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README.md

SIT Indonesia

Facundo Muñoz
January 04, 2023

Analysis of Sterile-Insect Technique (SIT) Mark-Release-Recapture (MRR) and pilot population-suppression trial data from Indonesia.

Main objective:

  • Determine whether the release numbers were sufficient to induce 80% sterility in the wild Aedes aegypti population (egg hatch rates, induced sterility, number of eggs, competitiveness (with and without bootstrapping method) of the pilot vs control sites in Indonesia.

Reports

Project structure

  • data/: Original data files, as they were received.

    I don't touch them at all. I may even set read-only permissions on them. I typically track versions (even if sometimes they are binary files) for reproducibility.

  • doc/: Supporting documents, papers, etc. that are not produced by me, but are useful or needed for reference.

    Binary documents in PDF or doc(x) formats are untracked (edit doc/.gitignore as needed). However there is a Notes.md for keeping a project log and a Makefile to compile the notes to PDF format.

  • public/: Dissemination material in HTML format (reports, slides). Everything here will be published automatically on line by GitLab Pages.

  • src/: Source code for everything. Functions, figures, reports, analyses.

    The .Rmd files produce RMarkdown reports (compiled into public/).

    Helper functions are in functions.R. The rest are ancilliary files. Write \LaTeX macros into before_body.tex and specific \LaTeX packages into preamble.tex. Include bibliographic references in BibTeX format into the .bib file. You can change the bibliographic style in the .csl file by whatever style you prefer.

  • .gitignore specifies which files are not to be tracked.

  • .gitlab-ci.yml configures GitLab's continuous integration in order to produce GitLab Pages based from README.md and files within public/.

  • README.md is the current file. It will become the index page of the GitLab Pages website, and can include links to compiled reports for dissemination.

  • _targets.R is the main file of the project. It consists of a list of targets that need to be computed using functions and code therein. These targets are R objects than can be referred to from within the Rmd files to produce the reports.

    Some of the targets load or clean up the data sets producing intermediate objects that are used by others in turn, others make figures and others are meant to compile the reports themselves.