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Jofre Espigule-Pons

[Notebook] Biodiversity: The Great Horned Owl (Bubo virginianus)

Jofre Espigule-Pons, Wolfram Research

Posted 1 year ago

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This is going to be my first post on a series of computational explorations on different animal species and biodiversity related topics. Last week on a late night walk, during the Wolfram Tech Conference, I got lucky and I heard one great horned owl singing on the parking lot of Champaigns football stadium. That’s why I’m going to start the series with this species. Listen to my recorded sound on SoundCloud here.

Since this post is actually a cloud embedded notebook, we can easily display a cool intro video using EmbeddedService:

EmbeddedService[{"YouTube","bt3X8MJgJWo"}]

In[]:=

Out[]=

Species Built-in Data

One way of obtaining the species entity of a great horned owl is by using Interpreter:

gHornedOwl=Interpreter["Species"]["Great Horned Owl"]

In[]:=

great horned owl

Out[]=

Once we have the entity of the species, we can check its associated properties, like its, “ScientificName”, “SpeciesAuthority”, and “Image”:

Column

great horned owl

SPECIES SPECIFICATION

[{"ScientificName","SpeciesAuthority","Image"}]

In[]:=

Bubo virginianus

Gmelin, 1788

Out[]=

A quick way to check all properties available for a species is by using “Dataset”:

great horned owl

SPECIES SPECIFICATION

["Dataset"]

In[]:=

alternate common names	
alternate scientific names	
body temperature	—
class	Class:Aves
common name	great horned owl
family	Family:Strigidae
genus	Genus:Bubo
image
infraspecies	—
kingdom	Kingdom:Animalia
length	(18.1102to24.8031)in
maximum recorded lifespan	29yr
maximum speed	—
name	great horned owl
number of members	13
order	Order:Strigiformes
parent entity	Genus:Bubo
phylum	Phylum:Chordata
scientific name	Bubo virginianus
sibling taxa	{ … 17 }
showing 1–20 of 27

Out[]=

Alternatively, we can also use SpeciesData which is equivalent to EntityValue:

length=SpeciesData

great horned owl

SPECIES SPECIFICATION

,"Length"

In[]:=

(18.1102to24.8031)

Out[]=

EntityValue

great horned owl

SPECIES SPECIFICATION

,"Length"

In[]:=

(18.1102to24.8031)

Out[]=

Since I’m not American, I need to convert the units to metric system in order to get a picture of the size of great horned owls:

UnitConvert[length,"Centimeters"]

In[]:=

(46.to63.)

Out[]=

Oh, Wow! They are actually bigger than I expected.

We can also easily get other eagle owl species using “Siblings”:

otherEagleOwls=SpeciesData[gHornedOwl,"Siblings"]

In[]:=



spotted eagle-owl

pharaoh eagle-owl

blakiston'sfish owl

Eurasian eagle-owl

Bubo capensis

Bubo cinerascens

Bubo coromandus

Verreaux's eagle-owl

Bubo leucostictus

Bubo magellanicus

spot-bellied eagle-owl

philippine eagle-owl

Bubo poensis

snowy owl

Bubo shelleyi

Bubo sumatranus

Bubo vosseleri



Out[]=

eagleOwls=Append[otherEagleOwls,gHornedOwl];

In[]:=

Now, we can easily create a MenuView with most of existing eagle owls species around the globe:

MenuView[DeleteMissing[Thread[Rule[eagleOwls,SpeciesData[eagleOwls,"Image"]]],2],13]

In[]:=

great horned owl

Out[]=

Or what other subspecies of Great Horned Owl do exist using “SubEntities”:

subspecies=gHornedOwl["SubEntities"]

In[]:=



Bubo virginianus subsp. algistus

Bubo virginianus subsp. elachistus

Bubo virginianus subsp. heterocnemis

Northwestern Horned Owl

Bubo virginianus subsp. mayensis

Bubo virginianus subsp. mesembrinus

Bubo virginianus subsp. nacurutu

Bubo virginianus subsp. nigrescens

Bubo virginianus subsp. pacificus

Virginia great horned owl

St.Michael horned owl

Western horned owl

Bubo virginianus subsp. virginianus



Out[]=

Visualizing a Taxonomic Graph for Eagle Owls

We can easily create a customized taxonomic graph for eagle owls using “TaxonomyGraph” and Graph directives:

{taxonomyGraph,taxonomicSequence,siblings}=SpeciesData[gHornedOwl,{"TaxonomyGraph","TaxonomicSequence","Siblings"}];

In[]:=

GraphtaxonomyGraph,ImageSize800,VertexLabels

Thread[

]

,VertexStyleDirective[Brown,Opacity[0.8]],VertexSize2,EdgeStyleGray,VertexLabelStyleDirective[FontSize13,Bold]

Map of occurrences of Great Horned Owls using iNaturalist data

Once you create an iNaturalist account (free), it’s fairly easy to import a CVS file with all owl observations from Illinois state and we need to setup the directory where we stored the CSV file:

$path="/Users/jofre/species-functions-and-data/iNaturalist/Imported files from Platform";SetDirectory[$path];

In[]:=

Amazingly, we can automatically import the CSV file as a nice Dataset using SemanticImport:

data=SemanticImport["owls_observations_Illinois.csv"];

In[]:=

Using GeoGraphics creating a map of Illinois with all owls observations is pretty straightforward:

owlsDistribution=GeoGraphics{Red,PointSize[0.01],Point@GeoPosition[Values@Normal@data[All,{"latitude","longitude"}]]},GeoRange

Illinois, United States

ADMINISTRATIVE DIVISION

,ImageSizeLarge

In[]:=

Out[]=

Let’s create a MenuView with all different species:

Get list of owl species on the dataset and exclude the sub-species:

illiniSpecies=Delete[Union@Normal@data[All,"scientific_name"],{{-3},{-1}}]

In[]:=

{Aegolius acadicus,Asio flammeus,Asio otus,Athene cunicularia,Bubo scandiacus,Bubo virginianus,Megascops,Megascops asio,Strigidae,Strigiformes,Strix varia,Tyto alba}

Out[]=

MenuView@MapWith{species=#,entity=Interpreter["Species"][#]},entityLabeledGeoGraphics{Orange,PointSize[0.02],Point@GeoPosition[Values@Normal@data[Select[#["scientific_name"]species&],{"latitude","longitude"}]]},GeoRange

Illinois, United States

ADMINISTRATIVE DIVISION

,ImageSizeLarge,entity["Image"]&,illiniSpecies

In[]:=

great horned owl

Out[]=

Combining data from different Maps:

Here, my original idea was to explore multiple geographical data by combining it on a same map, just to show some of the GeoGraphics capabilities that Wolfram Language offers. We will create a density map of Illinois wind farms, a wind vector map and finally combine them with the one from owls occurrences:

Illinois wind farms

Here, I’m going to use some code from Emmanuel Garcés Medina’s WTC19 presentation on Geo Visualizations:

windfarms=

wind farms

;

density=GeoSmoothHistogramwindfarms,RegionFunction->

Illinois, United States

ADMINISTRATIVE DIVISION

,GeoRange

Illinois, United States

ADMINISTRATIVE DIVISION



In[]:=

Wind Vector Map of Illinois

vectors=WindVectorDataRandomGeoPosition

Illinois, United States

ADMINISTRATIVE DIVISION

,200,Now,"DownwindGeoVector"

windplot=GeoVectorPlotvectors,RegionFunction->

Illinois, United States

ADMINISTRATIVE DIVISION



In[]:=

Combine all outputs

Show[density,windplot,owlsDistribution]

Out[]=

Identify Great Horned Owl species via audio samples

We can try to automatically identify the great horned owl song that I recorded using my phone near Champaign’s Football Stadium:

owlChampaign=


00:00	00:02

;

First, let’s try AudioIdentify built-in function, analogue to ImageIdentify:

AudioIdentify[owlChampaign,"animal",AcceptanceThreshold.1]

In[]:=

bird

Out[]=

Spectrogram[owlChampaign,Method"MelFrequency"]

In[]:=

Out[]=

We can use a high and a low pass filter to improve the quality of the audio:

filteredOwlChampaign=HighpassFilter[LowpassFilter[owlChampaign,

800

300

]

In[]:=


00:00	00:02

Out[]=

Spectrogram[HighpassFilter[LowpassFilter[owlChampaign,

800

300

],Method"MelFrequency"]

In[]:=

Out[]=

Import audio files from iNaturalist of the most common owls found in Illinois:

As we previously did, it’s fairly easy to import a CSV file with all owl observations with audio from North America:

$path="/Users/jofre/species-functions-and-data/Identify Species via audio/";SetDirectory[$path];

In[]:=

Again, we can automatically import the CSV file as a nice Dataset using SemanticImport:

dataset=SemanticImport["US_Owls_audios.csv"]

observed_on_string

observed_on

time_observed_at

time_zone

out_of_range

user_id

user_login

created_at

updated_at

quality_grade

license

url

image_url

sound_url

tag_list

description

id_please

num_identification_agreements

num_identification_disagreements

captive_cultivated

oauth_application_id

place_guess

latitude

longitude

positional_accuracy

geoprivacy

taxon_geoprivacy

coordinates_obscured

positioning_method

positioning_device

species_guess

scientific_name

common_name

iconic_taxon_name

taxon_id

307780

2013-06-20 12:12am

Thu 20 Jun 2013

2013-06-20 04:12:00 UTC

Eastern Time (US & Canada)

false

10787

maractwin

2013-06-22 03:02:05 UTC

2019-05-30 22:04:50 UTC

research

CC-BY

http://www.inaturalist.org/observations/307780

—

Recorded from my bedroom window. First time I've heard or seen an owl here. It ⋱

false

—

Porter Square, Cambridge MA

42.3889

-71.1194

1602

open

false

Eastern Screech-Owl

Megascops asio

Eastern Screech-Owl

Aves

19765

361064

2013-08-09

Fri 9 Aug 2013

Eastern Time (US & Canada)

false

12036

zaccota

2013-08-10 02:55:43 UTC

2016-06-23 03:25:26 UTC

research

CC-BY-NC

http://www.inaturalist.org/observations/361064

—

https://static.inaturalist.org/sounds/291.m4a?1502824207

false

—

Starksboro, VT

44.2576

-73.0479

190

false

Barred Owl (Strix varia)

Strix varia

Barred Owl

Aves

19893

373032

Sun Aug 18 2013 20:46:32 GMT-0700 (PDT)

Sun 18 Aug 20