In Dmirandae/geocleaMT-1: A Package to Clean/Test Georeferenced Data

knitr::opts_chunk$set(echo = TRUE)

To obtain the occurrences reported for the Biogeographic Choco in the Global Biodiversity Information Facility (GBIF) (Telenius2011), we will go to GBIF website and follow the next pathway:

>  Data
>  Explore occurences (Fig. 1)

Figure 1. Accessing to explore occurences in GBIF

>  Georeferenced records
>  Add a filter
>  Location (Fig. 2)

Figure 2. Add the Location Filter

>  Location Box
>  Draw tools: Undefined (Fig. 3)

Figure 3. Drawing the polygon.

Then, we draw the area of interest (in our case, The Biogeographic Choco form (sensu lato: Hernandez-Camacho et al 1992), see Fig. 3), and click on:

> Apply

We will download a specific taxon using again the `add filter' tool. For example, we will download all occurrences of mammals reported by GBIF for The Biogeographic Choco (Fig. 3-4), as was used in the example in R-Alarcon and Miranda-Esquivel (submitted).

Figure 4. Add the scientific name filter.

For this example, we will use a selection of 35 species from the example in R-Alarcon and Miranda-Esquivel (submitted). These 35 species are the best candidates because they present all possible issues we can face in a standard dataset.

> Add Filter
> Scientific name (Fig. 5)

Figure 5. Applying the filter.

> Download (Fig. 6)

Figure 6. Click on Download.

The best file format to download is as a zip file, because it brings the complete information in the Darwin Core Standard (Wieczorek et al. 2012). Keep in mind that you must be registered at GBIF website.

After download the zip file, we have a folder with some information files. The file which have the occurrences data is the called `occurrences.text'. If you want to read it, note that the separator is TAB.

Dmirandae/geocleaMT-1 documentation built on Nov. 18, 2019, 6:26 p.m.