dwc-analysis

A clojure library to perform fast analysis on darwincore occurrences.

Best used with dwc lib.

Usage

Using leningen:

[dwc-analysis "0.0.26"]

All functions expect and vector of hash-maps that represent the occurrences, such as:

[
  {:occurrenceID "foo1" :decimalLatitude 10.10 :decimalLongitude 20.20}
  {:occurrenceID "foo2" :decimalLatitude 10.12 :decimalLongitude 20.24}
]

And must of them return GeoJSON conforming objects on the "geo" propertie, ready to put on a map.

AOO

Calculates area of occupancy (in kilometers) using a grid-size (default to 2 kilometers), and the polygons cells that match with the count of matches per cell in geojson format.

(use 'dwc-analysis.aoo)

(aoo occurrences) 
(aoo occurrences 10) (comment "grid-size of 10km")
=> {:area 100000
    :geo {
      :type "FeatureCollection",
      :features [
        {:type "Feature",
         :geometry {
           :type "Polygon",
           :coordinates [[ ... ]]
         }
        }
      ]
    }
   }

EOO

Calculates the extent of occurrencce and returns the mininum convex polygon and area in kilometers:

(use 'dwc-analysis.eoo)
 
(eoo occurrences)
=> {:area 100000
    :geo {
      :type "FeatureCollection",
      :features [
        {:type "Feature",
         :geometry {
           :type "Polygon",
           :coordinates [[ ... ]]
         }
        }
      ]
    }
  }

Clusters

Performs clustering of occurrences identifing conglomerates by following:

Identify maximum distance between points
Buffer all points with radius as 10% of maximum distance
Union all buffers that overlaps

(use 'dwc-analysis.clusters) (clusters occurrences) => {:count 10 :area 10000 :buffers { :type "FeatureCollection", :features [ {:type "Feature", :geometry { :type "Polygon", :coordinates [[ ... ]] } } ] } :geo { :type "FeatureCollection", :features [ {:type "Feature", :geometry { :type "Polygon", :coordinates [[ ... ]] } } ] } }

Note: The radius calculation is to be changed to a mean distance based of a minimum spaning tree.

Quality Analysis

A simplistic quality analysis based on completeness.

Identification: id(occurrenceID), collector(recordedBy and recordNumber), date (day, month and year), identification(identifiedBy) and taxonomy (family and (scientificName or genus+specificEpithet))
Georeference: valida decimalLatitude/decimalLongitude, locality, country/state/municipality, precision and datum
Abundance: number of records
Linage: age/currency of record

(use 'dwc-analysis.quality) (analyse occurrences) => {:abundance 2.0 :identification 1.0 :georeference 4.5 :linage 3.5 :grades [ :each_occurrence_graded]}

Risk Analysis

I don't feel confident about this yet

Perform an automated risk analysis loosily based on IUCN methodology, applying only geospatial distribution data:

Categories:

Adapted from the IUCN Red List Categories and Criteria:

Criteria B

B1 (EOO)
EOO < 100km² = CR
EOO < 5000km² = EN
EOO < 20000km² = VU
B2 (AOO)
AOO < 10km² = CR
AOO < 500km² = EN
AOO < 2000km² = VU

The below information SHOULD apply, but I don't have an algorithm to calculate this values, so for the evaluation to happen we allow it to happen without them.'

Must also:
Locations = 1 for CR
Locations <= 5 for EN
Locations <= 10 for VU
AND one of
decline of population, eoo or aoo
extreme fluctuation of population, eoo or aoo

VU D2

(AOO < 20km² OR Locations <= 5) AND a threat (but we cant assess threats yet).

Usage:

(require 'dwc-analysis.risk)

(assess {:aoo 4 :eoo 256 :locations 1 :decline true})
  => [{ :category "X" :criteria "Xxn" :reason "Locations" } ... ]

It returns all possible classifications, ordered by bigger risk, all parameters are optional.

ALL

Perform all analysis, also dividing the occurrences by historic (> 50 years old) and recent.

Usage:

 (use 'dwc-analysis.all)

 (all-analysis occurrences)
  => {
    :quality {
      :abundance 0.0
      :identification 0.0
      :georeference 0.0
      :linage 0.0
    },
    :occurrences {
      :count 10,
      :recent [],
      :count_recent 0,
      :historic [],
      :count_historic 0
    }
    :points {
      :count 10,
      :recent [],
      :count_recent 0,
      :historic [],
      :count_historic 0
      :geo {:type "FeatureCollection" :features []}
    },
    :eoo {
      :all {},
      :historic {},
      :recent {}
    }
    :aoo {
      :all {},
      :historic {},
      :recent {}
    }
    :clusters {
      :all {},
      :historic {},
      :recent {}
    }
    :risk-assessment []
  }

License

MIT

biodivdev / dwc-analysis