Jeffrey Imai-Eaton jeffeaton

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 / 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 / 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 / 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"))