Jeff Imai-Eaton jeffeaton

jeffeaton / phia-cd4-by-cascade_2024-05-02.R

Created May 3, 2024 05:31

PHIA survey analysis of CD4 <200 by care cascade stage

	library(dplyr)
	library(readr)
	library(tidyr)
	library(forcats)
	library(haven)
	library(survey)

	phia_path <- "~/Data/household surveys/PHIA/datasets"

	cmr2017phia <- rdhs::read_zipdata(file.path(phia_path, "CMR/datasets/302 CAMPHIA 2017-2018 Adult Biomarker Dataset (DTA).zip"))

jeffeaton / phia-incidence-extract_2024-04-25.R

Created May 1, 2024 13:12

PHIA HIV incidence survey extract for UNAIDS Reference Group incidence analysis

	library(dplyr)
	library(readr)
	library(tidyr)
	library(forcats)
	library(haven)
	library(survey)

	## devtools::install_github("jeffeaton/svyincid")
	library(svyincid)

jeffeaton / ahd-first90-sim_2024-04-27.R

Created April 28, 2024 20:59

Extract Shiny90 output and aggregate for cryptococcal meningitis CD4 <200 inputs

	library(dplyr)
	library(brio)
	library(readr)
	library(first90) # remotes::install_github("mrc-ide/first90release")


	#' ## Define functions

	get_pjnz_shiny90_filename <- function (pjnz) {
	files <- utils::unzip(pjnz, list = TRUE)$Name

jeffeaton / pjnz-frr-input-update.R

Last active October 7, 2022 09:37

Function to update FRR fitting input in Spectrum PJNZ file

	## Requires library eppasm

	dpsub <- function(dp, tag, rows, cols, tagcol = 1) {
	dp[which(dp[, tagcol] == tag) + rows, cols]
	}


	read_frr_fit_input <- function(pjnz) {

	dp <- eppasm::read_dp(pjnz)

jeffeaton / epp-xml-anc-update.R

Last active December 16, 2022 05:04

Function to update ANC data in EPP XML file within Spectrum PJNZ

	library(xml2)
	library(epp)

	eppd_overwrite_matrix <- function (xm, mat) {

	if (!xml_attr(xm, "class") %in% c("[D", "[I"))
	stop("Tried to invoke .parse_matrix() on array node not of class '[D' or '[I'.")

	m_rows <- as.integer(xml_attr(xm, "length"))
	stopifnot(nrow(mat) == m_rows)

jeffeaton / adjust_datapack_export2021.R

Last active March 8, 2021 09:26

Adjust PEPFAR Data Pack export for 2021 specification

	#' This function saves an updated data pack export CSV in the same directory as
	#' the Naomi output package file
	#'
	#' Example:
	#'
	#' file <- "~/Downloads/MWI_20210308-090536_naomi_spectrum_digest.zip" ## !! REPLACE HERE
	#' adjust_datapack_export2021(file)
	#'

	adjust_datapack_export2021 <- function(naomi_output_package) {

jeffeaton / malawi-census-2018-district-population-projections.R

Last active December 8, 2020 09:50

Malawi Census 2018 District population projections (2018-2043)

	library(dplyr)
	library(pdftools)
	library(readr)
	library(stringr)
	library(tidyr)

	url <- "http://www.nsomalawi.mw/images/stories/data_on_line/demography/census_2018/Thematic_Reports/Population%20Projections%202018-2050.pdf"

	file <- tempfile(fileext = ".pdf")
	download.file(url, file)

jeffeaton / subset-naomi-output-package.R

Last active March 29, 2020 20:39

	#' This script is an example of the function subset_output_package() to load,
	#' subset, and resave the Naomi output package.
	#'
	#' The arguments to the function are:
	#'
	#' * path: file path to the output package.
	#' * output_path: file path to save the new subsetted package (end in .zip).
	#' * area_id: vector of area_ids to keep or drop.
	#' * area_level: vector of area_levels to keep or drop.
	#' * sex: vector of sexes to keep or drop.

jeffeaton / shiny90-datapack-extract.R

Last active February 12, 2020 12:36

Function to export proportion aware of status by age and sex from .shiny90 output file

	#' Export proportion aware by five year age group from Shiny90
	#'
	#' Export estimates for proportion aware of status from a Shiny90
	#' output file to five-year age groups 15-19 to 50+.
	#'
	#' @param shiny90_path file path to .shiny90 digest file.
	#' @param out_path output path to save CSV of proportion aware.
	#' @param year year(s) to generate estimates; an integer or a vector of integers.
	#'
	#' @return

jeffeaton / shiny90-datapack-extract.R

Created February 6, 2020 06:33

Function to export proportion aware of status by age and sex from .shiny90 output file

	#' Export proportion aware by five year age group from Shiny90
	#'
	#' Export estimates for proportion aware of status from a Shiny90
	#' output file to five-year age groups 15-19 to 50+.
	#'
	#' @param shiny90_path file path to .shiny90 digest file.
	#' @param out_path output path to save CSV of proportion aware.
	#' @param year year(s) to generate estimates; an integer or a vector of integers.
	#'
	#' @return