How to use this template

1. If you want to start a new repository, click on Use this template and then Create a new repository. If the repository was created for you, skip this step.
2. Copy the relevant issues from the template repository to your new repository.
3. Delete this section of the README.
4. Follow the instructions in the issues.

Template README and Guidance

INSTRUCTIONS: Include a brief project summary here, as well as short instructions for how to run the code in the repository. This may be simple, or may involve many complicated steps. It should be a simple list, no excess prose. Strict linear sequence. If more than 4-5 manual steps, please wrap a master program/Makefile around them, in logical sequences. Examples follow.

• Edit programs/config.do to adjust the default path
• Run programs/00_setup.do once on a new system to set up the working environment.
• Download the data files referenced above. Each should be stored in the prepared subdirectories of data/, in the format that you download them in. Do not unzip. Scripts are provided in each directory to download the public-use files. Confidential data files requested as part of your FSRDC project will appear in the /data folder. No further action is needed on the replicator's part.
• Run programs/01_master.do to run all steps in sequence.

Contents

• Comments for replicators
• Computational requirements
• Description of programs/code
• List of final outputs
• List of datasets
• Acknowledgements

Comments for replicators

• programs/00_setup.do: will create all output directories, install needed ado packages.
  • If wishing to update the ado packages used by this archive, change the parameter update_ado to yes. However, this is not needed to successfully reproduce the manuscript tables.
• programs/01_dataprep:
  • These programs were last run at various times in 2018.
  • Order does not matter, all programs can be run in parallel, if needed.
  • A programs/01_dataprep/master.do will run them all in sequence, which should take about 2 hours.
• programs/02_analysis/master.do.
  • If running programs individually, note that ORDER IS IMPORTANT.
  • The programs were last run top to bottom on July 4, 2019.
• programs/03_appendix/master-appendix.do. The programs were last run top to bottom on July 4, 2019.
• Figure 1: The figure can be reproduced using the data provided in the folder “2_data/data_map”, and ArcGIS Desktop (Version 10.7.1) by following these (manual) instructions:
  • Create a new map document in ArcGIS ArcMap, browse to the folder “2_data/data_map” in the “Catalog”, with files "provinceborders.shp", "lakes.shp", and "cities.shp".
  • Drop the files listed above onto the new map, creating three separate layers. Order them with "lakes" in the top layer and "cities" in the bottom layer.
  • Right-click on the cities file, in properties choose the variable "health"... (more details)

Computational requirements

INSTRUCTIONS: In general, the specific computer code used to generate the results in the article will be within the repository that also contains this README. However, other computational requirements - shared libraries or code packages, required software, specific computing hardware - may be important, and is always useful, for the goal of replication. Some example text follows.

Software Requirements

INSTRUCTIONS: List all of the software requirements, up to and including any operating system requirements, for the entire set of code. It is suggested to distribute most dependencies together with the replication package if allowed, in particular if sourced from unversioned code repositories, Github repos, and personal webpages. In all cases, list the version you used.

• Stata (code was last run with version 15)
  • the program "0_setup.do" will install all dependencies locally, and should be run once.
• Python 3.6.4
  • the file "requirements.txt" lists these dependencies, please run "pip install -r requirements.txt" as the first step. See https://pip.readthedocs.io/en/1.1/requirements.html for further instructions on using the "requirements.txt" file.
• R 3.4.3
  • the file "0_setup.R" will install all dependencies (latest version), and should be run once prior to running other programs.

Controlled randomness

INSTRUCTIONS: Some estimation code uses random numbers, almost always provided by pseudorandom number generators (PRNGs). For reproducibility purposes, these should be provided with a deterministic seed, so that the sequence of numbers provided is the same for the original author and any replicators. While this is not always possible, it is a requirement by many journals’ policies. The seed should be set once, and not use a time-stamp. If using parallel processing, special care needs to be taken. If using multiple programs in sequence, care must be taken on how to call these programs, ideally from a main program, so that the sequence is not altered.

Random seed is set at line ___ of program ____

Memory and Runtime Requirements

INSTRUCTIONS: Memory and compute-time requirements may also be relevant or even critical. Some example text follows. It may be useful to break this out by Table/Figure/section of processing. For instance, some estimation routines might run for weeks, but data prep and creating figures might only take a few minutes.

Approximate time needed to reproduce the analyses on a standard (CURRENT YEAR) desktop machine: ______

Description of programs/code

INSTRUCTIONS: Give a high-level overview of the program files and their purpose.

• Programs in programs/01_dataprep will extract and reformat all datasets referenced above. The file programs/01_dataprep/master.do will run them all.
• Programs in programs/02_analysis generate all tables and figures in the main body of the article. The program programs/02_analysis/master.do will run them all. Each program called from master.do identifies the table or figure it creates (e.g., 05_table5.do). Output files are called appropriate names (table5.tex, figure12.png) and should be easy to correlate with the manuscript.
• Programs in programs/03_appendix will generate all tables and figures in the online appendix. The program programs/03_appendix/master-appendix.do will run them all.
• Ado files have been stored in programs/ado and the master.do files set the ADO directories appropriately.
• The program programs/00_setup.do will populate the programs/ado directory with updated ado packages, but for purposes of exact reproduction, this is not needed. The file programs/00_setup.log identifies the versions as they were last updated.
• The program programs/config.do contains parameters used by all programs, including a random seed. Note that the random seed is set once for each of the two sequences (in 02_analysis and 03_appendix). If running in any order other than the one outlined below, your results may differ.

List of final outputs

INSTRUCTIONS: Your programs should clearly identify the tables and figures as they appear in the manuscript, by number. Sometimes, this may be obvious, e.g. a program called "table1.do" generates a file called table1.png. Sometimes, mnemonics are used, and a mapping is necessary. In all circumstances, provide a list of tables and figures, identifying the program (and possibly the line number) where a figure is created.

Figure/Table #	Program	Line Number	Output file	Note
Table 1	02_analysis/table1.do		summarystats.csv
Table 2	02_analysis/table2and3.do	15	table2.csv
Table 3	02_analysis/table2and3.do	145	table3.csv
Figure 1	n.a. (no data)			Source: Herodus (2011)
Figure 2	02_analysis/fig2.do		figure2.png
Figure 3	02_analysis/fig3.do		figure-robustness.png	Requires confidential data

List of datasets

INSTRUCTIONS: In some cases, authors will provide one dataset (file) per data source, and the code to combine them. In others, in particular when data access might be restrictive, the replication package may only include derived/analysis data. Every file should be described. This can be provided as a Excel/CSV table, or in the table below. See a more detailed discussion on how to create these tables here.

Master data sets

Data set name	Location	Key	Foreign keys	Main variables	Created by
Village master	Data/MasterData/VillageMaster.dta	village_id		Treatment status, county, sub-county, location	Code/MasterData/create-village-master.do
Household master	Data/MasterData/HouseholdMaster.dta	hh_id	village_id	GPS location, Enrollment status	Code/MasterData/create-hh-master.do

Raw data

Data set name	Location	Unit of observation	Key	Foreign keys	Main variables	Instrument/source
Chlorine tests	Data/Raw/ChlorineTests.csv	Household-time	hh_id date	village_id	Chlorine residual test result	Link to survey instrument or data provider documentation
Household survey	Data/Raw/HouseholdSurvey.csv	Household	hh_id	village_id	Chlorine use (self-reported), migration

Tidy data

Data set name	Location	Unit of observation	Key	Foreign keys	Main variables	Created by
Chlorine tests	Data/Tidy/ChlorineTests.dta	Household-time	hh_id date	village_id	Chlorine residual test result	Code/Tidy/tidy-chlorine.do
Household tidy	Data/Tidy/HouseholdTidy.dta	Household	hh_id	village_id	Chlorine use (self-reported), migration	Code/Tidy/tidy-hh.do
Children tidy	Data/Tidy/ChildrenTidy.dta	Household-child	child_id	hh_id	Data of birth, date of death, symptoms	Code/Tidy/tidy-child.do

Intermediate/constructed data

Data set name	Location	Unit of observation	Key	Foreign keys	Main variables	Created by
Children constructed	Data/Constructed/ChildrenConstructed.dta	Household-child	child_id	hh_id	Age at death, cause of death	Code/Construct/construct-child.do
Household constructed	Data/Constructed/HouseholdConstructed.dta	Household	hh_id	village_id	Chlorine use (self-reported, tested), exposure to treatment	Code/Construct/construct-hh.do

Analysis/final data

Data set name	Location	Unit of observation	Key	Main variables	Created by
Children final	Data/Analysis/ChildrenFinal.dta	Child	child_id	Treatment status, death indicator, cause of death, chlorine use, exposure to treatment	Code/Construct/create-children-final.do

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Acknowledgements

This file was adapted from the Social Science Data Editors website. For the latest version, visit https://social-science-data-editors.github.io/template_README/