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

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Introduction

T this document describes how to use rOceansNew and R package for exploring spatial trends in marine biodiversity and conservation. Here have examples of functions to access and explore spatial patterns of marine biodiversity.

Second example, exploring shark biodiversity trends of the genus Carharhinidae

Compute a abundance grid

data(Carcharhinidae_total_checked)

Carcharhinidae_abundance_10 = oceanAbundGrid(occurrences = Carcharhinidae_total_checked, cell_size=10)

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

Carcharhinidae_abundance_1 = oceanAbundGrid(occurrences = Carcharhinidae_total_checked, cell_size=1)

Carcharhinidae_abundance_0.5 = oceanAbundGrid(occurrences = Carcharhinidae_total_checked, cell_size=0.5)

Visualize abundance

par(mfrow=c(2,2))
oceanMaps(Carcharhinidae_abundance_10, logScale=T, main="Carcharhinidae abundance (10x10)")
oceanMaps(Carcharhinidae_abundance_5, logScale=T, main="Carcharhinidae abundance (5x5)")
oceanMaps(Carcharhinidae_abundance_1, logScale=T, main="Carcharhinidae abundance (1x1)")
oceanMaps(Carcharhinidae_abundance_0.5, logScale=T, main="Carcharhinidae abundance (0.5x0.5)")
par(mfrow=c(1,1))

Exploring envioronmental drivers of abundance patterns

abundance_environ_df = invisible(oceanEnv(biod_grid = Carcharhinidae_abundance_1,
                                biodiv_metric = "abundance", 
                                plot=T, 
                                log_scale=T))

Computing species abundance matrix - and several diversity metrics

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

# Visualizing diversity metrics
par(mfrow=c(2,2))
oceanMaps(Carcharhinidae_diversity[[2]], main = "Carcharhinidae richness")
oceanMaps(Carcharhinidae_diversity[[3]], main = "Carcharhinidae Shannon Diversity")
oceanMaps(Carcharhinidae_diversity[[4]], main = "Carcharhinidae Simpson Diversity")
par(mfrow=c(1,1))

Exploring envioronmental drivers of abundance patterns

diversity_env_df = invisible(oceanEnv(biod_grid = Carcharhinidae_diversity[[2]],
                                biodiv_metric = "richness", 
                                plot=T, 
                                log_scale=T))

Exploring biodiversity hotspots and vulnerability of these hotspots to warming

Carcharhinidea_hotspots = oceanHotspots(biodiversity_grid = Carcharhinidae_diversity[[2]], 
                          hotspot_map=T, main = "Hotspots and coldspots of shark diversity")


hotspots_vulnerb <- oceanVulnerab(biodiversity_grid = Carcharhinidea_hotspots,
                     map_climtatic_impacts = F, plot_histograms = T)