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species.R
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species.R
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library(data.table)
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#' See [species].
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species_matrix <- matrix(
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data = c(
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"abrachyrhynchus", "unknown", "Pink-footed goose",
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"acalliptera", "unknown", "Eastern happy",
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"acarolinensis", "shortlived", "Anole lizard",
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"acchrysaetos", "unknown", "Golden eagle", # (bird, Aquila chrysaetos chrysaetos)
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"acitrinellus", "unknown", "Midas child", # (fish)
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"amelanoleuca", "positive", "Panda",
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"amexicanus", "leaveout", "Mexican tetra", # (fish)
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"anancymaae", "unknown", "Ma's night monkey",
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"aocellaris", "unknown", "Clown anemonefish", # (fish)
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"apercula", "unknown", "Orange clownfish",
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"aplatyrhynchos", "shortlived", "Duck",
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"apolyacanthus", "unknown", "Spiny chromis", # (fish)
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"applatyrhynchos", "unknown", "Duck",
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"atestudineus", "unknown", "Climbing perch",
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"bbbison", "unknown", "American bison",
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"bgrunniens", "unknown", "Yak",
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"bihybrid", "replicative", "Bos indicus hybrid",
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"bmusculus", "unknown", "Blue whale",
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"bmutus", "unknown", "Wild yak",
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"bsplendens", "unknown", "Siamese fighting fish",
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"btaurus", "replicative", "Cow",
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"bthybrid", "replicative", "Bos taurus hybrid",
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"cabingdonii", "unknown", "Abington island giant tortoise",
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"capalliatus", "unknown", "Angola colobus", # (primate)
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"caperea", "unknown", "Brazilian guinea pig",
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"catys", "unknown", "Sooty mangabey",
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"cauratus", "unknown", "Goldfish", # (fish)
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"ccaeruleus", "unknown", "Blue tit", # (bird)
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"ccapucinus", "unknown", "Capuchin",
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"ccarpio", "unknown", "Common carp", # (fish)
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"cdromedarius", "unknown", "Arabian camel",
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"celegans", "shortlived", "Worm",
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"cfamiliaris", "replicative", "Dog",
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"cgchok1gshd", "unknown", "Chinese hamster",
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"cgobio", "unknown", "Channel bull blenny", # (fish)
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"cgpicr", "unknown", "Chinese hamster (PICR)",
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"charengus", "unknown", "Atlantic herring", # (fish)
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"chircus", "replicative", "Goat",
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"choffmanni", "positive", "Sloth", # lifespan 20-30 years
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"chyarkandensis", "unknown", "Yarkand deer",
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"cintestinalis", "leaveout", "Ciona intestinalis",
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"cjacchus", "replicative", "Marmoset",
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"cjaponica", "unknown", "Japanese quail",
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"clanigera", "unknown", "Long-tailed chinchilla",
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"cldingo", "unknown", "Dingo",
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"clfamiliaris", "replicative", "Dog",
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"clumpus", "unknown", "Lumpfish", # (fish)
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"cmilii", "unknown", "Elephant shark", # (fish)
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"cpbellii", "unknown", "Painted turtle",
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"cporcellus", "shortlived", "Guinea pig",
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"cporosus", "unknown", "Australian saltwater crocodile",
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"cpugnax", "unknown", "Ruff", # (bird)
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"csabaeus", "replicative", "African Green Monkey", # (Chlorocebus sabaeus)
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"csavignyi", "negative", "Ciona savignyi", # (early deep sea)
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"csemilaevis", "unknown", "Tongue sole", # (fish)
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"csyrichta", "unknown", "Tarsier",
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"cvariegatus", "unknown", "Sheepshead minnow", # (fish)
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"cwagneri", "unknown", "Chacoan peccary", # (pig)
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"dclupeoides", "unknown", "Denticle herring",
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"dlabrax", "unknown", "European seabass", # (fish)
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"dleucas", "unknown", "Beluga whale", # (mammal)
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"dmelanogaster", "shortlived", "Fruitfly",
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"dnovemcinctus", "negative", "Armadillo",
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"dordii", "shortlived", "Kangaroo rat",
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"drerio", "shortlived", "Zebrafish",
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"eaasinus", "unknown", "Donkey",
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"eburgeri", "unknown", "Hagfish", # (fish)
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"ecaballus", "replicative", "Horse",
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"ecalabaricus", "unknown", "Reedfish", # (fish)
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"eelectricus", "unknown", "Electric eel", # (fish)
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"eeuropaeus", "shortlived", "Hedgehog",
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"elucius", "unknown", "Northern pike", # (fish)
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"enaucrates", "unknown", "Live sharksucker", # (fish)
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"etelfairi", "shortlived", "Lesser hedgehog tenrec",
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"falbicollis", "leaveout", "Flycatcher", # (bird)
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"fcatus", "replicative", "Cat",
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"fheteroclitus", "unknown", "Mummichog", # (fish)
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"gaculeatus", "leaveout", "Stickleback", # (fish)
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"gaffinis", "unknown", "Western mosquitofish", # (fish)
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"gevgoodei", "unknown", "Goodes thornscrub tortoise",
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"gfortis", "unknown", "Medium gound-finch", # (bird)
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"ggallus", "shortlived", "Chicken",
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"ggorilla", "replicative", "Gorilla",
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"gmorhua", "leaveout", "Cod",
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"gwilldenowi", "unknown", "Blunt-snouted clingfish",
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"hburtoni", "unknown", "Burton's mouthbrooder", # (fish)
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"hcomes", "unknown", "Tiger sail seahorse",
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"hgfemale", "unknown", "Naked mole-rat female",
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"hhucho", "unknown", "Huchen", # (fish)
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"hsapiens", "replicative", "Human",
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"ipunctatus", "unknown", "Channel catfish", # (fish)
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"itridecemlineatus", "shortlived", "Squirrel",
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"jhyemalis", "unknown", "Dark-eyed junco", # (bird)
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"jjaculus", "unknown", "Lesser Egyptian jerboa", # (rodent)
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"kmarmoratus", "unknown", "Mangrove rivulus", # (fish)
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"lafricana", "replicative", "Elefant",
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"lbergylta", "unknown", "Ballan wrasse", # (fish)
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"lcalcarifer", "unknown", "Barramundi perch", # (fish)
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"lcanadensis", "unknown", "Lynx",
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"lchalumnae", "leaveout", "Coelacanth", # (fish)
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"lcrocea", "unknown", "Large yellow croaker", # (fish)
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"llaticaudata", "unknown", "Blue-ringed sea krait", # (snake)
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"lleishanense", "unknown", "Leishan spiny toad", # (reptile)
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"loculatus", "leaveout", "Spotted gar", # (fish)
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"marmatus", "unknown", "Zig-zag eel", # (fish)
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"mauratus", "unknown", "Golden Hamster", # (rodent)
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"mcaroli", "unknown", "Ryukyu mouse", # (rodent)
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"mdomestica", "leaveout", "Mus m. domesticus",
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"meugenii", "negative", "Wallaby",
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"mfascicularis", "replicative", "Crab-eating macaque",
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"mfuro", "shortlived", "Ferret", # (rodent)
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"mgallopavo", "shortlived", "Turkey", # (bird)
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"mleucophaeus", "unknown", "Drill", # (primate)
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"mlucifugus", "shortlived", "Microbat",
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"mmmarmota", "unknown", "Alpine marmot",
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"mmola", "unknown", "Ocean sunfish", # (fish)
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"mmonoceros", "unknown", "Narwhal", # (mammal)
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"mmoschiferus", "unknown", "Siberian musk deer",
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"mmulatta", "replicative", "Macaque", # (primate)
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"mmurdjan", "unknown", "Pinecone soldierfish", # (fish)
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"mmurinus", "replicative", "Lemur", # - of particular interest since so small but a primate
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"mmusculus", "negative", "Mouse", # (rodent)
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"mnemestrina", "replicative", "Pig-tailed macaque", # (primate)
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"mochrogaster", "unknown", "Prairie vole", # (rodent)
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"mpahari", "unknown", "Shrew mouse", # (rodent)
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"mpfuro", "unknown", "Ferret", # (rodent)
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"mspicilegus", "unknown", "Steppe mouse", # (rodent)
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"mspretus", "unknown", "Algerian mouse", # (rodent)
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"mundulatus", "unknown", "Budgerigar",
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"mvitellinus", "unknown", "Golden-collared manakin",
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"mzebra", "unknown", "Zebra mbuna", # (fish)
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"nbrichardi", "unknown", "Lyretail cichlid", # (fish)
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"neugenii", "unknown", "Wallaby",
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"nfurzeri", "unknown", "Turquoise killifish", # (fish)
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"ngalili", "unknown", "Upper Galilee mountains blind mole rat",
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"nleucogenys", "replicative", "Gibbon",
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"nmeleagris", "unknown", "Helmeted guineafowl", # (bird)
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"nnaja", "unknown", "Indian cobra", # (snake)
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"nscutatus", "unknown", "Mainland tiger snake",
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"nvison", "unknown", "American mink",
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"oanatinus", "negative", "Platypus",
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"oarambouillet", "unknown", "Sheep",
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"oaries", "replicative", "Sheep (texel)",
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"ocuniculus", "unknown", "Rabbit",
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"odegus", "unknown", "Degu",
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"ogarnettii", "positive", "Bushbaby", # (https://en.wikipedia.org/wiki/Galago)
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"ojavanicus", "unknown", "Javanese ricefish", # (fish)
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"okisutch", "unknown", "Coho salmon", # (fish)
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"olatipes", "leaveout", "Japahese rice fish", # (fish - Oryzias latipes)
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"olhni", "unknown", "Japanese rice fish (HNI)", # (fish)
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"olhsok", "unknown", "Japanese rice fish", # (fish)
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"omelastigma", "unknown", "Indian rice fish", # (fish)
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"omykiss", "unknown", "Oncorhynchus mykiss", # (fish)
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"oniloticus", "leaveout", "Nile tilapia", # (fish - Oreochromis niloticus)
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"oprinceps", "shortlived", "Pika", # (Ochotona princeps) (https://en.wikipedia.org/wiki/Pika) - max age 7 years, closest to rabbits
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"osinensis", "unknown", "Chinese medaka", # (fish)
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"otshawytscha", "unknown", "Chinook salmon", # (fish)
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"pabelii", "replicative", "Orang utan", # # (primate)
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"panubis", "replicative", "Olive baboon",
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"pcapensis", "shortlived", "Hyrax", # (mammal)
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"pcatodon", "unknown", "Sperm whale", # (mammal)
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"pcinereus", "unknown", "Koala", # (mammal)
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"pcoquereli", "unknown", "Coquerel's sifaka",
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"pformosa", "leaveout", "Amazon mollie", # (fish)
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"pkingsleyae", "unknown", "P. kingsleyae", # (fish) # Paramormyrops kingsleyae
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"platipinna", "unknown", "Sailfin molly", # (fish)
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"pleo", "unknown", "Lion",
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"pmajor", "unknown", "Great Tit", # (bird)
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"pmarinus", "leaveout", "Lamprey", # (https://en.wikipedia.org/wiki/Lamprey) (Neunaugen) (fish)
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"pmbairdii", "unknown", "Northern American deer mouse", # latin broken
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"pmuralis", "unknown", "Common wall lizard", # (reptile)
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"pnattereri", "unknown", "Red-bellied piranha", # (fish)
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"pnyererei", "unknown", "Makobe Island cichlid", # (fish)
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"ppaniscus", "replicative", "Bonobo",
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"ppardus", "unknown", "Leopard",
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"pranga", "unknown", "Indian glassy fish", # (fish)
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"preticulata", "unknown", "Guppy", # (fish)
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"psimus", "unknown", "Greater bamboo lemur", # (primate)
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"psinensis", "maybe", "Chinese softshell turtle", # (https://en.wikipedia.org/wiki/Chinese_softshell_turtle)
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"psinus", "unknown", "Vaquita", # (mammal)
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"ptaltaica", "unknown", "Tiger",
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"ptephrosceles", "unknown", "Ugandan red Colobus",
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"ptextilis", "unknown", "Eastern brown snake", # (snake)
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"ptroglodytes", "replicative", "Chimp", # (primate)
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"pvampyrus", "unknown", "Megabat",
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# "pvampyrus", "leaveout", "Megabat", # incomplete Ensembl build
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"rbieti", "unknown", "Black snub-nosed monkey", # (primate)
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"rferrumequinum", "unknown", "Greater horseshoe bat",
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"rnorvegicus", "negative", "Rat", # (rodent)
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"rroxellana", "unknown", "Golden snub-nosed monkey", # (primate)
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"saraneus", "shortlived", "Shrew", # (https://en.wikipedia.org/wiki/Shrew)
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"saurata", "unknown", "Gilthead seabream", # (fish)
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"sbboliviensis", "unknown", "Bolivian squirrel monkey", # (primate)
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"scanaria", "unknown", "Common canary", # (bird)
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"scaustralis", "unknown", "African austrich", # (bird)
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"scerevisiae", "shortlived", "Yeast",
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"sdumerili", "unknown", "Greater amberjack", # (fish)
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"sfasciatus", "unknown", "Jewelled Blenny", # (fish)
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"sformosus", "unknown", "Asian arowana", # (fish)
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"sgrahami", "unknown", "Golden-line barbel", # (fish)
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"shabroptila", "unknown", "Kakapo (parrot)", # (bird)
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"sharrisii", "shoatlived", "Tasmanian devil",
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"sldorsalis", "unknown", "Yellowtail amberjack", # (fish)
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"slucioperca", "unknown", "Pike-perch", # (fish)
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"smaximus", "unknown", "Turbot", # (fish)
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"smerianae", "unknown", "Argentine black and white tegu", # (fish)
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"sorbicularis", "unknown", "Orbiculate cardinalfish",
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"spunctatus", "unknown", "Tuatara",
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"spartitus", "unknown", "Bicolor damselfish", # (fish)
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"ssalar", "unknown", "Atlantic salmon", # (fish)
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"sscrofa", "replicative", "Pig", # (mammal)
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"strutta", "unknown", "River trout", # (fish)
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"svulgaris", "unknown", "Eurasian red squirrel", # (rodent)
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"tbelangeri", "leaveout", "Tree shrew", # (https://en.wikipedia.org/wiki/Treeshrew)
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"tctriunguis", "unknown", "Three-toad box turtle", # (reptile)
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"tgelada", "replicative", "Gelada", # (primate)
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"tguttata", "shortlived", "Zebra finch", # (bird)
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"tnigroviridis", "leaveout", "Tetraodon", # (fish)
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"trubripes", "leaveout", "Fugu", # (fish)
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"tsyrichta", "leaveout", "Tarsius/Carlito syrichta", # (https://en.wikipedia.org/wiki/Tarsier)
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"ttruncatus", "maybe", "Dolphin", # (mammal)
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"uamericanus", "unknown", "American black bear", # (mammal)
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"umaritimus", "unknown", "Polar bear", # (mammal)
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"uparryii", "unknown", "Arctic ground squirrel", # (rodent)
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"vpacos", "maybe", "Alpaca", # (https://en.wikipedia.org/wiki/Alpaca)
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"vursinus", "unknown", "Common wombat",
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"vvulpes", "unknown", "Red fox", # (mammal)
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"xcouchianus", "unknown", "Monterrey platyfish",
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"xmaculatus", "shortlived", "Platyfish ",
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"xtropicalis", "shortlived", "Frog", # (reptile)
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"zalbicollis", "unknown", "White-throated sparrow" # (bird)
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),
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ncol = 3,
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byrow = TRUE,
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)
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colnames(species_matrix) <- c("id", "group", "label")
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#' Constant data on species in Ensembl Mart.
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#'
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#' This is a data table with the following columns:
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#' - `id`: An unique identifier for the species (based on the latin name).
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#' - `group`: Whether and how the species has replicative aging.
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#' - `label`: A human readable, english label.
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species <- data.table(species_matrix)
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