https://github.com/pakillo/exclosures-almoraima
Research compendium for "Impactos de la herbivoría por ungulados en las comunidades de plantas leñosas del Parque Natural Los Alcornocales""
https://github.com/pakillo/exclosures-almoraima
ecology r r-package reproducible-paper research-compendium rmarkdown
Last synced: about 1 year ago
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Research compendium for "Impactos de la herbivoría por ungulados en las comunidades de plantas leñosas del Parque Natural Los Alcornocales""
- Host: GitHub
- URL: https://github.com/pakillo/exclosures-almoraima
- Owner: Pakillo
- License: other
- Created: 2018-08-01T12:31:25.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2018-08-01T14:09:50.000Z (almost 8 years ago)
- Last Synced: 2025-03-20T16:57:52.546Z (about 1 year ago)
- Topics: ecology, r, r-package, reproducible-paper, research-compendium, rmarkdown
- Language: TeX
- Size: 1.89 MB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
Awesome Lists containing this project
README
---
title: Impactos de la herbivoría por ungulados en las comunidades de plantas leñosas del Parque Natural Los Alcornocales
date: "`r Sys.Date()`"
output: github_document
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
[](https://zenodo.org/badge/latestdoi/143153398)
Research compendium (code and data) used for the following publication:
Rodríguez-Sánchez F, Luque-Oliva V & Jurado V. (2018) Impactos de la herbivoría por ungulados en las comunidades de plantas leñosas del Parque Natural Los Alcornocales. *Almoraima*, en prensa.
The manuscript, written in Rmarkdown, can be read [here](https://github.com/Pakillo/exclosures-Almoraima/blob/master/manuscript/cercados_Almoraima.md). The submitted Word file is [here](https://github.com/Pakillo/exclosures-Almoraima/blob/master/manuscript/cercados_Almoraima.docx).
Compendium DOI: https://doi.org/10.5281/zenodo.1325107
CITATION:
Rodríguez-Sánchez F, Luque-Oliva V & Jurado V. (2018) Research compendium for "Impactos de la herbivoría por ungulados en las comunidades de plantas leñosas del Parque Natural Los Alcornocales" (Version 1.0.0). Zenodo. https://doi.org/10.5281/zenodo.1325107
## Installation
In order to run the analyses you will need to install the package first:
```{r eval = FALSE}
devtools::install_github("Pakillo/exclosures-Almoraima")
```
## Usage
There is a [`makefile.R`](https://github.com/Pakillo/exclosures-Almoraima/blob/master/makefile.R) that runs each step of the analysis in the appropriate order.
```{r eval=FALSE}
library(exclosures)
#### READ AND PRE-PROCESS DATA #####
## Read site info
read_siteinfo("data-raw/sites_info_raw.csv")
## Read and prepare species info
read_sppinfo(sppdata = "data-raw/species_info_raw.csv")
## Read and process raw cover data
read_rawcover(rawcover = "data-raw/exclosures_cover_raw.csv", tr.length = 25)
## Read and prepare damage data
read_damage("data-raw/exclosure_damage_raw.csv")
## Prepare dataset
make_dataset()
#### EXPLORATORY ANALYSIS ####
rmarkdown::render("analyses/EDA.Rmd")
#### MANUSCRIPT ####
rmarkdown::render("manuscript/cercados_Almoraima.Rmd")
```