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index.Rmd
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---
title: "Global Register of Introduced and Invasive Species - Belgium"
author: Peter Desmet, Lien Reyserhove, Damiano Oldoni
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
github-repo: trias-project/unified-checklist
output:
bookdown::gitbook:
split_by: rmd
df_print: paged
config:
search: no
sharing:
facebook: no
twitter: no
all: []
---
```{r index-setup, include = FALSE}
knitr::opts_chunk$set(
echo = FALSE, # Exclude code from output by default
warning = FALSE,
message = FALSE,
rownames.print = FALSE # Option for df_print = paged
)
```
This document contains and describes all the steps in creating a unified checklist of alien species in Belgium and was developed for the [Tracking Invasive Alien Species (TrIAS) project](http://trias-project.be). By running this document in R, it will create all the necessary data files for the unified checklist.
For more general information, see:
- [GitHub repository](https://github.com/trias-project/unified-checklist)
- [Dataset on GBIF](https://doi.org/10.15468/xoidmd)
Load libraries:
```{r echo = TRUE}
library(tidyverse) # To do data science
library(tidylog) # To provide feedback on dplyr functions
library(magrittr) # To use %<>% pipes
library(here) # To find files
library(janitor) # To clean input data
library(openxlsx) # To write Excel files
library(digest) # To generate hashes
library(rgbif) # To use GBIF services
library(furrr) # To allow parallel downloads
library(progressr) # To show progress bar for parallel downloads
# devtools::install_github("trias-project/trias")
library(trias) # To use functions developed for TrIAS
```
Setup the number of simultaneous workers for parallel downloads.
```{r echo = FALSE}
future::plan(multisession, workers = 2)
```
Setup the progress bars for fetching data from GBIF.
```{r echo = FALSE}
progressr::handlers(progressr::handler_progress("[:bar] | :percent ~:eta remaining"))
```