey	threemc_ppc
Posterior Predictive Distribution and checks on OOS survey	threemc_ppc2
Produce Data Matrices for Modelling	threemc_prepare_model_data

Package: threemc 0.1.45

threemc: (Matt's) Multi-Level Model of Male Circumcision in Sub-Saharan Africa

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