In monteroserra/rOceansNew: Spatial Trends in Marine Biodiversity and Conservation

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Introduction

This document describes how to use rOceans, an R package for exploring spatial trends in marine biodiversity and conservation. Here we have a examples of usage for explore spatial patterns of biodiversity in scleractinian corals of the genus Acropora.

(1) Download rOceansNew from GitHub and load the package

invisible(devtools::install_github("monteroserra/rOceansNew"))
invisible(library(rOceansNew))

Function #2 oceanDataCheck

Allows merging, checking, filtering the raw data from OBIS and/or GBIF into a common standard database. It removes occurrences with inconsistent or inconmplete taxonomic information, land-based occurrences, and duplicate occurrences.

For this set of functions, we first need to access and download data from GBIF (www.gbif.org) and OBIS (www.iobis.org).

Here I show an example with data of species within the genus Acropora that were directly downloaded from the website on June 2018. The data can be accessed from my GitHub repository "monteroserra/rOceanData" or using data()

#Accesing raw datasets
data(Acropora_GBIF) 
data(Acropora_OBIS)

#Checking OBIS or GBIF individually
Acropora_OBIS_checked = oceanDataCheck(OBIS_occurrences = Acropora_OBIS, source = "OBIS")

Acropora_GBIF_checked = oceanDataCheck(GBIF_occurrences = Acropora_GBIF, source = "GBIF")

Merging OBIS and GBIF Datasets, and checking for taxonomic and geographic issues

Acropora_Total_Checked = oceanDataCheck(GBIF_occurrences = Acropora_GBIF,
                                        OBIS_occurrences = Acropora_OBIS,
                                        source = "GBIF_&_OBIS")

monteroserra/rOceansNew documentation built on May 13, 2019, 1:09 p.m.