In annakrystalli/OBIShmpr: Link and query OBIS occurence data with a variety of marine habitat data

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OBIShmpr

The goal of OBIShmpr is to link and query OBIS occurence data with a variety of marine habitat data.

Data Sources

• Bio-ORACLE & MARSPEC data accesed through sdmpredictors:

  a set of GIS rasters providing geophysical, biotic and environmental data for surface and benthic marine realms. Accessed via sdmpredictors

• sedmaps [Synthetic map of the NW European

  Shelf sedimentary environment](https://www.earth-syst-sci-data.net/10/109/2018/essd-10-109-2018.pdf) data product 10.15129/1e27b806-1eae-494d-83b5-a5f4792c46fc 0.125◦ by 0.125◦ resolution synthetic maps of continuous properties of the north-west European sedimentary environment. The maps are a blend of gridded survey data, statistically modelled values based on distributions of bed shear stress due to tidal currents and waves and bathymetric properties.

  • percentage compositions of mud, sand and gravel;
  • porosity and permeability;
  • median grain size of the whole sediment and of the sand and the gravel fractions;
  • carbon and nitrogen content of sediments;
  • percentage of seabed area covered by rock;
  • mean and maximum depth-averaged tidal velocity and wave orbital velocity at the seabed; and mean monthly natural disturbance rates.

• EMODnet Seabed Habitat maps

Installation

You can install the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("EMODnet/OBIShmpr")

Example

Get habitat data for a species

library(OBIShmpr)

An example with one species

This is an example of how to run the above code for a single species - we use Scytothamnus fasciculatus, Aphia ID 325567, chosen as it has just 6 OBIS records so should run reasonably quickly.

Choose some layers to extract data from

sp_id <- 325567
layers <- c("BO2_nitratemax_bdmin", "BO_parmax", "BO2_tempmax_bdmax", "permeability", 
"tidal_vel_max", "april")

obis_match_habitat(sp_id, layers = layers)

layer_codes <- c("BO_ph", "BO_phosphate", 
                 "BO2_phosphatemean_bdmax", 
                 "BO_nitrate", "BO2_nitratemean_bdmax", 
                 "surface_nitrogen", "tn", "surface_carbon",
                 "BO_sstmean", "BO_sstmin", "BO_sstmax", 
                 "MS_biogeo13_sst_mean_5m", "MS_biogeo14_sst_min_5m",
                 "MS_biogeo15_sst_max_5m")

Palinurus elephas

Next I use the AphiaID for Palinurus elephas.

species_id <- worrms::wm_name2id("Palinurus elephas")

data <- OBIShmpr::obis_match_habitat(
    sp_id = species_id, 
    layers = layer_codes,
    geometry = bbox_nwes)

data

library(ggplot2)
world <- rnaturalearth::ne_countries(scale = "medium", returnclass = "sf")


ggplot() +
    geom_sf(data = world) +
    geom_sf(data = data, aes(color = BO_ph) ) +
    coord_sf(crs = 3035,
             xlim = c(2426378.0132, 7093974.6215),
             ylim = c(1308101.2618, 5446513.5222)) +
    theme_bw() +
    ggtitle("Palinurus elephas",
            subtitle = paste0('AphiaID = ', species_id))

annakrystalli/OBIShmpr documentation built on Oct. 4, 2020, 6:37 a.m.