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Merge pull request #8 from ealarsen/abund-el
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Merge new work from working branch.
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ealarsen authored May 11, 2023
2 parents a6c6edb + 364b82e commit 1f6519b
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187 changes: 187 additions & 0 deletions NABA_abund_taxa.csv
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"","group","ScientificName","CommonName","count.recs","mean.abund"
"1","RE","Thymelicus lineola","European Skipper",2568,521.993380062305
"2","RE","Satyrium calanus","Banded Hairstreak",2412,13.9705638474295
"3","RE","Satyrium titus","Coral Hairstreak",1914,7.45036572622779
"4","RE","Satyrium liparops","Striped Hairstreak",1253,3.62330407023144
"5","RE","Satyrium acadica","Acadian Hairstreak",797,11.6863237139272
"6","RE","Satyrium edwardsii","Edwards' Hairstreak",785,24.6853503184713
"7","RE","Lycaena hyllus","Bronze Copper",776,4.75
"8","RE","Satyrium caryaevorum","Hickory Hairstreak",584,5.78938356164384
"9","RE","Lycaena epixanthe","Bog Copper",420,68.6904761904762
"10","RE","Satyrium","Satyrium",141,4.97872340425532
"11","RE","Lycaeides melissa samuelis","'Karner' Melissa Blue",109,82.954128440367
"12","RE","Lycaena dione","Gray Copper",85,3.65882352941176
"13","RE","Lycaena helloides","Purplish Copper",85,5.03529411764706
"14","RE","Lycaena dorcas","Dorcas Copper",77,19.038961038961
"15","RE","Satyrium favonius ontario","'Northern' Oak Hairstreak",50,2.12
"16","RE","Lycaeides idas","Northern Blue",29,45.6551724137931
"17","RE","Satyrium favonius","Oak Hairstreak",28,1.92857142857143
"18","RE","Satyrium favonius favonius","'Southern' Oak Hairstreak",21,1.38095238095238
"19","RE","Lycaeides melissa","Melissa Blue",16,58.5
"20","RE","Hesperia comma","Common Branded Skipper",14,1.64285714285714
"21","RL","Phyciodes tharos","Pearl Crescent",5433,63.5422418553285
"22","RL","Colias eurytheme","Orange Sulphur",5126,45.8536870854467
"23","RL","Colias philodice","Clouded Sulphur",4954,48.045014129996
"24","RL","Everes comyntas","Eastern Tailed-Blue",4789,40.4234704531217
"25","RL","Speyeria cybele","Great Spangled Fritillary",4703,40.7010418881565
"26","RL","Cercyonis pegala","Common Wood-Nymph",4310,58.1408352668213
"27","RL","Euphyes vestris","Dun Skipper",4229,27.6214235043746
"28","RL","Ancyloxypha numitor","Least Skipper",4031,19.7685437856611
"29","RL","Limenitis archippus","Viceroy",3934,8.40747330960854
"30","RL","Megisto cymela","Little Wood-Satyr",3738,32.4232209737828
"31","RL","Limenitis arthemis astyanax","Red-spotted Purple",3684,17.6224212812161
"32","RL","Wallengrenia egeremet","Northern Broken-Dash",3033,17.0956149027366
"33","RL","Anatrytone logan","Delaware Skipper",2825,12.4722123893805
"34","RL","Enodia anthedon","Northern Pearly-eye",2707,8.64351680827484
"35","RL","Erynnis horatius","Horace's Duskywing",2405,31.8794178794179
"36","RL","Asterocampa celtis","Hackberry Emperor",2264,61.2875441696113
"37","RL","Lycaena phlaeas","American Copper",2153,31.618671620994
"38","RL","Satyrodes appalachia","Appalachian Brown",1982,9.4021190716448
"39","RL","Erynnis baptisiae","Wild Indigo Duskywing",1905,14.3459317585302
"40","RL","Boloria bellona","Meadow Fritillary",1881,16.3014354066986
"41","RL","Polites origenes","Crossline Skipper",1792,5.99330357142857
"42","RL","Satyrodes eurydice","Eyed Brown",1777,21.4991558806978
"43","RL","Thorybes pylades","Northern Cloudywing",1623,4.65187923598275
"44","RL","Pholisora catullus","Common Sootywing",1555,9.64565916398714
"45","RL","Asterocampa clyton","Tawny Emperor",1545,68.4932038834951
"46","RL","Euphydryas phaeton","Baltimore Checkerspot",1434,31.1338912133891
"47","RL","Chlosyne nycteis","Silvery Checkerspot",1431,24.3221523410203
"48","RL","Polites mystic","Long Dash",1420,13.8415492957746
"49","RL","Poanes hobomok","Hobomok Skipper",1377,8.24328249818446
"50","RL","Speyeria aphrodite","Aphrodite Fritillary",1376,19.374273255814
"51","RL","Thorybes bathyllus","Southern Cloudywing",1363,5.33382245047689
"52","RL","Calycopis cecrops","Red-banded Hairstreak",1338,9.65844544095665
"53","RL","Pyrgus communis","Common Checkered-Skipper",1147,9.4202266782912
"54","RL","Phyciodes selenis","Northern Crescent",1145,90.7257641921397
"55","RL","Poanes zabulon","Zabulon Skipper",1103,13.2284678150499
"56","RL","Limenitis arthemis arthemis","White Admiral",1067,20.1490159325211
"57","RL","Poanes viator","Broad-winged Skipper",1037,37.1957569913211
"58","RL","Achalarus lyciades","Hoary Edge",952,5.33088235294118
"59","RL","Poanes massasoit","Mulberry Wing",870,14.0735632183908
"60","RL","Euphyes conspicua","Black Dash",849,13.7290930506478
"61","RL","Boloria selene","Silver-bordered Fritillary",815,6.31411042944785
"62","RL","Coenonympha tullia","Common Ringlet",765,29.5450980392157
"63","RL","Euphyes dion","Dion Skipper",726,5.59228650137741
"64","RL","Speyeria atlantis","Atlantis Fritillary",673,22.3551263001486
"65","RL","Cyllopsis gemma","Gemmed Satyr",492,3.66463414634146
"66","RL","Speyeria","Speyeria",428,16.7733644859813
"67","RL","Limenitis arthemis","Red-spotted Admiral",370,45.5513513513514
"68","RL","Colias interior","Pink-edged Sulphur",365,31.2
"69","RL","Enodia portlandia","Southern Pearly-eye",337,4.2700296735905
"70","RL","Erynnis","Erynnis",319,3.96238244514107
"71","RL","Amblyscirtes vialis","Common Roadside-Skipper",312,4.04487179487179
"72","RL","Amblyscirtes aesculapius","Lace-winged Roadside-Skipper",286,4.07342657342657
"73","RL","Staphylus hayhurstii","Hayhurst's Scallopwing",283,3.34982332155477
"74","RL","Chlosyne harrisii","Harris' Checkerspot",279,7.60573476702509
"75","RL","Erynnis icelus","Dreamy Duskywing",264,4.75378787878788
"76","RL","Panoquina panoquin","Salt Marsh Skipper",261,69.27969348659
"77","RL","Erynnis juvenalis","Juvenal's Duskywing",259,4.87258687258687
"78","RL","Problema byssus","Byssus Skipper",238,7.97899159663866
"79","RL","Thorybes confusis","Confused Cloudywing",233,2.70386266094421
"80","RL","Calephelis virginiensis","Little Metalmark",230,7.4
"81","RL","Colias","Colias",227,18.9030837004405
"82","RL","Coenonympha tullia inornata","'Inornate' Common Ringlet",216,36.75
"83","RL","Speyeria diana","Diana Fritillary",210,8.03333333333333
"84","RL","Enodia creola","Creole Pearly-eye",192,3.765625
"85","RL","Hesperia sassacus","Indian Skipper",179,3.84916201117318
"86","RL","Neonympha areolata","Georgia Satyr",176,13.3181818181818
"87","RL","Poanes aaroni","Aaron's Skipper",147,53.578231292517
"88","RL","Carterocephalus palaemon","Arctic Skipper",144,7.84027777777778
"89","RL","Euphyes bimacula","Two-spotted Skipper",140,6.64285714285714
"90","RL","Chlosyne gorgone","Gorgone Checkerspot",138,10.0579710144928
"91","RL","Calephelis borealis","Northern Metalmark",115,18.8695652173913
"92","RL","Phyciodes batesii","Tawny Crescent",101,3.6039603960396
"93","RL","Boloria","Boloria",100,3.47
"94","RL","Euphyes arpa","Palmetto Skipper",100,7.74
"95","RL","Poanes yehl","Yehl Skipper",99,5.65656565656566
"96","RL","Erynnis lucilius","Columbine Duskywing",98,22.1428571428571
"97","RL","Euphyes dukesi","Dukes' Skipper",83,6.60240963855422
"98","RL","Erynnis funeralis","Funereal Duskywing",82,4.03658536585366
"99","RL","Euphyes pilatka","Palatka Skipper",81,2.87654320987654
"100","RL","Speyeria idalia","Regal Fritillary",75,109.946666666667
"101","RL","Problema bulenta","Rare Skipper",74,14.7027027027027
"102","RL","Polites baracoa","Baracoa Skipper",72,17.4027777777778
"103","RL","Erynnis martialis","Mottled Duskywing",68,3.32352941176471
"104","RL","Polygonus leo","Hammock Skipper",56,10.6071428571429
"105","RL","Amblyscirtes hegon","Pepper and Salt Skipper",53,2.18867924528302
"106","RL","Euphyes berryi","Berry's Skipper",49,4.12244897959184
"107","RL","Thorybes","Thorybes",47,1.78723404255319
"108","RL","Asterocampa","Asterocampa",43,2.13953488372093
"109","RL","Calephelis mutica","Swamp Metalmark",40,8.05
"110","RL","Atrytonopsis hianna","Dusted Skipper",38,2.60526315789474
"111","RL","Plebejus saepiolus","Greenish Blue",38,7.84210526315789
"112","RL","Amblyscirtes carolina","Carolina Roadside-Skipper",31,14.3870967741935
"113","RL","Hesperia attalus","Dotted Skipper",30,5.43333333333333
"114","RL","Speyeria atlantis atlantis","'Atlantis' Atlantis Fritillary",30,13.2
"115","RL","Amblyscirtes belli","Bell's Roadside-Skipper",27,2.44444444444444
"116","RL","Amblyscirtes reversa","Reversed Roadside-Skipper",27,5.51851851851852
"117","RL","Erynnis brizo","Sleepy Duskywing",25,1.8
"118","RL","Chlosyne","Chlosyne",24,7.83333333333333
"119","RL","Amblyscirtes alternata","Dusky Roadside-Skipper",21,1.76190476190476
"120","RL","Hesperia meskei","Meske's Skipper",20,3.5
"121","RL","Megathymus cofaqui","Cofaqui Giant-Skipper",16,1.75
"122","RL","Hesperia leonardus","Leonard's Skipper",15,6.53333333333333
"123","RL","Oeneis jutta","Jutta Arctic",15,4.93333333333333
"124","RL","Strymon martialis","Martial Scrub-Hairstreak",15,1.93333333333333
"125","RL","Oarisma poweshiek","Poweshiek Skipperling",13,9
"126","RL","Everes amyntula","Western Tailed-Blue",10,7.9
"127","RL","Oeneis macounii","Macoun's Arctic",10,3.9
"128","RL","Poanes","Poanes",8,1.25
"129","RL","Boloria eunomia","Bog Fritillary",7,3
"130","RL","Oeneis chryxus","Chryxus Arctic",5,6.2
"131","RL","Oeneis melissa","Melissa Arctic",5,61.8
"132","RL","Limenitis arthemis artXast","Hybrid arthemisXastyanax",4,2.25
"133","RL","Euphyes","Euphyes",3,9
"134","RL","Boloria freija","Freija Fritillary",2,3
"135","RL","Boloria frigga","Frigga Fritillary",2,7
"136","RL","Erebia rossii","Ross' Alpine",2,6.5
"137","RL","Neonympha mitchellii","Mitchell's Satyr",2,2
"138","RL","Oeneis polixenes","Polixenes Arctic",2,9
"139","RL","Colias gigantea","Giant Sulphur",1,1
"140","RL","Colias nastes","Labrador Sulphur",1,5
"141","RL","Colias palaeno","Palaeno Sulphur",1,1
"142","RL","Pyrgus centaureae","Grizzled Skipper",1,3
"143","RP","Pieris rapae","Cabbage White",5470,170.783729433272
"144","RP","Papilio glaucus","Eastern Tiger Swallowtail",5383,26.0926992383429
"145","RP","Epargyreus clarus","Silver-spotted Skipper",5253,42.2109270892823
"146","RP","Papilio polyxenes","Black Swallowtail",4443,9.25455773126266
"147","RP","Papilio troilus","Spicebush Swallowtail",4152,15.895472061657
"148","RP","Celastrina ladon neglecta","'Summer' Spring Azure",3575,22.9264335664336
"149","RP","Strymon melinus","Gray Hairstreak",2762,9.43374366401159
"150","RP","Polites themistocles","Tawny-edged Skipper",2543,7.19150609516319
"151","RP","Battus philenor","Pipevine Swallowtail",1930,15.7678756476684
"152","RP","Papilio cresphontes","Giant Swallowtail",1452,6.62741046831956
"153","RP","Eurytides marcellus","Zebra Swallowtail",1297,17.6622976098689
"154","RP","Celastrina ladon","Spring Azure",1265,9.90197628458498
"155","RP","Lerema accius","Clouded Skipper",1074,9.47299813780261
"156","RP","Papilio canadensis","Canadian Tiger Swallowtail",671,13.6661698956781
"157","RP","Pieris napi","Mustard White",406,20.5467980295567
"158","RP","Callophrys gryneus","Juniper Hairstreak",379,6.5778364116095
"159","RP","Leptotes cassius","Cassius Blue",345,47.231884057971
"160","RP","Callophrys gryneus gryneus","'Olive' Juniper Hairstreak",291,6.40549828178694
"161","RP","Parrhasius m-album","White M Hairstreak",258,2.32170542635659
"162","RP","Glaucopsyche lygdamus","Silvery Blue",187,13.7593582887701
"163","RP","Papilio","Papilio",148,4.35135135135135
"164","RP","Atlides halesus","Great Purple Hairstreak",147,3.64625850340136
"165","RP","Pieris","Pieris",83,6.1566265060241
"166","RP","Brephidium isophthalma","Eastern Pygmy-Blue",81,30.2962962962963
"167","RP","Celastrina ladon ladon","'Spring' Spring Azure",79,12.0379746835443
"168","RP","Celastrina neglectamajor","Appalachian Azure",71,9.02816901408451
"169","RP","Pieris napi oleracea","'Veined' Mustard White",71,11.2676056338028
"170","RP","Nastra neamathla","Neamathla Skipper",53,2.05660377358491
"171","RP","Celastrina","Celastrina",45,5.06666666666667
"172","RP","Autochton cellus","Golden Banded-Skipper",39,10.9487179487179
"173","RP","Callophrys niphon","Eastern Pine Elfin",39,26
"174","RP","Callophrys augustinus","Brown Elfin",21,4.61904761904762
"175","RP","Callophrys","Callophrys",11,23.4545454545455
"176","RP","Callophrys hesseli","Hessel's Hairstreak",10,1
"177","RP","Callophrys eryphon","Western Pine Elfin",7,9.14285714285714
"178","RP","Callophrys polios","Hoary Elfin",7,1.57142857142857
"179","RP","Papilio aristodemus","Schaus' Swallowtail",5,3.8
"180","RP","Callophrys henrici","Henry's Elfin",3,1.33333333333333
"181","RP","Callophrys irus","Frosted Elfin",2,1
"182","RP","Euchloe olympia","Olympia Marble",2,2.5
"183","RP","Anthocharis midea","Falcate Orangetip",1,2
"184","RP","Callophrys gryneus sweadneri","'Sweadner's' Juniper Hairstreak",1,1
"185","RP","Celastrina ladon humulus","'Hops' Spring Azure",1,8
"186","RP","Celastrina ladon serotina","'Cherry-gall' Spring Azure",1,1
15 changes: 14 additions & 1 deletion code/abundance_analysis.R
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ theme_set(theme_sjplot())
###PHENO DATA
load("data/derived/pheno.RData")
#### ENV DATA
load("data/derived/env.input.RData")
load("data/derived/env.input.new.RData")
pheno1<-pheno.quant %>%
dplyr::select(q50,year,cell,code)

Expand Down Expand Up @@ -68,6 +68,19 @@ naba.1<-naba.1 %>% mutate(MonthF=as.factor(ObsMonth), ObsDay=as.numeric(format(a

save(naba.1, file="data/abund.input1005.RData")

(n.cellyr.summary<-naba.1 %>%
group_by(cell, code) %>%
summarize(x1=1) %>%
group_by(code) %>%
summarize(cs1=sum(x1))
)

(pdev.sum<-pheno.dev %>%
group_by(cell, code) %>%
summarize(x1=1) %>%
group_by(code) %>%
summarize(cs1=sum(x1))
)

ggplot(data=naba.1, aes(x=onset.dev, y=log.abund, color=code)) +
geom_smooth(method="lm")
Expand Down
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