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DIVA
(Data Interpolating Variational Analysis) and DIVAnd
(DIVA in n dimensions) are software tools designed to generate gridded maps of continuous variables such as sea water temperature, salinity or oxygen concentration. The main advantages over other interpolation or analysis method are:
DIVAnd
is a multi-dimensional generalization (Barth et al., 2014), written in the Julia language, with a new mathematical formulation with respect to the previous DIVA
code.
This directory provides the codes and tools to
DIVAnd
.The dataset to be processed contained only a binary information: presence or absence, and the objective is to derive a map showing the probability to encounter a given species, as illustrated below for Aequipecten opercularis.
The input data was provided by Herman et al (2020). The main data file is spe.csv
, it contains all sampling events as rows, and the most frequent species (occurrence >200) as columns. The first columns specify sampling event and location. All columns are coded as ‘pa’ (for presence/absence) followed by the AphiaID
of the species. In the separate file specieslist.csv
you find the names of the species corresponding to their AphiaID
. You also find the total number of events where the species has been found.
A species can have value 1 (present), 0 (looked for but absent) and NA (not looked for). The NA values must be disregarded when making maps. They do not contain information about either presence or absence. There are NAs in the file because some datasets only look for a subset of species.
The information about the occurrence of a species is obtained with the function read_coords_species
defined in the script BenthosInterp.jl
. The species are selected by using the AphiaID.
This directory contains the notebooks for the preparation and analysis of the data, as well as the generation of the figures.
For a given species, two heatmaps are computed: one of the presence, the other for the absences. Then the probability (between 0 and 1) is computed using the following formula:
d = npre * dens_pre / (npre * dens_pre + nabs * dens_abs)
where
npre
is the total number of absence data points;nabs
is the total number of absence data point;dens_pre
is the heatmap obtained with the presence data only;dens_abs
is the heatmap obtained with the absence data only.If we have only presence data, the 2nd term of the denominator is zero and the probability reduces to the presence heatmap. The absence data decrease the ratio and hence the probability.
product/netCDF
plot_results_map.ipynb
: notebook in Python
to create the figures using the ETRS89 Lambert Azimuthal Equal Area coordinate reference system of 2001 (EPGS 3035
).product/figures
and consist of
You need Julia 1.5 (or later) available from https://julialang.org/downloads/. The following Julia packages required to run this code can be installed with:
using Pkg
Pkg.add("DIVAnd")
Pkg.add("DelimitedFiles")
Pkg.add("Dates")
Pkg.add("NCDatasets")
Pkg.add("GridInterpolations")
Pkg.add("Interpolations")
Pkg.add("Missings")
if plots are to be created with Julia, those packages are also required:
Pkg.add("PyCall")
Pkg.add("PyPlot")
Pkg.add("Proj4")
Two types of analysis are performed:
1-UniformL
)2-VariableL
).For both analysis, 2 types of products are created (described in the next section):
jpg
format).Barth, A., Beckers, J.-M., Troupin, C., Alvera-Azcárate, A., and Vandenbulcke, L.(2014): divand-1.0: n-dimensional variational data analysis for ocean observations, Geosci. Model Dev., 7, 225–241, https://doi.org/10.5194/gmd-7-225-2014.
Herman, P.M.J., Stolte, W., van der Heijden, L. 2020. Summary presence/absence maps of macro-endobenthos in the greater North Sea, based on nearly 100,000 samples from 65 assembled monitoring data sets. Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund. Available at: https://www.emodnet-biology.eu/data-catalog?module=dataset&dasid=6617
The code, written in Julia
, is distributed through GitHub: https://github.com/EMODnet/EMODnet-Biology-Benthos-Interpolated-Maps
Please cite this product as: A. Barth, P. Hermann and C. Troupin (2020). Probability maps for different benthos species in the North Sea. Integrated data products created under the European Marine Observation Data Network (EMODnet) Biology project (EASME/EMFF/2017/1.3.1.2/02/SI2.789013), funded by the European Union under Regulation (EU) No 508/2014 of the European Parliament and of the Council of 15 May 2014 on the European Maritime and Fisheries Fund.
The code is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
Available to download in:
https://www.emodnet-biology.eu/data-catalog?module=dataset&dasid=6617
This link downloads a zip file containing a local copy of this git repository with the data products in the ./product/
subdirectory. The scripts and workflows included in this local git repository may differ from the pipelines included in this remote repository on GitHub as we continue to improve the product. To see the differences between the local copy of the git repository you downloaded and the latest version on GitHub, open the git bash console and type:
$ git fetch origin master
$ git diff origin/master
If you want to update the local copy of the git repository you downloaded to the latest development version, run the following line:
$ git pull
If you are unsure about how to use git, please check the installation guide of the git book: https://git-scm.com/book
A. Barth, P. Hermann and C. Troupin
Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CÉCI), funded by the Fonds de la Recherche Scientifique de Belgique (F.R.S.-FNRS) under Grant No. 2.5020.11 and by the Walloon Region"