R/data-documentation.R

In mrc-ide/naomi: Naomi Model for Subnational HIV Estimates

#' Programme data: Malawi routine HIV service delivery data
#'
#' Datasets containing Malawi National HIV programme quarterly reported data
#' about:
#' * Reported number currently on ART.
#' * Number of women receiving antenatal care and final antenatal HIV testing.
#'
#' @format
#'
#'  TODO: Link to demo_areas dataset
#'  `demo_art_number` is a dataset with 2042 observations on the following 5 variables:
#'  \describe{
#'    \item{\code{area_id}}{District area id -- see demo_areas dataset.}
#'    \item{\code{sex}}{Sex as a character vector -- all values are "both".}
#'    \item{\code{age_group}}{Value "Y015_999" is age 15+, "Y000_014" is age 0-14.}
#'    \item{\code{calendar_quarter}}{Calendar quarter.}
#'    \item{\code{art_current}}{Number currently on ART at the end of the quarter.}
#'    \item{\code{art_new}}{Number newly initiated ART during the quarter.}
#'   }
#'
#'  TODO: Link to demo_areas dataset
#'  `demo_anc_testing` is a dataset with 923 observations on the following 8 variables:
#'  \describe{
#'    \item{\code{area_id}}{District area id -- see demo_areas dataset.}
#'    \item{\code{quarter_id}}{Quarter ID (integer).}
#'    \item{\code{anc_clients}}{Number of unique ANC clients during quarter.}
#'    \item{\code{anc_known_pos}}{Number of ANC clients already known to be HIV positive prior to first ANC visit and not tested for HIV.}
#'    \item{\code{anc_already_art}}{Number of ANC clients already on ART prior to first ANC visit.}
#'    \item{\code{anc_tested}}{Number of ANC clients tested for HIV and received result.}
#'    \item{\code{anc_tested_pos}}{Number of ANC clients testing HIV postive.}
#'    \item{\code{anc_known_pos}}{Number of ANC clients not tested for HIV due to documented recent HIV negative status (optional).}
#'    \item{\code{births_facility}}{Number of life births recorded at health facilities..}
#'  }
#'
#' @source
#' Department of HIV & AIDS, Minitry of Health, Malawi.
#' \url{http://hiv.health.gov.mw/index.php/our-documents}
#'
#' @details
#'
#' Data are sourced from quarterly reporting spreadsheets produced via the Quarterly
#' Integrated HIV Program Reports and publicly available from Malawi Ministry of
#' Health: Department of HIV & AIDS website.
#'
#' Data are provided by the Ministry of Health, Malawi with the following disclaimer:
#'
#' 1. The data in this file are owned by the Ministry of Health (MOH), Malawi.
#'
#' 2. These data are shared in order to support the National HIV Program.
#'
#' 3. Data in this file may not be used by Third Parties for further analysis and
#'    dissemination without prior written approval of the Director of the Department
#'    for HIV and AIDS, MOH.
#'
#' 4. Patient-level data are routinely collected by health facility staff using
#'    standard monitoring tools. This file contains facility-level aggregates that
#'    have been generated by facility staff and that were verified from primary
#'    records during quarterly National HIV Program Supervision (coordinated of the
#'    Department of HIV and AIDS). While every effort is made to ensure high data
#'    quality, individual records may not be complete and accurate.
#'
#' 5. The official interpretation of these data is presented in Quarterly Integrated
#'    HIV Program Reports and any divergent interpretation may be misleading and is
#'    not supported by the MOH. Analysis and interpretation of the data requires
#'    detailed understsanding of the methods and constraints of the Malawi's National
#'    M&E System.
#'
#' The number of ART by age 0-14 and age 15+ is not reported in aggregate quarterly
#' reporting data. For model illustration purposes, this is approximated as 94% of
#' all ART clients are age 15+ based on Spectrum model outputs which were validated
#' against age distributions from electronic medical records by the Malawi HIV
#' estimates team.
#'
#' Dataset could contain one observation per district per quarter for all 32 districts
#' for all quarters between Q3 2011 and Q3 2018, but the number of observations is
#' fewer than 32 * 29 = 928 due to a few missing observations.
#'
#'
#' @seealso \code{\link{quarter_labels}}, \code{\link{get_age_groups}}.
#'
"demo_anc_testing"

#' @rdname demo_anc_testing
"demo_art_number"