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jamesgrecian/habitat preference gam.r

Last active August 15, 2018 20:40
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Example script to generate habitat preference GAM using telemetry data and random pseudo-absence points
Raw
habitat preference gam.r
#####################################################
### Some pointers for habitat preference analysis ###
#####################################################
#Load in libraries
require(sf)
require(tidyverse)
require(viridis)
require(rworldmap)
require(raster)
require(gdistance)
#Define projection - UTM 30N in this case
prj = "+proj=utm +zone=30 +ellps=WGS84 +datum=WGS84 +units=m +no_defs"
#Load in the world shapefile from rworldmap and force to same CRS as the telemetry data will be...
CP <- as(raster::extent(-20, 10, 45, 65), "SpatialPolygons")
proj4string(CP) <- sp::CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
proj4string(countriesLow) <- sp::CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
world_shp <- rgeos::gIntersection(countriesLow, CP, byid=T, drop_lower_td = T)
world_utm = sp::spTransform(world_shp, CRS(prj))
#Most habitat preference analysis of telemetry data centres on comparing presence locations (the locations)
#with absence data (pseudo-absences generated according to some principles)
#Load in some example telemetry data
dat <- structure(list(DateTime = structure(c(1437739920, 1437740520,
1437741120, 1437741720, 1437742320, 1437742920, 1437743520, 1437744120,
1437744720, 1437745320, 1437745920, 1437746520, 1437747120, 1437747720,
1437748320, 1437748920, 1437749520, 1437750120, 1437750720, 1437751320,
1437751920, 1437752520, 1437753120, 1437753720, 1437754320, 1437754920,
1437755520, 1437756120, 1437756720, 1437757320, 1437757920, 1437758520,
1437759120, 1437759720, 1437760320, 1437760920, 1437761520, 1437762120,
1437762720, 1437763320, 1437763920, 1437764520, 1437765120, 1437765720,
1437766320, 1437766920, 1437767520, 1437768120, 1437768720, 1437769320,
1437769920, 1437770520, 1437771120, 1437771720, 1437772320, 1437772920,
1437773520, 1437774120, 1437774720, 1437775320, 1437775920, 1437776520,
1437777120, 1437777720, 1437778320, 1437778920, 1437779520, 1437780120,
1437780720, 1437781320, 1437781920, 1437782520, 1437783120, 1437783720,
1437784320, 1437784920, 1437785520, 1437786120, 1437786720, 1437787320,
1437787920, 1437788520, 1437789120, 1437789720, 1437790320, 1437790920,
1437791520, 1437792120, 1437792720, 1437793320, 1437793920, 1437794520,
1437795120, 1437795720, 1437796320, 1437796920, 1437797520, 1437798120,
1437798720, 1437799320, 1437799920, 1437800520, 1437801120, 1437801720,
1437802320, 1437802920, 1437803520, 1437804120, 1437804720, 1437805320,
1437805920, 1437806520, 1437807120, 1437807720, 1437808320, 1437808920,
1437809520, 1437810120, 1437810720, 1437811320, 1437811920, 1437812520,
1437813120, 1437813720, 1437814320, 1437814920, 1437815520, 1437816120,
1437816720, 1437817320, 1437817920, 1437818520, 1437819120, 1437819720,
1437820320, 1437820920, 1437821520, 1437822120, 1437822720, 1437823320,
1437823920, 1437824520, 1437825120, 1437825720, 1437826320, 1437826920,
1437827520, 1437828120, 1437828720, 1437829320, 1437829920, 1437935340,
1437935940, 1437936540, 1437937140, 1437937740, 1437938340, 1437938940,
1437939540, 1437940140, 1437940740, 1437941340, 1437941940, 1437942540,
1437943140, 1437943740, 1437944340, 1437944940, 1437945540, 1437946140,
1437946740, 1437947340, 1437947940, 1437948540, 1437949140, 1437949740,
1437950340, 1437950940, 1437951540, 1437952140, 1437952740, 1437953340,
1437953940, 1437954540, 1437955140, 1437955740, 1437956340, 1437956940,
1437957540, 1437958140, 1437958740, 1437959340, 1437959940, 1437960540,
1437961140, 1437961740, 1437962340, 1437962940, 1437963540, 1437964140,
1437964740, 1437965340, 1437965940, 1437966540, 1437967140, 1437967740,
1437968340, 1437968940, 1437969540, 1437970140, 1437970740, 1437971340,
1437971940, 1437972540, 1437973140, 1437973740, 1437974340, 1437974940,
1437975540, 1437976140, 1437976740, 1437977340, 1437977940, 1437978540,
1437979140, 1437979740, 1437980340, 1437980940, 1437981540, 1437982140,
1437982740, 1437983340, 1437983940, 1437984540, 1437985140, 1437985740,
1437986340, 1437986940, 1437987540, 1437988140, 1437988740, 1437989340,
1437989940, 1437990540, 1437991140, 1437991740, 1437992340, 1437992940,
1437993540, 1437994140, 1437994740, 1437995340, 1437995940, 1437996540,
1437997140, 1437997740, 1437998340, 1437998940, 1437999540, 1438000140,
1438000740, 1438001340, 1438001940, 1438002540, 1438003140, 1438003740,
1438004340, 1438004940, 1438005540, 1438006140, 1438006740, 1438007340,
1438007940, 1438008540, 1438009140, 1438009740, 1438010340, 1438010940,
1438011540, 1438012140, 1438012740, 1438013340, 1438013940, 1438014540,
1438015140, 1438015740, 1438016340, 1438016940, 1438017540, 1438018140,
1438018740, 1438019340, 1438019940, 1438020540, 1438021140, 1438021740,
1438022340, 1438022940, 1438023540, 1438024140, 1438024740, 1438025340,
1438025940, 1438026540, 1438027140, 1438027740, 1438028340, 1438028940,
1438029540, 1438187640, 1438188240, 1438188840, 1438189440, 1438190040,
1438190640, 1438191240, 1438191840, 1438192440, 1438193040, 1438193640,
1438194240, 1438194840, 1438195440, 1438196040, 1438196640, 1438197240,
1438197840, 1438198440, 1438199040, 1438199640, 1438200240, 1438200840,
1438201440, 1438202040, 1438202640, 1438203240, 1438203840, 1438204440,
1438205040, 1438205640, 1438206240, 1438206840, 1438207440, 1438208040,
1438208640, 1438209240, 1438209840, 1438210440, 1438211040, 1438211640,
1438212240, 1438212840, 1438213440, 1438214040, 1438214640, 1438215240,
1438215840, 1438216440, 1438217040, 1438217640, 1438218240, 1438218840,
1438219440, 1438220040, 1438220640, 1438221240, 1438221840, 1438222440,
1438223040, 1438223640, 1438224240, 1438224840, 1438225440, 1438226040,
1438226640, 1438227240, 1438227840, 1438228440, 1438229040, 1438229640,
1438230240, 1438230840, 1438231440, 1438232040, 1438232640, 1438233240,
1438233840, 1438234440, 1438235040, 1438235640, 1438236240, 1438236840,
1438237440, 1438238040, 1438238640, 1438239240, 1438239840, 1438240440,
1438241040, 1438241640, 1438242240, 1438242840, 1438243440, 1438244040,
1438244640, 1438245240, 1438245840, 1438246440, 1438247040, 1438247640,
1438248240, 1438248840, 1438249440, 1438250040, 1438250640, 1438251240,
1438251840, 1438252440, 1438253040, 1438253640, 1438254240, 1438254840,
1438255440, 1438256040, 1438256640, 1438257240, 1438257840, 1438258440,
1438259040, 1438259640, 1438260240, 1438260840, 1438261440, 1438262040,
1438262640, 1438263240, 1438263840, 1438264440, 1438265040, 1438265640,
1438266240, 1438266840, 1438267440, 1438268040, 1438601100, 1438601700,
1438602300, 1438602900, 1438603500, 1438604100, 1438604700, 1438605300,
1438605900, 1438606500, 1438607100, 1438607700, 1438608300, 1438608900,
1438609500, 1438610100, 1438610700, 1438611300, 1438611900, 1438612500,
1438613100, 1438613700, 1438614300, 1438614900, 1438615500, 1438616100,
1438616700, 1438617300, 1438617900, 1438618500, 1438619100, 1438619700,
1438620300, 1438620900, 1438621500, 1438622100, 1438622700, 1438623300,
1438623900, 1438624500, 1438625100, 1438625700, 1438626300, 1438626900,
1438627500, 1438628100, 1438628700, 1438629300, 1438629900, 1438630500,
1438631100, 1438631700, 1438632300, 1438632900, 1438633500, 1438634100,
1438634700, 1438635300, 1438635900, 1438636500, 1438637100, 1438637700,
1438638300, 1438638900, 1438639500, 1438640100, 1438640700, 1438641300,
1438641900, 1438642500, 1438643100, 1438643700, 1438644300, 1438644900,
1438645500, 1438646100, 1438646700, 1438647300, 1438647900, 1438648500,
1438649100, 1438649700, 1438650300, 1438650900, 1438651500, 1438652100,
1438652700, 1438653300, 1438653900, 1438654500, 1438655100, 1438655700,
1438656300, 1438656900, 1438657500, 1438658100, 1438658700, 1438659300,
1438659900, 1438660500, 1438661100, 1438661700, 1438662300, 1438662900,
1438663500, 1438664100, 1438664700, 1438665300, 1438665900, 1438666500,
1438667100, 1438667700, 1438668300, 1438668900, 1438669500, 1438670100,
1438670700, 1438671300, 1438671900, 1438672500, 1438673100, 1438673700,
1438674300, 1438674900, 1438675500, 1438676100, 1438676700, 1438677300,
1438677900, 1438678500, 1438679100, 1438679700, 1438680300, 1438680900,
1438681500, 1438682100, 1438682700, 1438683300, 1438683900, 1438684500,
1438685100, 1438685700, 1438686300, 1438686900, 1438687500, 1438688100,
1438688700, 1438689300, 1438689900, 1438690500, 1438691100, 1438691700,
1438692300, 1438692900, 1438693500, 1438694100, 1438694700, 1438695300,
1438695900, 1438696500, 1438697100, 1438697700, 1438698300, 1438698900,
1438699500, 1438700100, 1438700700, 1438701300, 1438701900, 1438702500,
1438703100, 1438703700, 1438704300, 1437643320, 1437643920, 1437644520,
1437645120, 1437645720, 1437646320, 1437646920, 1437647520, 1437648120,
1437648720, 1437649320, 1437649920, 1437650520, 1437651120, 1437651720,
1437652320, 1437652920, 1437653520, 1437654120, 1437654720, 1437655320,
1437655920, 1437656520, 1437657120, 1437657720, 1437658320, 1437658920,
1437659520, 1437660120, 1437660720, 1437661320, 1437661920, 1437662520,
1437663120, 1437663720, 1437664320, 1437664920, 1437665520, 1437666120,
1437666720, 1437667320, 1437667920, 1437668520, 1437669120, 1437669720,
1437670320, 1437670920, 1437671520, 1437672120, 1437672720, 1437673320,
1437673920, 1437674520, 1437675120, 1437675720, 1437676320, 1437676920,
1437677520, 1437678120, 1437678720, 1437679320, 1437679920, 1437680520,
1437681120, 1437681720, 1437682320, 1437682920, 1437683520, 1437684120,
1437684720, 1437685320, 1437685920, 1437686520, 1437687120, 1437687720,
1437688320, 1437688920, 1437689520, 1437690120, 1437690720, 1437691320,
1437691920, 1437692520, 1437693120, 1437693720, 1437694320, 1437694920,
1437695520, 1437696120, 1437696720, 1437697320, 1437697920, 1437698520,
1437699120, 1437699720, 1437700320, 1437700920, 1437701520, 1437702120,
1437702720, 1437703320, 1437703920, 1437704520, 1437705120, 1437705720,
1437706320, 1437706920, 1437707520, 1437708120, 1437708720, 1437709320,
1437709920, 1437710520, 1437711120, 1437711720, 1437712320, 1437712920,
1437713520, 1437714120, 1437714720, 1437715320, 1437715920, 1437716520,
1437717120, 1437717720, 1437718320, 1437718920, 1437719520, 1437720120,
1437720720, 1437721320, 1437721920, 1437722520, 1437723120, 1437723720,
1437724320, 1437724920, 1437725520, 1437726120, 1437726720, 1437727320,
1437727920, 1437728520, 1437729120, 1437729720, 1437730320, 1437730920,
1437899820, 1437900420, 1437901020, 1437901620, 1437902220, 1437902820,
1437903420, 1437904020, 1437904620, 1437905220, 1437905820, 1437906420,
1437907020, 1437907620, 1437908220, 1437908820, 1437909420, 1437910020,
1437910620, 1437911220, 1437911820, 1437912420, 1437913020, 1437913620,
1437914220, 1437914820, 1437915420, 1437916020, 1437916620, 1437917220,
1437917820, 1437918420, 1437919020, 1437919620, 1437920220, 1437920820,
1437921420, 1437922020, 1437922620, 1437923220, 1437923820, 1437924420,
1437925020, 1437925620, 1437926220, 1437926820, 1437927420, 1437928020,
1437928620, 1437929220, 1437929820, 1437930420, 1437931020, 1437931620,
1437932220, 1437932820, 1437933420, 1437934020, 1437934620, 1437935220,
1437935820, 1437936420, 1437937020, 1437937620, 1437938220, 1437938820,
1437939420, 1437940020, 1437940620, 1437941220, 1437941820, 1437942420,
1437943020, 1437943620, 1437944220, 1437944820, 1437945420, 1437946020,
1437946620, 1437947220, 1437947820, 1437948420, 1437949020, 1437949620,
1437950220, 1437950820, 1437951420, 1437952020, 1437952620, 1437953220,
1437953820, 1437954420, 1437955020, 1437955620, 1437956220, 1437956820,
1437957420, 1437958020, 1437958620, 1437959220, 1437959820, 1437960420,
1437961020, 1437961620, 1437962220, 1437962820, 1437963420, 1437964020,
1437964620, 1437965220, 1437965820, 1437966420, 1437967020, 1437967620,
1437968220, 1437968820, 1437969420, 1437970020, 1437970620, 1437971220,
1437971820, 1437972420, 1437973020, 1437973620, 1437974220, 1437974820,
1437975420, 1437976020, 1437976620, 1437977220, 1437977820, 1437978420,
1438105260, 1438105860, 1438106460, 1438107060, 1438107660, 1438108260,
1438108860, 1438109460, 1438110060, 1438110660, 1438111260, 1438111860,
1438112460, 1438113060, 1438113660, 1438114260, 1438114860, 1438115460,
1438116060, 1438116660, 1438117260, 1438117860, 1438118460, 1438119060,
1438119660, 1438120260, 1438120860, 1438121460, 1438122060, 1438122660,
1438123260, 1438123860, 1438124460, 1438125060, 1438125660, 1438126260,
1438126860, 1438127460, 1438128060, 1438128660, 1438129260, 1438129860,
1438130460, 1438131060, 1438131660, 1438132260, 1438132860, 1438133460,
1438134060, 1438134660, 1438135260, 1438135860, 1438136460, 1438137060,
1438137660, 1438138260, 1438138860, 1438139460, 1438140060, 1438140660,
1438141260, 1438141860, 1438142460, 1438143060, 1438143660, 1438144260,
1438144860, 1438145460, 1438146060, 1438146660, 1438147260, 1438147860,
1438148460, 1438149060, 1438149660, 1438150260, 1438150860, 1438151460,
1438152060, 1438152660, 1438153260, 1438153860, 1438154460, 1438155060,
1438155660, 1438156260, 1438156860, 1438157460, 1438158060, 1438158660,
1438159260, 1438159860, 1438160460, 1438161060, 1438161660, 1438162260,
1438162860, 1438163460, 1438164060, 1438164660, 1438165260, 1438165860,
1438166460, 1438167060, 1438167660, 1438168260, 1438168860, 1438169460,
1438170060, 1438170660, 1438171260, 1438171860, 1438172460, 1438173060,
1438173660, 1438174260, 1438174860, 1438175460, 1438176060, 1438176660,
1438177260, 1438177860, 1438178460, 1438179060, 1438179660, 1438180260,
1438180860, 1438181460, 1438182060, 1438182660, 1438183260, 1438183860,
1438184460, 1438185060, 1438185660, 1438186260, 1438186860, 1438187460,
1438188060, 1438188660, 1438189260, 1438189860, 1438190460, 1438191060,
1438191660, 1438192260, 1438192860, 1438193460, 1438194060, 1438194660,
1438195260, 1438195860, 1438196460, 1438197060, 1438197660, 1438198260,
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1438202460, 1438203060, 1438203660, 1438204260, 1438204860, 1438205460,
1438206060, 1438206660, 1438207260, 1438207860, 1438208460, 1438209060,
1438209660, 1438210260, 1438210860, 1438211460, 1438212060, 1438212660,
1438213260, 1438213860, 1438214460, 1438215060, 1438215660, 1438216260,
1438216860, 1438217460, 1438218060, 1438218660, 1438219260, 1438219860,
1438220460, 1438221060, 1438221660, 1438222260, 1438222860, 1438223460,
1438224060, 1438224660, 1438225260, 1438225860, 1438226460, 1438227060,
1438227660, 1438228260, 1438228860, 1438229460, 1438230060, 1438230660,
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1438238460, 1438239060, 1438239660, 1438240260, 1438240860, 1438241460,
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1438245660, 1438246260, 1438246860, 1438247460, 1438248060, 1438248660,
1438249260, 1438249860, 1438250460, 1438251060, 1438251660, 1438252260,
1438252860, 1438253460, 1438254060, 1438254660, 1438255260, 1438255860,
1438256460, 1438257060, 1438257660, 1438258260, 1438258860, 1438259460,
1438260060, 1438260660, 1438261260, 1438261860, 1438262460, 1438263060,
1438263660, 1438264260, 1438264860, 1438505400, 1438506000, 1438506600,
1438507200, 1438507800, 1438508400, 1438509000, 1438509600, 1438510200,
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1438514400, 1438515000, 1438515600, 1438516200, 1438516800, 1438517400,
1438518000, 1438518600, 1438519200, 1438519800, 1438520400, 1438521000,
1438521600, 1438522200, 1438522800, 1438523400, 1438524000, 1438524600,
1438525200, 1438525800, 1438526400, 1438527000, 1438527600, 1438528200,
1438528800, 1438529400, 1438530000, 1438530600, 1438531200, 1438531800,
1438532400, 1438533000, 1438533600, 1438534200, 1438534800, 1438535400,
1438536000, 1438536600, 1438537200, 1438537800, 1438538400, 1438539000,
1438539600, 1438540200, 1438540800, 1438541400, 1438542000, 1438542600,
1438543200, 1438543800, 1438544400, 1438545000, 1438545600, 1438546200,
1438546800, 1438547400, 1438548000, 1438548600, 1438549200, 1438549800,
1438550400, 1438551000, 1438551600, 1438552200, 1438552800, 1438553400,
1438554000, 1438554600, 1438555200, 1438555800, 1438556400, 1438557000,
1438557600, 1438558200, 1438558800, 1438559400, 1438560000, 1438560600,
1438561200, 1438561800, 1438562400, 1438563000, 1438563600, 1438564200,
1438564800, 1438565400, 1438566000, 1438566600, 1438567200, 1438567800,
1438568400, 1438569000, 1438569600, 1438570200, 1438570800, 1438571400,
1438572000, 1438572600, 1438573200, 1438573800, 1438574400, 1438575000,
1438575600, 1438576200, 1438576800, 1438577400, 1438578000, 1438578600,
1438579200, 1438579800, 1438580400, 1438699020, 1438699620, 1438700220,
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55.6217, 55.632, 55.6431, 55.6512, 55.6449, 55.6495, 55.6692,
55.6777, 55.6891, 55.7129, 55.7368, 55.7563, 55.7771, 55.7956,
55.8299, 55.8678, 55.9089, 55.95, 55.9845, 56.0182, 56.0451,
56.0709, 56.0708, 56.0802, 56.0672, 56.0347, 55.9932, 55.9502,
55.9329, 55.9146, 55.8784, 55.8234, 55.7832, 55.7549, 55.7199,
55.6902, 55.6365, 55.5864, 55.5529, 55.5151, 55.4819, 55.4455,
55.3948, 55.3437, 55.329, 55.3276, 55.3271, 55.3262, 55.3252,
55.324, 55.323, 55.3217, 55.3204, 55.3192, 55.3176, 55.3165,
55.3154, 55.3149, 55.3123, 55.3109, 55.3094, 55.3075, 55.3057,
55.3039, 55.3021, 55.3004, 55.2988, 55.2974, 55.2961, 55.2948,
55.2937, 55.2926, 55.2917, 55.2912, 55.2912, 55.2914, 55.2906,
55.293, 55.2924, 55.2931, 55.2938, 55.2947, 55.2953, 55.2953,
55.2914, 55.2854, 55.2736, 55.2788, 55.2818, 55.2915, 55.3026,
55.3059, 55.3266, 55.3449, 55.3609, 55.3783, 55.394, 55.4081,
55.4207, 55.4436, 55.4575, 55.4821, 55.4987, 55.5005, 55.5006,
55.5005, 55.5005, 55.5, 55.4998, 55.5112, 55.5214, 55.5258,
55.5289, 55.5288, 55.5282, 55.5273, 55.5277, 55.5354, 55.5533,
55.5635, 55.5704, 55.5709, 55.5759, 55.5826, 55.5815, 55.58,
55.5785, 55.5769, 55.5753, 55.574, 55.5727, 55.5715, 55.5701,
55.5691, 55.5705, 55.5846, 55.5835, 55.5828, 55.5816, 55.6194,
55.6494, 55.6646, 55.677, 55.6722, 55.6704, 55.6731, 55.6725,
55.679, 55.6841, 55.684, 55.681, 55.6823, 55.6877, 55.6899,
55.7131, 55.7414, 55.7573, 55.7515, 55.7523, 55.7617, 55.7722,
55.7819, 55.7854, 55.7882, 55.7759, 55.7773, 55.7691, 55.7449,
55.7374, 55.7377, 55.7475, 55.7583, 55.7772, 55.8251, 55.8734,
55.9201, 55.9518, 55.9739, 56.0057, 56.0507, 56.0739, 56.0727,
56.0547, 56.01, 55.9807, 55.9242, 55.8825, 55.8417, 55.8198,
55.801, 55.7939, 55.7793, 55.7653, 55.7452, 55.7331, 55.7395,
55.7502, 55.7533, 55.7722, 55.7754, 55.7785, 55.7734, 55.7745,
55.7729, 55.7765, 55.7804, 55.775, 55.7762, 55.7679, 55.7561,
55.7599, 55.7608, 55.75, 55.7509, 55.7518, 55.7508, 55.7499,
55.749, 55.7478, 55.7459, 55.7446, 55.7432, 55.7421, 55.7408,
55.7389, 55.7369, 55.7346, 55.7323, 55.7297, 55.7272, 55.7245,
55.722, 55.7195, 55.7166, 55.7141, 55.7116, 55.7088, 55.7062,
55.7037, 55.7009, 55.6988, 55.6963, 55.6942, 55.6918, 55.6898,
55.6876, 55.6857, 55.6838, 55.6823, 55.6807, 55.6792, 55.6777,
55.6757, 55.6737, 55.6926, 55.7231, 55.7345, 55.7361, 55.7292,
55.7204, 55.7177, 55.7218, 55.7347, 55.7334, 55.7339, 55.7333,
55.7377, 55.7571, 55.7519, 55.76, 55.804, 55.8149, 55.8348,
55.8407, 55.8487, 55.8566, 55.8619, 55.8718, 55.8731, 55.8734,
55.8877, 55.8973, 55.9047, 55.905, 55.9048, 55.9128, 55.9138,
55.9171, 55.9236, 55.9277, 55.9275, 55.9237, 55.9248, 55.9195,
55.9129, 55.9168, 55.9166, 55.9202, 55.9242, 55.9268, 55.9252,
55.9213, 55.9264, 55.9344, 55.9459, 55.9585, 55.9728, 55.9762,
55.9811, 55.9941, 56.0003, 56.0084, 56.0157, 56.0307, 56.0574,
56.0673, 56.0721, 56.0555, 56.0328, 56.0049, 55.9796, 55.9476,
55.9106, 55.8788, 55.8585, 55.8535, 55.8339, 55.8161, 55.7928,
55.7656, 55.7621, 55.7279, 55.7099, 55.7064, 55.7053, 55.7043,
55.7045, 55.7045, 55.7041, 55.7039, 55.6983, 55.6747, 55.6421,
55.596, 55.5974, 55.5618, 55.5398, 55.547, 55.5389, 55.5498,
55.5622, 55.5463, 55.5156, 55.5085, 55.5112, 55.4991, 55.4883,
55.4973, 55.4957, 55.4914, 55.4894, 55.4943, 55.4527, 55.4514,
55.4498, 55.4419, 55.4877, 55.4928, 55.5068, 55.4772, 55.4597,
55.4356, 55.4301, 55.4283, 55.4229, 55.4072, 55.43, 55.4301,
55.4303, 55.4307, 55.4314, 55.4325, 55.4335, 55.4349, 55.4366,
55.4385, 55.4402, 55.4421, 55.4438, 55.4455, 55.4477, 55.4497,
55.452, 55.4541, 55.4564, 55.4582, 55.4599, 55.4617, 55.4634,
55.4656, 55.4678, 55.4697, 55.4717, 55.4729, 55.4738, 55.4748,
55.4759, 55.4772, 55.478, 55.4782, 55.4791, 55.4794, 55.4796,
55.4797, 55.4797, 55.4793, 55.4784, 55.4772, 55.4763, 55.4759,
55.4751, 55.474, 55.4763, 55.4949, 55.5003, 55.5012, 55.4976,
55.5068, 55.5057, 55.5047, 55.5037, 55.5028, 55.5019, 55.5009,
55.5, 55.4993, 55.4986, 55.498, 55.5129, 55.5237, 55.5236,
55.5233, 55.5245, 55.5246, 55.5251, 55.5325, 55.5562, 55.5673,
55.5564, 55.5518, 55.5949, 55.5882, 55.5766, 55.5787, 55.567,
55.5681, 55.5675, 55.5619, 55.5543, 55.5579, 55.5705, 55.574,
55.6026, 55.6317, 55.6671, 55.7026, 55.7423, 55.7691, 55.7936,
55.8185, 55.8657, 55.9155, 55.9665, 56.0144, 56.0493, 56.0727,
56.0969, 56.1048, 56.1105, 56.1036, 56.1064, 56.1014, 56.0892,
56.0741, 56.0709, 56.0671, 56.0627, 56.0621, 56.0762, 56.0822,
56.1215, 56.1442, 56.1934, 56.2145, 56.2586, 56.2964, 56.3472,
56.405, 56.4252, 56.4256, 56.4266, 56.4237, 56.4161, 56.4138,
56.4288, 56.4428, 56.4365, 56.4259, 56.4426, 56.4535, 56.4955,
56.5557, 56.6109, 56.6809, 56.7109, 56.7087, 56.7196, 56.7405,
56.7797, 56.7958, 56.8135, 56.813, 56.8572, 56.9053, 56.9097,
56.8859, 56.8639, 56.8399, 56.8182, 56.8183, 56.8158, 56.809,
56.7914, 56.8205, 56.8377, 56.8489, 56.8346, 56.8317, 56.8314,
56.831, 56.8309, 56.8306, 56.8177, 56.7964, 56.7693, 56.7493,
56.7247, 56.7169, 56.6978, 56.6968, 56.6957, 56.6757, 56.6551,
56.6497, 56.6477, 56.6486, 56.6482, 56.6475, 56.6473, 56.6469,
56.6469, 56.646, 56.6351, 56.6353, 56.6353, 56.6355, 56.6354,
56.6354, 56.6356, 56.6358, 56.6364, 56.6368, 56.6373, 56.6379,
56.6383, 56.6388, 56.6396, 56.6405, 56.6413, 56.642, 56.6427,
56.6435, 56.6444, 56.6451, 56.6457, 56.6464, 56.6467, 56.647,
56.6476, 56.6479, 56.6483, 56.6484, 56.6487, 56.6489, 56.6492,
56.6492, 56.649, 56.6497, 56.649, 56.6484, 56.6515, 56.6379,
56.6306, 56.6528, 56.6573, 56.6585, 56.6584, 56.6496, 56.6463,
56.6241, 56.6166, 56.6053, 56.5989, 56.5688, 56.5376, 56.5132,
56.4844, 56.4595, 56.4413, 56.421, 56.4027, 56.3894, 56.3802,
56.358, 56.3369, 56.3094, 56.278, 56.2566, 56.239, 56.2133,
56.1972, 56.176, 56.153, 56.1243, 56.1077, 56.0873, 56.0801,
56.0837, 56.0904, 56.1116, 56.1329, 56.1576, 56.1697, 56.1829,
56.1888, 56.2093, 56.2259, 56.2471, 56.2566, 56.2668, 56.267,
56.2684, 56.2725, 56.2822, 56.2835, 56.2977, 56.3133, 56.3329,
56.3447, 56.3434, 56.355, 56.3587, 56.3603, 56.3596, 56.3528,
56.3526, 56.3777, 56.3674, 56.3606, 56.3653, 56.3736, 56.3927,
56.395, 56.3976, 56.3996, 56.4012, 56.4015, 56.404, 56.406,
56.41, 56.4065, 56.4145, 56.4246, 56.4258, 56.428, 56.4394,
56.4464, 56.4462, 56.4475, 56.449, 56.4499, 56.451, 56.4518,
56.4529, 56.4537, 56.4517, 56.447, 56.4746, 56.4745, 56.4749,
56.4753, 56.4753, 56.474, 56.4717, 56.4715, 56.4571, 56.4038,
56.4175, 56.4204, 56.4201, 56.4194, 56.4188, 56.4172, 56.4173,
56.4163, 56.4154, 56.4148, 56.4138, 56.4128, 56.4122, 56.4113,
56.4104, 56.4096, 56.4087, 56.4078, 56.4069, 56.4062, 56.4053,
56.4046, 56.4039, 56.4034, 56.403, 56.4027, 56.4023, 56.402,
56.402, 56.4019, 56.4019, 56.4018, 56.4018, 56.4018, 56.4019,
56.4023, 56.4023, 56.4031, 56.404, 56.4048, 56.4054, 56.4056,
56.4062, 56.4069, 56.4075, 56.4081, 56.4091, 56.4109, 56.4217,
56.3782, 56.3513, 56.3014, 56.263, 56.2693, 56.2491, 56.2037,
56.1531, 56.0691, 56.0764, 56.0829, 56.0836, 56.0821, 56.0992,
56.11, 56.1288, 56.1535, 56.1669, 56.1852, 56.2015, 56.2149,
56.2379, 56.2427, 56.2653, 56.2901, 56.3057, 56.3193, 56.3177,
56.3375, 56.3526, 56.385, 56.4162, 56.4299, 56.4564, 56.4619,
56.4534, 56.466, 56.4806, 56.4783, 56.4768, 56.4747, 56.4729,
56.4707, 56.4687, 56.4665, 56.4642, 56.4618, 56.4595, 56.4576,
56.4552, 56.4529, 56.4502, 56.4478, 56.4454, 56.4429, 56.4404,
56.4381, 56.4359, 56.4337, 56.4315, 56.4294, 56.4275, 56.4261,
56.4247, 56.4235, 56.4224, 56.4213, 56.4202, 56.4192, 56.4183,
56.4175, 56.4168, 56.4159, 56.415, 56.4203, 56.4436, 56.4585,
56.4809, 56.503, 56.5328, 56.5429, 56.5453, 56.5463, 56.5615,
56.5723, 56.5983, 56.6093, 56.614, 56.635, 56.6597, 56.6738,
56.6886, 56.7019, 56.7262, 56.7311, 56.7308, 56.7311, 56.7125,
56.6961, 56.6806, 56.6851, 56.6884, 56.6812, 56.684, 56.7052,
56.6895, 56.7066, 56.7203, 56.7321, 56.7576, 56.7855, 56.8136,
56.8421, 56.8644, 56.8717, 56.8843, 56.9053, 56.8952, 56.8748,
56.8595, 56.8553, 56.8596, 56.8899, 56.9196, 56.9374, 56.9641,
56.9766, 56.956, 56.9531, 56.9502, 56.9542, 56.9654, 56.9587,
56.9473, 56.9284, 56.8978, 56.9163, 56.9462, 56.9766, 57.0026,
57.0363, 57.0594, 57.0802, 57.1155, 57.1476, 57.1801, 57.2212,
57.2615, 57.2944, 57.3225, 57.3411, 57.3732, 57.4083, 57.4469,
57.4778, 57.5121, 57.5136, 57.5128, 57.5115, 57.5101, 57.5098,
57.5013, 57.5067, 57.5119, 57.5066, 57.5019, 57.4954, 57.4934,
57.4907, 57.5003, 57.5052, 57.5098, 57.5086, 57.5124, 57.5106,
57.509, 57.5129, 57.511, 57.509, 57.5072, 57.5048, 57.5026,
57.5005, 57.4983, 57.4959, 57.4934, 57.491, 57.4885, 57.4857,
57.483, 57.4807, 57.4781, 57.4753, 57.4727, 57.4701, 57.4673,
57.4649, 57.4626, 57.4601, 57.4576, 57.4556, 57.4531, 57.4509,
57.4488, 57.4469, 57.445, 57.4429, 57.4409, 57.4395, 57.438,
57.4366, 57.4352, 57.434, 57.4329, 57.4319, 57.4305, 57.4289,
57.4276, 57.4259, 57.4256, 57.4248, 57.4513, 57.4594, 57.4653,
57.465, 57.463, 57.4602, 57.4605, 57.4506, 57.4461, 57.4404,
57.4376, 57.4348, 57.4328, 57.4331, 57.4313, 57.4353, 57.439,
57.4303, 57.3828, 57.3362, 57.2989, 57.2523, 57.2112, 57.1746,
57.1397, 57.0943, 57.0527, 57.0357, 56.9866, 56.944, 56.9053,
56.8548, 56.8108, 56.7732, 56.7392, 56.7038, 56.6664, 56.6396,
56.6024, 56.5733, 56.541, 56.5198, 56.5033, 56.4912, 56.4637,
56.4427, 56.3984, 56.3429, 56.3002, 56.2699, 56.2353, 56.2015,
56.1746, 56.1498, 56.1213, 56.1012, 56.0836, 56.078, 56.0789,
56.0825, 56.0832, 56.0661, 56.0753, 56.0624, 56.048, 56.0269,
56.004, 55.995, 55.9903, 55.9851, 55.9732, 55.9621, 55.9575,
55.9503, 55.9341, 55.9175, 55.9089, 55.9119, 55.9199, 55.9288,
55.9323, 55.9308, 55.9376, 55.9385, 55.9244, 55.9109, 55.9117,
55.9121, 55.9124, 55.9252, 55.9687, 55.9817, 56.0147, 56.039,
56.0461, 56.07, 56.0781, 56.0694, 56.0598, 56.0521, 56.0442,
56.0395, 56.0463, 56.0947, 56.1058, 56.0947, 56.0909, 56.0746,
56.0949, 56.0872, 56.0863, 56.0853, 56.0807, 56.0897, 56.0894,
56.089, 56.0889, 56.0894, 56.0898, 56.0901, 56.1437, 56.1263,
56.107, 56.1138, 56.1166, 56.127, 56.1314, 56.1318, 56.1303,
56.1273, 56.1146, 56.0907, 56.0651, 56.0611, 56.0437, 56.0466,
56.0493, 56.0521, 56.0551, 56.0585, 56.0617, 56.065, 56.0684,
56.0716, 56.075, 56.0789, 56.082, 56.085, 56.0882, 56.0909,
56.0933, 56.0954, 56.0973, 56.0991, 56.1006, 56.1021, 56.103,
56.1036, 56.1043, 56.1046, 56.1048, 56.1048, 56.1043, 56.1036,
56.1028, 56.1018, 56.101, 56.0999, 56.0991, 56.0974, 56.0959,
56.0943, 56.0929, 56.0915, 56.0902, 56.0891, 56.0812, 56.0537,
56.0322, 56.014, 55.9934, 55.9821, 56.0283, 56.0676, 56.0771,
56.0761, 56.0733, 56.0791, 56.081, 56.0894, 56.0942, 56.1,
56.1084, 56.1243, 56.1356, 56.132, 56.1355, 56.1341, 56.1593,
56.1633, 56.1582, 56.1573, 56.147, 56.1296, 56.1144, 56.1033,
56.097, 56.1147, 56.1103, 56.1012, 56.1035, 56.1112, 56.1093,
56.1087, 56.1082, 56.1079, 56.1076, 56.1028, 56.0887, 56.0849,
56.0819, 56.0671, 56.0835, 56.0898, 56.091, 56.1138, 56.1167,
56.1171, 56.1177, 56.1199, 56.1216, 56.1235, 56.1253, 56.1273,
56.129, 56.1312, 56.133, 56.1349, 56.1371, 56.1397, 56.1419,
56.1443, 56.1468, 56.1493, 56.1515, 56.1537, 56.1556, 56.1577,
56.1595, 56.1608, 56.1621, 56.1632, 56.1641, 56.1647, 56.1656,
56.1664, 56.167, 56.1675, 56.1675, 56.1676, 56.1674, 56.1673,
56.1668, 56.1664, 56.1657, 56.1654, 56.1649, 56.1645, 56.1635,
56.1626, 56.1587, 56.1292, 56.1117, 56.0956, 56.0682, 56.0341,
56.0189, 56.0058, 56.0168, 56.0836, 56.1858, 56.288, 56.3403,
56.4154, 56.4686, 56.4985, 56.4882, 56.4824, 56.4703, 56.4625,
56.4688, 56.4418, 56.4821, 56.4971, 56.5049, 56.5007, 56.5014,
56.5029, 56.5004, 56.4999, 56.5022, 56.4896, 56.5021, 56.5133,
56.5211, 56.5273, 56.5397, 56.5534, 56.5612, 56.567, 56.5653,
56.5587, 56.5496, 56.5472, 56.5609, 56.564, 56.5692, 56.5722,
56.5724, 56.5656, 56.5582, 56.534, 56.5177, 56.5027, 56.4719,
56.4274, 56.3898, 56.3373, 56.2849, 56.2306, 56.1697, 56.1229,
56.0895, 56.0827, 56.0835, 56.0577, 56.0337, 56.0135, 56.0124,
56.0099, 55.9904, 55.99, 55.9895, 55.9893, 55.9686, 55.9679,
55.9532, 55.9243, 55.8806, 55.8372, 55.8169, 55.7826, 55.7662,
55.7647, 55.7592, 55.7588, 55.7593, 55.7586, 55.7581, 55.7315,
55.6769, 55.6321, 55.6244, 55.5915, 55.5374, 55.4817, 55.4396,
55.3814, 55.3693, 55.3696, 55.3701, 55.3707, 55.3788, 55.3802,
55.3816, 55.3827, 55.3698, 55.3556, 55.3606, 55.3657, 55.3664,
55.3512, 55.331, 55.327, 55.3284, 55.303, 55.3014, 55.3012,
55.303, 55.3106, 55.3101, 55.2919, 55.3167, 55.3166, 55.3184,
55.3199, 55.3205, 55.3215, 55.3228, 55.3237, 55.3972, 55.492,
55.5473, 55.6331, 55.7144, 55.7649, 55.7644, 55.7908, 55.8566,
55.9085, 55.9493, 55.9799, 56.0203, 56.0507)), .Names = c("DateTime",
"Bird", "Lon", "Lat"), row.names = c(NA, -1519L), spec = structure(list(
cols = structure(list(DateTime = structure(list(), class = c("collector_character",
"collector")), Bird = structure(list(), class = c("collector_integer",
"collector")), Lon = structure(list(), class = c("collector_double",
"collector")), Lat = structure(list(), class = c("collector_double",
"collector"))), .Names = c("DateTime", "Bird", "Lon", "Lat"
)), default = structure(list(), class = c("collector_guess",
"collector"))), .Names = c("cols", "default"), class = "col_spec"), class = c("tbl_df",
"tbl", "data.frame"))
#Group data_frame by animal ID
dat <- dat %>% group_by(Bird)
#The new sf package allows better manipulaton of spatial dataframes incl. improved plotting and on the fly transformations...
dat_sf <- st_as_sf(dat, coords = c("Lon", "Lat")) %>% st_set_crs("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
#i.e.
p1 = ggplot() +
geom_sf(data = st_transform(st_as_sf(world_shp), prj), fill = "dark grey") +
geom_sf(data = st_transform(st_as_sf(dat_sf), prj), aes(colour = Bird), show.legend = "point") +
coord_sf(xlim = c(-250000, 1000000), ylim = c(5500000, 6750000), crs = prj, expand = T) +
scale_colour_viridis(discrete = T) +
theme_bw()
print(p1)
print(p1 + facet_wrap(~Bird))
#To generate some absence points we need to decide on the 'available' area
#There are loads of different ways to do this
#One option is to draw a buffer around the breeding colony that is just a bit bigger than the maximum distance travelled by any individual
#Define breeding colony
colony = sp::SpatialPoints(coords = cbind(-6.25, 56.07), proj4string = CRS("+proj=longlat +datum=WGS84"))
colony_utm = sp::spTransform(colony, CRS(prj)) #project to UTM
#Estimate foraging range
fr <- max(sp::spDistsN1(pts = cbind(dat$Lon, dat$Lat), pt = colony, longlat = T))
#Buffer around colony
buff_1 = rgeos::gBuffer(colony_utm, width = 1.1*fr*1000) #110% buffer of foraging range in metres
buff_2 = rgeos::gIntersection(world_utm, buff_1, byid = T) #exclude the land
buff_3 = buff_1 - buff_2 #take difference between two
#Generate some random points in buffer
#How many points to we need?
#Start with a 1:1 presence:absence ratio
n <- nrow(dat)
rp = sp::spsample(buff_3, n, type = "random")
rp = as.data.frame(rp) #convert random points to dataframe
#Combine presence and absence points into single dataframe
#There are questions over whether the random points should be assigned to individuals
#i.e. each individual has n presences and n pseudo-absences
#or shoud the n pseudo-absences be assigned a new ID so they are estimated differently in the random effect structure of any model?
#Create presence data frame
#Remove lat lon and add UTM coordinates
dat1 <- dat %>%
ungroup() %>%
dplyr::select(-Lon, -Lat) %>%
mutate(x = st_coordinates(st_transform(st_as_sf(dat_sf), prj))[,1],
y = st_coordinates(st_transform(st_as_sf(dat_sf), prj))[,2])
#Generate psudeo-absence data frame using random points
dat0 <- dat1 %>%
ungroup %>%
mutate(x = rp$x,
y = rp$y)
#Add column that specifies presence or absence
dat1 <- dat1 %>%
mutate(used = 1)
dat0 <- dat0 %>%
mutate(used = 0)
#Combine together and reorder by bird and time
dat_df <- bind_rows(dat1, dat0) %>%
arrange(Bird, DateTime)
#Each animal now has one pseudo-absence for each presence
#Create spatial data frame
dat_sf <- st_as_sf(dat_df, coords = c("x", "y")) %>% st_set_crs(prj)
####################################
### Calculate distance to colony ###
####################################
#Many species are constrained by how far they can travel from the breeding colony
#Generate a grid over which to estimate biological distance - i.e. around land
#Base the size of the grid on the random point buffer
ras = raster(xmn = floor(st_bbox(buff_3)$xmin),
xmx = ceiling(st_bbox(buff_3)$xmax),
ymn = floor(st_bbox(buff_3)$ymin),
ymx = ceiling(st_bbox(buff_3)$ymax),
resolution = 10000) #1 km gridthis may be SLOW
crs(ras) <- crs(prj)
#Rasterize will set ocean to NA so we just inverse it
#and set water to "1"
#Land is equal to zero because it is "NOT" NA
mask <- rasterize(world_utm, ras)
ras <- is.na(mask)
#Set land to 999 make it expensive to cross but not "impossible"
ras[ras==0] <- 999
#Each cell now has value of 1 or 999, nothing else
#Create a Transition object from the raster
#This calculation will take time when resolution small
tr <- transition(ras, function(x) 1/mean(x), 8)
tr <- geoCorrection(tr, scl=FALSE)
#Calculate the cost distance across the grid from the colony of interest
R <- accCost(tr, colony_utm)
#Raster still shows the expensive travel over land
#Mask it out for sea travel only
R <- mask(R, mask, inverse=TRUE)
#It's still possible to get across land and into lakes
#Some very high values of cost skew the plot to look rubbish
#Draw histogram of distances, and line to check high values
hist(R, breaks = 1000)
abline(v = 10000000)
#Remove high values
R[R > 10000000] = NA
#R is now a raster of at sea distances to the focal colony
#Extract the distance from each animal location to the colony
dat_sf <- dat_sf %>%
mutate(dist = raster::extract(R, .))
#Dummey plot
ggplot() +
geom_boxplot(aes(x = factor(used), y = dist), data = dat_sf)
#######################################
### Extract some environmental data ###
#######################################
#To download bathymetry data
#ETOPO1 database hosted on the NOAA website
library(marmap)
bathy <- getNOAA.bathy(lon1=-20, lon2=10, lat1=45, lat2=65, resolution = 1)
plot(bathy, image=TRUE, deep=-6000, shallow=0, step=1000)
bat = marmap::as.raster(bathy)
#Write
raster::writeRaster(bat, filename = "~/bathy.asc", overwrite = T)
#Read and define projection
bathy = raster("~/bathy.asc")
raster::projection(bathy) = CRS("+proj=longlat +datum=WGS84")
#Raster resolution is x = 1070 and y = 1850
#Easier for spatial predictions if resolution of environmental covariates matches
#Project raster
bathy_utm = raster::projectRaster(bathy, crs = CRS(prj), res = 10000)
#Crop to same extent as distance raster
bathy_utm <- crop(bathy_utm, R)
#Extract the bathymetry underlying each point
dat_sf <- dat_sf %>%
mutate(bathy = raster::extract(bathy_utm, .))
#Dummy plot
ggplot() +
geom_boxplot(aes(x = factor(used), y = bathy), data = dat_sf)
######################################
### Example habitat preference GAM ###
######################################
require(mgcv)
#how many knots?
#what kind of splines?
m1 = gam(used ~ s(dist) + s(bathy) + s(Bird, bs = "re"), family = "binomial", data = dat_sf)
m2 = gam(used ~ s(bathy) + s(Bird, bs = "re"), family = "binomial", data = dat_sf)
m3 = gam(used ~ s(dist) + s(Bird, bs = "re"), family = "binomial", data = dat_sf)
m4 = gam(used ~ 1 + s(Bird, bs = "re"), family = "binomial", data = dat_sf)
AIC(m1, m2, m3, m4)
plot(m1, scale = 0)
hist(residuals(m1)) #these are not normal!
#temporal autocorrelation?
pacf(resid(m1), main = "pACF")
#what about spatial autocorrelation?
########################################
### Example predictions from the GAM ###
########################################
#Create dummy dataframe from rasters
newdata = rasterToPoints(R)
newdata <- as.tibble(newdata)
names(newdata)[3] <- "dist"
newdata <- newdata %>% mutate(bathy = extract(bathy_utm, newdata[,1:2]))
newdata <- newdata %>% mutate(Bird = 1) #dummy bird id
preds = predict(m1, newdata = newdata, exclude = "s(REF)")
newdata <- newdata %>% mutate(preds = exp(preds)) #exp as there are pseudo-absences
#dummy plot
ggplot() +
geom_raster(aes(x = x, y = y, fill = preds), data = newdata) +
coord_equal(ratio = 1) +
scale_fill_viridis()
#ends
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