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

Introduction - Diversity patterns in sharks using rOceans

This document describes how to use rOceans for computing spatial patterns of diversity in marine species using raw data directly downloaded from OBIS and GBIF. Here we have an example of usage for sharks of family Carcharhinidae.

(1) Download rOceans from GitHub and load the package

#devtools::install_github("monteroserra/rOceans")
library(rOceans)

Data access and visualization of spatial patterns in occurrences

For simplicity, we provide the dataset "Carcharhinidae_total_checked" which is the output obtained using oceanDataCheck() applied to raw datasets from OBIS and GBIF (see vignette 1 with Acropora example for more details on checking and filtering raw data)

data(Carcharhinidae_total_checked)

Carcharhinidae_abundance_5 = oceanAbundance(occurrences = Carcharhinidae_total_checked, cell_size=5)

#Visualize abundance
oceanMaps(Carcharhinidae_abundance_5, logScale=T, main="Carcharhinidae abundance")

Computing species abundance matrix - and several diversity metrics

Carcharhinidae_diversity = oceanDiversity(occurrences = Carcharhinidae_total_checked, print=F)

Raw species richness

oceanMaps(Carcharhinidae_diversity[[2]],logScale=T,main = "Raw richness")

Corrected species richness

Using a rarefaction techniques with a treshold set at 50 samples

oceanMaps(Carcharhinidae_diversity[[3]],logScale=T, main = "Corrected richness ")

Visualizing all diversity metrics

par(mfrow=c(2,2))
oceanMaps(Carcharhinidae_diversity[[2]],logScale=T,main = "Raw species richness")
oceanMaps(Carcharhinidae_diversity[[3]],logScale=T, main = "Corrected species richness ")
oceanMaps(Carcharhinidae_diversity[[4]], main = "Shannon Diversity")
oceanMaps(Carcharhinidae_diversity[[5]], main = "Simpson Diversity")

par(mfrow=c(1,1))