Overview

This repository consists of a data analysis pipeline of the World Health Organization, built in collaboration with Databrew LLC. It contains code for processing, analyzing, and visualizing data from a global arbovirus survey. The below instructions lay out how a developer can (a) prepare her repository for analysis by setting up data, (b) generate an analytical webpage / dashboard, (c) generate a “simplified” dataset for further analysis, and (d) generate a missingness report for operational and data collection monitoring.

Developer instructions

Setting up data

• Start by cloning this repository (if needed, instructions for cloning a repository from github are available here).
• Once you’ve got the repository on your local machine, in the main repo, create a folder named data. Populate it with the files in data.zip sent to you directly.
• Source prepare_data.R to create data.RData, combined_data.RData, and the simplified dataset simplified_dataset.csv.
• The contents of your arbovirus data folder should now look like this:

# tree
data
├── combined_data.RData
├── Copia_de_PAHO_key_indicator_spreadsheet_19_Nov_2021-Completo.xlsx
├── Country_level_summarized_responses.csv
├── Data_dictionary_Survey375147.csv
├── data.RData
├── PAHO_countries.csv
├── Regions_Countries.csv
├── region_shp.rda
├── results-survey375147.csv
├── simplified_dataset.csv
├── survey_375147_R_data_file.csv
├── survey_375147_R_syntax_file.R
├── who_afro.csv
├── who_shp.RData
└── world_shp.rda

Generating the global dashboard

• Change to the directory dashboard and set it as your working directory.
• Open create_pages.R in RStudio.
• Make sure that line 7 is commented out and that line 8 is not commented out:

# regions <- "EMRO"
regions <- c("AMRO","EMRO","EURO","SEARO","WPRO")

(Line 7 might show a region other than “EMRO”, but it should be commented out.)

• Source create_pages.R.
• Run rmarkdown::render_site.
• Using a web browser, open any of the .html pages in dashboard/_WHOA to launch the global dashboard.

Generating a regional dashboard

• Change to the directory dashboard and set it as your working directory.
• Open create_pages.R in RStudio.
• Make sure that line 8 is commented out and that line 7 is not commented out:

regions <- "EMRO"
# regions <- c("AMRO","EMRO","EURO","SEARO","WPRO")

• Change line 7 to specify the desired region; “EMRO” is shown here as an example.
• Source create_pages.R.
• Run rmarkdown::render_site.
• Using a web browser, open any of the .html pages in the directory determined by the desired region (dashboard/_AMRO, dashboard/_EMRO, dashboard/_EURO, dashboard/_SEARO, or dashboard/_WPRO) to launch the regional dashboard.

Generating missingness reports

• Open missingness/missing.Rmd in Rstudio
• Follow the instructions in missingness/instructions.md