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add the data prep by Greg
1 parent b14790a commit 14648b8

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data/01_ASDN_Readme.txt

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data/ASDN_Bird_eggs.csv

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data/ASDN_Bird_nests.csv

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data/ASDN_Camp_assignment.csv

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data/asdn-er-diagram.png

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data/bird_database.duckdb

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data/build-database

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#!/bin/bash
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rm -f bird_database.duckdb
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duckdb bird_database.duckdb < schema-build-script.sql

data/personnel.csv

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Abbreviation,Name
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agottesman,Aaron Gottesman
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asterling,Abby Sterling
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abradley,Adam Bradley
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akneidel,Alan Kneidel
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akataluk-primeau,Alannah Kataluk-Primeau
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aissisgaitok,Albert Issisgaitok
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amatsyna,Alexader Matsyna
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asoto,Alfredo Soto
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abuckley,Alvan Buckley
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ataqtaq,Amanda Taqtaq
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aguerra,Ana Guerra
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amines,Anaka Mines
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apopovkina,Anastasia Popovkina
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abankert,Andrew Bankert
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adoll,Andrew Doll
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aperry,Andrew Perry
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arbankert,Andrew R. Bankert
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asjohnson,Andrew S. Johnson
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abaltensperger,Andy Baltensperger
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ajohnson,Andy Johnson
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asmith,Angus Smith
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anja,Anja
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acorkery,Anne Corkery
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amould,Anthony Mould
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ancook,Ashley Nicole Cook
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atufts,Ashley Tufts
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amylnikova,Asya Mylnikova
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blalibert,Benoît Laliberté
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bkaselow,Billy Kaselow
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bwinn,Brad Winn
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bmwalker,Bradley M. Walker
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bwilkinson,Bradley Wilkinson
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bverheijen,Bram Verheijen
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bhiggins,Brendan Higgins
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bksandercock,Brett K. Sandercock
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bharrington,Brian Harrington
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brobinson,Brian Robinson
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bdalziel,Bronwyn Dalziel
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bhill,Brooke Hill
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cdavis,Caitlin Davis
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cbishop,Caitlyn Bishop
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cmorcos,Camila Morcos
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clahoda,Candace Lahoda
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cjrguerra,Carlos Jose Ruiz Guerra
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clishman,Carmen Lishman
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codwyer,Carol O'Dwyer
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cdoucet,Catherine Doucet
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cpham,Catherine Pham
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cwoodworth,Chelsea Woodworth
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cgratto-trevor,Cheri Gratto-Trevor
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chojnowski,Cheryl Hojnowski
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csmith,Chris Smith
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cbrunner,Christina Brunner
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canderson,Christine Anderson
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chelms,Clinton Helms
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cmurchison,Colleen Murchison
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dgough,Danielle Gough
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dedwards,Darryl Edwards
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dmcgeachy,Dave Mcgeachy
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dsaalfeld,Dave Saalfeld
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dattagutaluk,David Attagutaluk
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dblank,David B. Lank
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dhodkinson,David Hodkinson
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dpavlik,David Pavlik
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dward,David Ward
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dturner,Devin Turner
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dsolovyeva,Diana Solovyeva
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dborden,Diane Borden
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dfillman,Don Fillman
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djleandry,Don-Jean Léandry
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dmcrae,Doug McRae
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dkessler,Dylan Kessler
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ecorp,Edward Corp
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epierce,Elin Pierce
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epayne,Elizabeth Payne
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epero,Ellen Pero
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egirard,Eloise Girard
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echalifour,Émilie Chalifour
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edastrous,Emilie D'Astrous
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eweiser,Emily Weiser
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edavis,Emma Davis
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ereed,Eric Reed
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estroud,Eric Stroud
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eescajeda,Erica Escajeda
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enol,Erica Nol
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ekwon,Eunbi Kwon
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fylin,Fang-Yee Lin
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fsgagnon,Fanny Senez Gagnon
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fsanders,Felicia Sanders
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fsmith,Fletcher Smith
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frousseaux,Francois Rousseaux
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fstetler,Frank Stetler
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gmccune,Gennyne Mccune
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gpavlyukov,Georgiy Pavlyukov
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gracey,Gerry Racey
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gholmes,Gillian Holmes
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gdanilov,Gleb Danilov
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gsedash,Gleb Sedash
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ggilchrist,Grant Gilchrist
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gsolovyev,Grigory Solovyev
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gszor,Guillaume Szor
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hspecht,Hannah Specht
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hcraig,Heather Craig
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hhelling,Heidi Helling
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hbatcheller,Hope Batcheller
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idavies,Ian Davies
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ijong,Ian Jong
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jeschenroeder,Jackman Eschenroeder
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jkorol,Jaimlyn Korol
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jcaville,James Caville
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jhughey,Jared Hughey
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jmarin,Javier Marin
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jiron,Jean Iron
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jflamarre,Jean-François Lamarre
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jrjulian,Jean-Remi Julian
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jzamuido,Jeisson Zamuido
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jcoughlan,Jennifer Coughlan
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jgale,Jennifer Gale
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jkardiak,Jennifer Kardiak
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jcunningham,Jenny Cunningham
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jhixon,Jerrid Hixon
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jhupp,Jerry Hupp
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jrobinson,Jill Robinson
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jsauer,Jim Sauer
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jpanipak,Joanna Panipak
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jliebezeit,Joe Liebezeit
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jbety,Joël Bêty
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jperz,Johanna Perz
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jbrunjes,John Brunjes
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jdiener,John Diener
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jlautenbach,Jonathan Lautenbach
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jotis,José Otis
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jbelliveau,Julie Belliveau
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jdanby,Julie Danby
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jkelso,Julie Kelso
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jwebber,Julie Webber
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jloshchagina,Julya Loshchagina
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kaward,Kara-Anne Ward
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kreischke,Karissa Reischke
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kmatsyna,Katya Matsyna
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knuyaviak,Kayla Nuyaviak
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ksheimreif,Kayla Sheimreif
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kabraham,Ken Abraham
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kkalasz,Kevin Kalasz
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kkardynal,Kevin Kardynal
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kpietrzak,Kevin Pietrzak
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kbennett,Kim Bennett
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kjones,Kim Jones
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kgrond,Kirsten Grond
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kbeckmann,Kristina Beckmann
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kbertrand,Kyle Bertrand
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khogrefe,Kyle Hogrefe
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lkoloski,Laura Koloski
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lmckinnon,Laura McKinnon
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lpaquette,Laurence Paquette
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lrenzel,Leah Renzel
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lmercier,Léonie Mercier
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lyen,Leslie Yen
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lworing,Lewis W. Oring
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lbachellier,Lisa Bachellier
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lkennedy,Lisa Kennedy
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lpirie,Lisa Pirie
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lpollock,Lisa Pollock
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lgoodrick,Lizzie Goodrick
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ljolicoeur,Ludovic Jolicoeur
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lpadegimas,Lukas Padegimas
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lburlingame,Luke Burlingame
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mvheyden,Madeline Vander Heyden
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mmcconnell,Madison McConnell
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myyang,Man-Yu Yang (Mona)
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magiroux,Marie-Andrée Giroux
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mcfrenette,Marie-Christine Frenette
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mtrudel,Marion Trudel
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mdodds,Mark Dodds
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mgibson,Mark Gibson
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mlafaver,Mark Lafaver
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mpeck,Mark Peck
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mpatenaude-monette,Martin Patenaude-Monette
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mheung,Mary Heung
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mjones,Mary Jones
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mbirarda,Matt Birarda
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mmichaud,Matt Michaud
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msmith,Matt Smith
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mmudge,Mckenzie Mudge
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mmccloskey,Meagan Mccloskey
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mboldenow,Megan Boldenow
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mchown,Melanie Chown
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mvezina,Melanie Vezina
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mwilson,Melanie Wilson
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mmcgarvey,Metta Mcgarvey
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mbwunder,Michael B. Wunder
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mevers,Michael Evers
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mharing,Michaela Haring
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mballvanzee,Michelangelo Ballvanzee
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mallen,Mike Allen
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mburrell,Mike Burrell
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mqrunnut,Mike Qrunnut
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mettuvgii,Mikhail Ettuvgii
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mtrottier-paquet,Myriam Trottier-Paquet
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nmveld,Naomi Manin'T Veld
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nhentze,Nathan Hentze
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nkirby,Nathan Kirby
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nrsenner,Nathan R. Senner
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nlecomte,Nicolas Lecomte
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ncook,Nicole Cook
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nmacdonald,Nicole MacDonald
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nboulanger-lapointe,Noémie Boulanger-Lapointe
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ojames,Oliver James
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ohicks,Olivia Hicks
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oguy,Other Guy
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proyer-boutin,Pascal Royer-Boutin
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pherzog,Patrick Herzog
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psmith,Paul Smith
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pwoodard,Paul Woodard
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pchilton,Penelope Chilton
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pbertrand,Philippe Bertrand
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rhildebrandt,Reid Hildebrandt
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rlanctot,Richard Lanctot
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rgates,River Gates
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rnakoochee,Roberta Nakoochee
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rhunnewell,Robin Hunnewell
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radugan,Ronan A. Dugan
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rharned,Ronnie Harned
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rchurchwell,Roy Churchwell
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rhammond,Ruby Hammond
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rburner,Ryan Burner
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sfranks,Samantha Franks
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sjeswiet,Sarah Jeswiet
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sneima,Sarah Neima
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ssaalfeld,Sarah Saalfeld
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sflemming,Scott Flemming
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sfreeman,Scott Freeman
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svartanyan,Sergey Vartanyan
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scarvey,Shannon Carvey
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smbillerman,Shawn M. Billerman
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sskinner,Shelby Skinner
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sschulte,Shiloh Schulte
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sbuckell,Simon Buckell
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ssapora,Slade Sapora
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sbrown,Stephen Brown
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sparmiter,Stephen Parmiter
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sbennett,Steve Bennett
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shart,Steve Hart
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skendall,Steve Kendall
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skolbe,Steve Kolbe
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svissault,Steve Vissault
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ssheedy,Sydney Sheedy
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tdoyle,Terry Doyle
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tfarrugia,Thomas Farrugia
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triecke,Thomas Riecke
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tmankis,Tobias Mankis
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tstclair,Toby St Clair
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tesson,Tommy Esson
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tkydd,Tyler Kydd
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tdonnelly,Tyrone Donnelly
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vamarualik,Valerie Amarualik
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vloverti,Vanessa Loverti
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vbaranyuk,Vasily Baranyuk
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vkokhanova,Vera Kokhanova
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vputinski,Victoria Putinski
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vjirinec,Vitek Jirinec
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wkennerley,Will Kennerley
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wenglish,Willow English
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yhhsu,Yu-Hsun Hsu (Echo)
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zharris,Zack Harris
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zlebrun-southcott,Zoe Lebrun-Southcott
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cmontgomerie,Claire Montgomerie
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emagnuson,Emily Magnuson
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mcorrell,Maureen Correll

data/schema-build-script.sql

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.nullvalue -NULL-
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CREATE TABLE Species (
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Code VARCHAR PRIMARY KEY,
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Common_name VARCHAR UNIQUE NOT NULL,
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Scientific_name VARCHAR, -- can't make NOT NULL, missing data in some rows
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Relevance VARCHAR
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);
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COPY Species FROM 'species.csv' (header TRUE);
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CREATE TABLE Site (
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Code VARCHAR PRIMARY KEY,
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Site_name VARCHAR UNIQUE NOT NULL,
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Location VARCHAR NOT NULL,
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Latitude FLOAT NOT NULL CHECK (Latitude BETWEEN -90 AND 90),
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Longitude FLOAT NOT NULL CHECK (Longitude BETWEEN -180 AND 180),
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Area FLOAT NOT NULL CHECK (Area > 0),
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UNIQUE (Latitude, Longitude)
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);
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COPY Site FROM 'site.csv' (header TRUE);
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CREATE TABLE Personnel (
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Abbreviation VARCHAR PRIMARY KEY,
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Name VARCHAR UNIQUE NOT NULL
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);
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COPY Personnel FROM 'personnel.csv' (header TRUE);
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CREATE TABLE Camp_assignment (
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Year INTEGER NOT NULL CHECK (Year BETWEEN 1950 AND 2015),
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Site VARCHAR NOT NULL,
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Observer VARCHAR NOT NULL,
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Start DATE,
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"End" DATE,
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FOREIGN KEY (Site) REFERENCES Site (Code),
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FOREIGN KEY (Observer) REFERENCES Personnel (Abbreviation),
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CHECK (Start <= "End"),
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CHECK (Start BETWEEN (Year||'-01-01')::DATE AND (Year||'-12-31')::DATE),
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CHECK ("End" BETWEEN (Year||'-01-01')::DATE AND (Year||'-12-31')::DATE)
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);
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COPY Camp_assignment FROM 'ASDN_Camp_assignment.csv' (header TRUE);
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CREATE TABLE Bird_nests (
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Book_page VARCHAR,
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Year INTEGER NOT NULL CHECK (Year BETWEEN 1950 AND 2015),
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Site VARCHAR NOT NULL,
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Nest_ID VARCHAR PRIMARY KEY,
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Species VARCHAR NOT NULL,
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Observer VARCHAR,
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Date_found DATE NOT NULL
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CHECK (
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Date_found BETWEEN (Year||'-01-01')::DATE
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AND (Year||'-12-31')::DATE
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),
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how_found VARCHAR CHECK (how_found IN ('searcher', 'rope', 'bander')),
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Clutch_max INTEGER CHECK (Clutch_max BETWEEN 0 AND 20),
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floatAge FLOAT CHECK (floatAge BETWEEN 0 AND 30),
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ageMethod VARCHAR CHECK (ageMethod IN ('float', 'lay', 'hatch')),
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FOREIGN KEY (Site) REFERENCES Site (Code),
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FOREIGN KEY (Species) REFERENCES Species (Code),
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FOREIGN KEY (Observer) REFERENCES Personnel (Abbreviation)
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);
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COPY Bird_nests FROM 'ASDN_Bird_nests.csv' (header TRUE);
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CREATE TABLE Bird_eggs (
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Book_page VARCHAR,
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Year INTEGER NOT NULL CHECK (Year BETWEEN 1950 AND 2015),
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Site VARCHAR NOT NULL,
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Nest_ID VARCHAR NOT NULL,
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Egg_num INTEGER NOT NULL CHECK (Egg_num BETWEEN 1 AND 20),
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Length FLOAT NOT NULL CHECK (Length > 0 AND Length < 100),
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Width FLOAT NOT NULL CHECK (Width > 0 AND Width < 100),
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PRIMARY KEY (Nest_ID, Egg_num),
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FOREIGN KEY (Site) REFERENCES Site (Code),
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FOREIGN KEY (Nest_ID) REFERENCES Bird_nests (Nest_ID)
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);
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COPY Bird_eggs FROM 'ASDN_Bird_eggs.csv' (header TRUE);

data/site.csv

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Code,Site name,Location,Latitude,Longitude,Total_Study_Plot_Area_(ha)
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barr,Barrow,"Alaska, USA",71.3,-156.6,220.4
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burn,Burntpoint Creek,"Ontario, Canada",55.2,-84.3,63.0
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bylo,Bylot Island,"Nunavut, Canada",73.2,-80.0,723.6
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cakr,Cape Krusenstern,"Alaska, USA",67.1,-163.5,54.1
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cari,Canning River Delta,"Alaska, USA",70.1,-145.8,722.0
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chau,Chaun River Delta,"Chukotka, Russia",68.8,170.6,248.2
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chur,Churchill,"Manitoba, Canada",58.7,-93.8,866.9
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coat,Coats Island,"Nunavut, Canada",62.9,-82.5,1239.1
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colv,Colville River Delta,"Alaska, USA",70.4,-150.7,324.8
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eaba,East Bay,"Nunavut, Canada",64.0,-81.7,1205.5
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iglo,Igloolik,"Nunavut, Canada",69.4,-81.6,59.8
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ikpi,Ikpikpuk,"Alaska, USA",70.6,-154.7,174.1
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lkri,Lower Khatanga River,"Krasnoyarsk, Russia",72.9,106.1,270.9
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made,Mackenzie River Delta,"Northwest Territories, Canada",69.4,-135.0,667.3
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nome,Nome,"Alaska, USA",64.4,-164.9,90.1
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prba,Prudhoe Bay,"Alaska, USA",70.3,-148.6,120.0

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