jeffeaton

read_zipdta <- function(zfile){
  tmp <- tempfile()
  on.exit(unlink(tmp))
  return(foreign::read.dta(unzip(zfile, grep(".dta", unzip(zfile, list=TRUE)$Name, TRUE, value=TRUE), exdir=tmp)))
}

jeffeaton

#' ---
#' title: "<title>"
#' author: Jeff Eaton
#' output: pdf_document
#' ---
#'

##+ setup, include=FALSE
library(knitr)
opts_chunk$set(tidy=TRUE, warning=FALSE, cache=TRUE, message=FALSE)

jeffeaton

devtools::install_github("mrc-ide/hivmappr@shiny")


## 1. Bundle app using `rsconnect` internals.

appDir <- "~/Documents/Code/R/hivmappr/inst/shiny/hivmappr/"

appPath <- appDir
target <- rsconnect:::deploymentTarget(appPath,
                                       appName = NULL,

jeffeaton

library(scam)
library(rstan)
library(ggplot2)

set.seed(0)
n <- 200
x1 <- runif(n)*6-3
f1 <- 3*exp(-x1^2) # unconstrained term
f1 <- (f1-min(f1))/(max(f1)-min(f1)) # function scaled to have range [0,1]
x2 <- runif(n)*4-1;

jeffeaton

#' 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

#' 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

#' 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

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

#' 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

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)