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biodiversity-puerto-wilches

Object y objetives

The main objective of this repository is to share R and SQL code which we used to manage data and analyse the baseline biodiversity in Puerto Wilches, Santander, Colombia. This project has been conducted around a project of fracking test phase in this municipality, since then fracking projects have been paused in Colombia. One of the main interesting part of this study is that a very extensive biodiversity sampling effort have been conducted by the Instituto Alexander von Humboldt, concerning plants, insects, other arthropods, birds and mammals, as a collaboration with the ANH (Agencia Nacional de Hidrocarburos).

Content

The repository includes:

  1. folder database: data integration in a postgreSQL database ( code in R y SQL, presented as Rmarkdown files).
  2. folder analyses: includes analyses code (mainly in R, presented in Rmarkdown files)

Requirements

In order to run the codes presented in this repository, you will need:

  • PostgreSQL
  • postgis extension
  • pandoc
  • R with the following packages:
    • rmarkdown
    • knitr
    • DiagrammeRsvg
    • dm
    • ggplot2
    • htmltools
    • iNEXT
    • kableExtra
    • leaflet
    • openxlsx
    • png
    • readxl
    • rpostgis
    • sp
    • RPostgreSQL
    • rsvg
    • sqldf
    • vegan

You will need to create an empty Postgres database called "fracking", which may be done in bash by:

createdb fracking

In postgreSQL, call for the postgis extension by entering:

CREATE EXTENSION postgis;

We recommend the use of pgpass to be able to connect to the database without needing to give the password (nor the host in a server based setup).

Rmarkdown documents

Most of the codes of this repository are presented in rmarkdown document (Rmd extension).

You may render them as github documents with the following command in R:

rmarkdown::render("filename.Rmd")

However, since github document are not easy to read on a local machine, you may want to use:

rmarkdown::render("filename.Rmd", output_format="html_document")

If you have a functional latex distribution on your computer (see tinytex R package to install one otherwise), you may even create pdf report out of the rmarkdown files using:

rmarkdown::render("filename.Rmd", output_format="pdf_document")