The user must prepare a set of
files before running the workflow. These files can be uploaded previously in
the “personal space”, or in each step of the workflow.
1. Occurrences Dataset:
Dataset of species occurrences. It should be a .txt file contained within a
.zip file with TSV (tab separated values), up to 6 columns, and its first row
should contain the following column headers:
-
decimalLatitude (numeric): the
latitude of the observed specimen expressed in decimal degree in WGS 84
coordinate system (EPSG:4326)
-
decimalLongitude (numeric): the
longitude of the observed specimen expressed in decimal degree in WGS 84
coordinate system (EPSG:4326)
-
scientificName (text): the
scientific name of the species
- year (numeric): the year
of the observation
2. Alien Taxonomy
Dataset: List of alien species scientific names. It should be a .txt file
contained within a .zip file with TSV (tab separated values), with 2 columns,
and its first row contains the headers:
-
scientificName (text): the
scientific name of the alien species
-
dispersionRadius (numeric): a
species potential daily range (as an individual trait, not an observation
property), expressed in meter. A default value of 50 meters is used if the
field is not provided.
3. CIMPAL paths of
introduction: Paths of introduction for each NIS taxa. It should be a .csv
file (with TSV) in a matrix format with the first column listing the pathways of
introduction categories and the subsequent n columns headers (first row)
being the alien species scientific names <scientificName1>, which must
match the names in the input file used in Alien Taxonomy Dataset Uploader
(field scientificName):
-
row names (column 1)
(text): “SpSciName”; “ALL”; <path1>; <path2>; <path3>; …
-
column headers
(column 2 to n+1) (text): <scientificNameA>; <scientificNameB>; <scientificNameC>; …
-
(matrix cells)
binary value (0/1) (integer): indicates if the pathway of introduction
applies (1) or not (0) to a given alien species. In row ‘ALL’ always indicate
(1): this will allow you to generate the cumulative CIMPAL index for all
species, not filtered by pathway of introduction.
4. Weight file: List of values of impact for
each taxon inside of each biotope. It should be a .csv file (with TSV) in a
matrix format with the first column listing the alien species names scientificName and the subsequent
n columns’ headers (first row) being the n habitat names <habitatname>. These names
must correspond to the names of each spatial layer uploaded in as Biotopes shapefiles
and must be written in lower case. The cells in the matrix correspond
to the value of the Magnitude of Impact (MoI):
- (column 1) scientificName (text): the
scientific name of the alien species must match the names in the input file
used in Alien Taxonomy Dataset Uploader (field scientificName)
-
(row 1, column 2 to
n+1) <habitatname> (text): the
habitat names (lower case) must match spatial layers habitat names in input
files 5 Biotopes.zip (<habitatname>)
-
(matrix cells)
(integer): score of the Magnitude of Impact (MoI) of each species in each
habitat, according to the scoring protocol adopted by the user.
5. Biotope shapefiles:
Spatial layers for each habitat. It should be a set of shapefiles contained
within a .zip file. Each file should be named as single_<habitatname>.shp (write all habitat names in lower case). Please
make sure that the names in the shape file match the names in the weight
file. Project the habitat shapefiles in LAEA (EPSG:3035).
6. Zones shapefiles: Spatial
layer(s) for aggregating results. It should be one or more shapefiles
contained within a .zip file. The zone shapefile must be in LAEA (EPSG:3035),
and it must also contain a numeric field named "id_habitat" identifying each zone (unique
zone code 1 to n).
Heliana Teixeira, CESAM Centre for Environmental and Marine Studies, Biology Department, University of Aveiro
Julien Radoux, UCLouvain