Neotoma Bookdown Manual

Development of the Neotoma Paleoecology Database manual in the form of a Bookdown document. This is a revision of the ReStructured Markdown Neotoma manual, and as such has its own GitHub repository.

Contributors

This project is an open project, and contributions are welcome from any individual. All contributors to this project are bound by a code of conduct. Please review and follow this code of conduct as part of your contribution.

• Simon Goring

Tips for Contributing

Issues and bug reports are always welcome. Code clean-up, and feature additions can be done either through pull requests to project forks or branches.

All products of the Throughput Annotation Project are licensed under an MIT License unless otherwise noted.

How to use this repository

This repository is managed as a Bookdown project using R and SQL scripts to demonstrate use of the Neotoma Database. The connection to the database is managed through a file that is ignored in .gitignore. This file needs to be added to the repository before the Bookdown project is compiled.

connect_remote.json

A file in JSON format that is used as the connection string for the database. If you use a Neotoma snapshot to work with the database locally, your connect_remote.json file will look like this:

json { "host": "localhost", "port": 5432, "database": "neotoma", "user": "postgres", "password": "postgres", }

If you intend to continue tracking your version of this repository and want to push to a public code repository then ensure that the file connect_remote.json is included in your .gitignore file.

All references and images should be included in the assets folder, split into text and image folders. Images should be clearly labelled.

Workflow Overview

The project uses R. All required packages are included in the file requirements.txt. In package load (in the file index.Rmd) the requirements file is loaded into the project and the pacman package is used to load all the required packages using p_load(). Implied in all of this is that the package bookdown is used in this project.

This repository comes with a bash script that can be used to compile the project on Linux and Mac computers by calling bash renderBookdown.sh. This script will render the Bookdown document to an HTML file that can be directly navigated.

System Requirements

This project was developed using R (v4.2+) using both RStudio and Visual Studio Code. To properly render the document requires the use of pandoc (v2.17+).

Data Requirements

This Bookdown version of the manual directly calls data from the Neotoma database, either using the neotoma2 R package, or through calls using SQL.

Key Outputs

This project generates an HTML document that can be read as a manual.

Metrics

This project is to be evaluated using the following metrics:

• Complete rendering of the manual (generally from the past version)
• All SQL queries re-written to reflect Postgres standard SQL
• Addition of R code to mimic the SQL calls