{ "_id": "6a10143facfb0bcc41c83a3d", "Package": "mcmsupply", "Type": "Package", "Title": "Estimating Public and Private Sector Contraceptive Market Supply\nShares", "Version": "1.0.3", "Authors@R": "c(person(\"Hannah\", \"Comiskey\", email=\"hannahcomiskey68@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Niamh\", \"Cahill\", role = \"aut\"),\nperson(\"Leontine\", \"Alkema\", role =\"aut\"))", "Description": "Family Planning programs and initiatives typically use\nnationally representative surveys to estimate key indicators of\na country’s family planning progress. However, in recent years,\nroutinely collected family planning services data (Service\nStatistics) have been used as a supplementary data source to\nbridge gaps in the surveys. The use of service statistics comes\nwith the caveat that adjustments need to be made for missing\nprivate sector contributions to the contraceptive method supply\nchain. Evaluating the supply source of modern contraceptives\noften relies on Demographic Health Surveys (DHS), where many\ncountries do not have recent data beyond 2015/16. Fortunately,\nin the absence of recent surveys we can rely on statistical\nmodel-based estimates and projections to fill the knowledge\ngap. We present a Bayesian, hierarchical, penalized-spline\nmodel with multivariate-normal spline coefficients, to account\nfor across method correlations, to produce\ncountry-specific,annual estimates for the proportion of modern\ncontraceptive methods coming from the public and private\nsectors. This package provides a quick and convenient way for\nusers to access the DHS modern contraceptive supply share data\nat national and subnational administration levels, estimate,\nevaluate and plot annual estimates with uncertainty for a\nsample of low- and middle-income countries. Methods for the\nestimation of method supply shares at the national level are\ndescribed in Comiskey, Alkema, Cahill (2022)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "URL": "https://hannahcomiskey.github.io/mcmsupply/,\nhttps://github.com/hannahcomiskey/mcmsupply", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev make libharfbuzz-dev jags libicu-dev libjpeg-dev\nlibpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev\nlibssl-dev libx11-dev zlib1g-dev", "Repository": "https://hannahcomiskey.r-universe.dev", "Date/Publication": "2026-03-22 21:56:19 UTC", "RemoteUrl": "https://github.com/hannahcomiskey/mcmsupply", "RemoteRef": "HEAD", "RemoteSha": "a6f30a0a04b52b780a86d6a973738df1a1e00647", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-21 09:02:56 UTC", "User": "root" }, "Author": "Hannah Comiskey [aut, cre],\nNiamh Cahill [aut],\nLeontine Alkema [aut]", "Maintainer": "Hannah Comiskey ", "MD5sum": "18380f284dcc82f6dd2615b16cb8e739", "_user": "hannahcomiskey", "_type": "src", "_file": "mcmsupply_1.0.3.tar.gz", "_fileid": "8ae27df33c5657606009054ba48818765786ed7f622db8d6dbb67cc6ab7fb486", "_filesize": 1158792, "_sha256": "8ae27df33c5657606009054ba48818765786ed7f622db8d6dbb67cc6ab7fb486", "_created": "2026-05-21T09:02:56.000Z", "_published": "2026-05-22T08:30:55.905Z", "_distro": "noble", "_jobs": [ { "job": 77343972473, "time": 210, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7131669125" }, { "job": 77343972906, "time": 185, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7131660809" }, { "job": 77343972780, "time": 166, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7131654191" }, { "job": 77343972851, "time": 140, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", 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"_maintainer": { "name": "Hannah Comiskey", "email": "hannahcomiskey68@gmail.com", "login": "hannahcomiskey", "description": "", "uuid": 56960311 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "haven", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rvest", "role": "Imports" }, { "package": "survey", "role": "Imports" }, { "package": "openxlsx", "role": "Imports" }, { "package": "R2jags", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "tidyverse", "role": "Imports" }, { "package": "tidybayes", "role": "Imports" }, { "package": "runjags", "role": "Imports" }, { "package": "rjags", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "abind", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "plyr", "role": "Imports" 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This array is used to inform the Normal prior of the subnational-level intercept in the single-country subnational model.", "object": "subnational_alpha_cms_hat", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "subnational_estimated_correlations", "title": "The estimated subnational-level correlations between the rates of change in methods", "object": "subnational_estimated_correlations", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "row", "column", "public_cor", "private_cor" ], "rows": 10, "table": true, "tojson": true }, { "name": "subnational_inv.sigma_delta_hat", "title": "The median estimate for the subnational-level precision matrix of the delta.k terms in the multi-country subnational model. This array is used to inform the multi-variate normal prior in the single-country subnational model.", "object": "subnational_inv.sigma_delta_hat", "class": [ "array" ], "fields": [], "table": false, "tojson": true }, { "name": "subnational_tau_alpha_pms_hat", "title": "subnational_tau_alpha_pms_hat The median estimates of the precision for the subnational-level country, sector-, method-specific intercepts in the multi-country subnational model. This vector is used to inform the precision in the Normal prior of the subnational-level intercept in single-country subnational models.", "object": "subnational_tau_alpha_pms_hat", "class": [ "array" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "calculate_SE_data_from_DTA", "title": "Calculate Standard Errors and Variance-Covariance Matrices for DHS Subnational Estimates", "topics": [ "calculate_SE_data_from_DTA" ] }, { "page": "check_data_freshness", "title": "Check Data Freshness Against DHS Reference", "topics": [ "check_data_freshness" ] }, { "page": "Country_and_area_classification", "title": "The Country and area classification according to the United Nations Standaistical Division, Standard country or area codes for statistical use (M49). Adapted for use in FP2030 by the Track20 project. A subset of data from the United Nations country classifications", "topics": [ "Country_and_area_classification" ] }, { "page": "country_names", "title": "The names of the countries with national and subnational administration level data stored", "topics": [ "country_names" ] }, { "page": "DEFT_DHS_database", "title": "DEFT_DHS_database A database of the design effects for some of the DHS surveys in the national and subnational datasets. Due to due to multistage and clustering of the DHS sample, the average standard error is increased by a design effect (DEFT) factor over that in an equivalent simple random sample.", "topics": [ "DEFT_DHS_database" ] }, { "page": "get_data", "title": "Wrapper function that retrieves the DHS data used for modelling the proportion of modern contraceptives supplied by the public and private sectors at the national and subnational administration levels.", "topics": [ "get_data" ] }, { "page": "get_posterior_P_samps", "title": "Function to pull the complete posterior sample for the national method-supply share estimates. Functionality for the subnational models is still under development.", "topics": [ "get_posterior_P_samps" ] }, { "page": "get_subnational_modelinputs", "title": "Get JAGS model inputs", "topics": [ "get_modelinputs", "get_subnational_modelinputs" ] }, { "page": "harvest_dhs", "title": "Harvest DHS Dataset Availability", "topics": [ "harvest_dhs" ] }, { "page": "national_estimated_correlations_bivarlogitnormal", "title": "The estimated national-level correlations between the rates of change in methods", "topics": [ "national_estimated_correlations_bivarlogitnormal" ] }, { "page": "national_FPsource_data", "title": "DHS survey observations for the proportion of modern contraceptives supplied by the public and private sectors at the national level", "topics": [ "national_FPsource_data" ] }, { "page": "national_FPsource_format", "title": "A checklist for ensuring national-level custom data is appropriate to be used for estimation", "topics": [ "national_FPsource_format" ] }, { "page": "national_FPsource_VARCOV_bivarlogitnormal", "title": "An array of variance-covariance matrices transformed onto the logit-scale via the delta method. Each matrix corresponds to the DHS survey logit-transformed observations for the proportion of modern contraceptives supplied by the public and private sectors at the national level", "topics": [ "national_FPsource_VARCOV_bivarlogitnormal" ] }, { "page": "national_inv_sigma_delta_hat_bivarlogitnorm", "title": "The median estimate for the national-level variance-covariance matrix of the delta.k terms in the multi-country national model.", "topics": [ "national_inv_sigma_delta_hat_bivarlogitnorm" ] }, { "page": "national_tau_alpha_cms_hat_bivarlogitnorm", "title": "The median estimates of the precision for the national-level country, sector-, method-specific intercepts in the multi-country national model. This vector is used to inform the precision in the Normal prior of the national-level intercept in single-country national models.", "topics": [ "national_tau_alpha_cms_hat_bivarlogitnorm" ] }, { "page": "national_theta_rms_hat_bivarlogitnorm", "title": "The median estimates of the national-level sub-continental, sector-, method-specific intercepts in the multi-country national model. This array is used to inform the Normal prior of the country-level intercept in the single-country national model.", "topics": [ "national_theta_rms_hat_bivarlogitnorm" ] }, { "page": "national_varcov_order_bivarlogitnormal", "title": "The order of observations to join the variance-covariance array data and the DHS survey observations for the proportion of modern contraceptives supplied by the public and private sectors at the national level", "topics": [ "national_varcov_order_bivarlogitnormal" ] }, { "page": "plot_estimates", "title": "Wrapper function to plot the JAGS estimates", "topics": [ "plot_estimates" ] }, { "page": "pull_estimates", "title": "Function to pull method-supply share median estimates and credible intervals for a given year and country.", "topics": [ "pull_estimates" ] }, { "page": "run_jags_model", "title": "Wrapper function to run the jags model for estimating the proportion of modern contraceptive methods supplied by the public & private Sectors using a Bayesian hierarchical penalized spline model for the national and subnational administration levels", "topics": [ "run_jags_model" ] }, { "page": "subnat_FPsource_data", "title": "DHS survey observations for the proportion of modern contraceptives supplied by the public and private sectors at the subnational administration level.", "topics": [ "subnat_FPsource_data" ] }, { "page": "subnat_FPsource_format", "title": "A checklist for ensuring subnational-level custom data is appropriate to be used for estimation", "topics": [ "subnat_FPsource_format" ] }, { "page": "subnational_alpha_cms_hat", "title": "The median estimates of the subnational-level country, sector-, method-specific intercepts in the multi-country subnational model. This array is used to inform the Normal prior of the subnational-level intercept in the single-country subnational model.", "topics": [ "subnational_alpha_cms_hat" ] }, { "page": "subnational_estimated_correlations", "title": "The estimated subnational-level correlations between the rates of change in methods", "topics": [ "subnational_estimated_correlations" ] }, { "page": "subnational_inv.sigma_delta_hat", "title": "The median estimate for the subnational-level precision matrix of the delta.k terms in the multi-country subnational model. This array is used to inform the multi-variate normal prior in the single-country subnational model.", "topics": [ "subnational_inv.sigma_delta_hat" ] }, { "page": "subnational_tau_alpha_pms_hat", "title": "subnational_tau_alpha_pms_hat The median estimates of the precision for the subnational-level country, sector-, method-specific intercepts in the multi-country subnational model. 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