Philippa Kaur

Centro de Investigação em Biodiversidade e Recursos Genéticos/Research Network in Biodiversity and Evolutionary Biology, Campus Agrário de Vairão, Universidade do Porto, Vairão, PortugalNuno Queiroz, Ana Couto, Marisa Vedor, Ivo da Costa, Gonzalo Mucientes & António M. SantosMarine Biological Association of the United Kingdom, Plymouth, UKNuno Queiroz, Nicolas E. Humphries, Lara L. Sousa, Samantha J. Simpson, Emily J. Southall & David W. SimsDepartamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, PortugalMarisa Vedor & António M. SantosUWA Oceans Institute, Indian Ocean Marine Research Centre, University of Western Australia, Crawley, Western Australia, AustraliaAna M. M. SequeiraSchool of Biological Sciences, University of Western Australia, Crawley, Western Australia, AustraliaAna M. M. SequeiraSpanish Institute of Oceanography, Santa Cruz de Tenerife, SpainFrancisco J. AbascalAbercrombie and Fish, Port Jefferson Station, NY, USADebra L. AbercrombieMarine Biology and Aquaculture Unit, College of Science and Engineering, James Cook University, Cairns, Queensland, AustraliaKatya Abrantes, Adam Barnett, Richard Fitzpatrick & Marcus SheavesInstitute of Natural and Mathematical Sciences, Massey University, Palmerston North, New ZealandDavid Acuña-MarreroUniversidade Federal Rural de Pernambuco (UFRPE), Departamento de Pesca e Aquicultura, Recife, BrazilAndré S. Afonso, Natalia P. A. Bezerra, Fábio H. V. Hazin, Fernanda O. Lana, Bruno C. L. Macena & Paulo TravassosMARE, Marine and Environmental Sciences Centre, Instituto Politécnico de Leiria, Peniche, PortugalAndré S. AfonsoMARE, Laboratório Marítimo da Guia, Faculdade de Ciências da Universidade de Lisboa, Cascais, PortugalPedro Afonso, Jorge Fontes & Frederic VandeperreInstitute of Marine Research (IMAR), Departamento de Oceanografia e Pescas, Universidade dos Açores, Horta, PortugalPedro Afonso, Jorge Fontes, Bruno C. L. Macena & Frederic VandeperreOkeanos – Departamento de Oceanografia e Pescas, Universidade dos Açores, Horta, PortugalPedro Afonso, Jorge Fontes & Frederic VandeperreDepartment of Environmental Affairs, Oceans and Coasts Research, Cape Town, South AfricaDarrell Anders, Michael A. Meÿer, Sarika Singh & Laurenne B. SnydersLarge Marine Vertebrates Research Institute Philippines, Jagna, PhilippinesGonzalo AraujoFins Attached Marine Research and Conservation, Colorado Springs, CO, USARandall ArauzPrograma Restauración de Tortugas Marinas PRETOMA, San José, Costa RicaRandall ArauzMigraMar, Olema, CA, USARandall Arauz, Sandra Bessudo Lion, Eduardo Espinoza, Alex R. Hearn, Mauricio Hoyos, James T. Ketchum, A. Peter Klimley, Cesar Peñaherrera-Palma, George Shillinger, German Soler & Patricia M. ZárateInstitut de Recherche pour le Développement, UMR MARBEC (IRD, Ifremer, Univ. Montpellier, CNRS), Sète, FrancePascal Bach, Antonin V. Blaison, Laurent Dagorn, John D. Filmalter, Fabien Forget, Francois Poisson, Marc Soria & Mariana T. TolottiBiology Department, University of Massachusetts Dartmouth, Dartmouth, MA, USADiego Bernal & Heather MarshallRed Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaMichael L. Berumen, Jesse E. M. Cochran & Carlos M. DuarteFundación Malpelo y Otros Ecosistemas Marinos, Bogota, ColombiaSandra Bessudo Lion, Felipe Ladino, Lina Maria Quintero & German SolerHopkins Marine Station of Stanford University, Pacific Grove, CA, USABarbara A. Block, Taylor K. Chapple, George Shillinger & Timothy D. WhiteDepartment of Biological Sciences, Florida International University, North Miami, FL, USAMark E. Bond, Demian D. Chapman & Yannis P. PapastamatiouInstituto de Ciências do Mar, Universidade Federal do Ceará, Fortaleza, BrazilRamon BonfilSchool of Fishery and Aquatic Sciences, University of Washington, Seattle, WA, USACamrin D. BraunBiology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USACamrin D. Braun & Simon R. ThorroldShark Research and Conservation Program, Cape Eleuthera Institute, Eleuthera, BahamasEdward J. Brooks, Annabelle Brooks & Sean WilliamsUniversity of Exeter, Exeter, UKAnnabelle BrooksSouth Atlantic Environmental Research Institute, Stanley, Falkland IslandsJudith BrownDepartment of Biological Sciences, The Guy Harvey Research Institute, Nova Southeastern University, Dania Beach, FL, USAMichael E. Byrne, Mahmood Shivji, Jeremy J. Vaudo & Bradley M. WetherbeeSchool of Natural Resources, University of Missouri, Columbia, MO, USAMichael E. ByrneLife and Environmental Sciences, University of Iceland, Reykjavik, IcelandSteven E. CampanaSchool of Marine Science and Policy, University of Delaware, Lewes, DE, USAAaron B. CarlisleMassachusetts Division of Marine Fisheries, New Bedford, MA, USAJohn Chisholm & Gregory B. SkomalMarine Research Facility, Jeddah, Saudi ArabiaChristopher R. Clarke & James S. E. LeaPSL, Labex CORAIL, CRIOBE USR3278 EPHE-CNRS-UPVD, Papetoai, French PolynesiaEric G. CluaAgence de Recherche pour la Biodiversité à la Réunion (ARBRE), Réunion, Marseille, FranceEstelle C. CrocheletInstitut de Recherche pour le Développement, UMR 228 ESPACE-DEV, Réunion, Marseille, FranceEstelle C. CrocheletSave Our Seas Foundation–D’Arros Research Centre (SOSF-DRC), Geneva, SwitzerlandRyan Daly & Clare A. Keating DalySouth African Institute for Aquatic Biodiversity (SAIAB), Grahamstown, South AfricaRyan Daly, John D. Filmalter, Enrico Gennari & Alison A. KockDepartment of Fisheries Evaluation, Fisheries Research Division, Instituto de Fomento Pesquero (IFOP), Valparaíso, ChileDaniel Devia CortésSchool of Biological, Earth and Environmental Sciences, University College Cork, Cork, IrelandThomas K. Doyle & Luke HarmanMaREI Centre, Environmental Research Institute, University College Cork, Cork, IrelandThomas K. DoyleCollege of Science and Engineering, Flinders University, Adelaide, South Australia, AustraliaMichael Drew, Matthew Heard & Charlie HuveneersDepartment of Conservation, Auckland, New ZealandClinton A. J. DuffySouth African Institute for Aquatic Biodiversity, Geological Sciences, UKZN, Durban, South AfricaThor EriksonDireccion Parque Nacional Galapagos, Puerto Ayora, Galapagos, EcuadorEduardo EspinozaAustralian Institute of Marine Science, Indian Ocean Marine Research Centre (UWA), Crawley Western Australia, Crawley, AustraliaLuciana C. Ferreira, Mark G. Meekan & Michele ThumsDepartment of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA, USAFrancesco FerrettiOCEARCH, Park City, Utah, USAG. Chris FischerBedford Institute of Oceanography, Dartmouth, Nova Scotia, CanadaMark Fowler, Warren Joyce & Anna MacDonnellNational Institute of Water and Atmospheric Research, Wellington, New ZealandMalcolm P. Francis & Warrick S. LyonBeneath the Waves, Herndon, VA, USAAustin J. GallagherRosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USAAustin J. Gallagher, Neil Hammerschlag & Emily R. NelsonOceans Research Institute, Mossel Bay, South AfricaEnrico GennariDepartment of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South AfricaEnrico Gennari & Alison TownerSARDI Aquatic Sciences, Adelaide, South Australia, AustraliaSimon D. Goldsworthy & Paul J. RogersZoological Society of London, London, UKMatthew J. Gollock & Fiona LlewellynGalapagos Whale Shark Project, Puerto Ayora, Galapagos, EcuadorJonathan R. GreenGriffith Centre for Coastal Management, Griffith University School of Engineering, Griffith University, Gold Coast, Queensland, AustraliaJohan A. GustafsonSaving the Blue, Cooper City, FL, USATristan L. GuttridgeSmithsonian Tropical Research Institute, Panama City, PanamaHector M. GuzmanLeonard and Jayne Abess Center for Ecosystem Science and Policy, University of Miami, Coral Gables, FL, USANeil HammerschlagGalapagos Science Center, San Cristobal, Galapagos, EcuadorAlex R. HearnUniversidad San Francisco de Quito, Quito, EcuadorAlex R. HearnBlue Water Marine Research, Tutukaka, New ZealandJohn C. HoldsworthUniversity of QueenslandBrisbane, Queensland, AustraliaBonnie J. HolmesMicrowave Telemetry, Columbia, MD, USALucy A. Howey & Lance K. B. JordanPelagios-Kakunja, La Paz, MexicoMauricio Hoyos & James T. KetchumMote Marine Laboratory, Center for Shark Research, Sarasota, FL, USARobert E. Hueter, John J. Morris & John P. TyminskiBiological Sciences, University of Windsor, Windsor, Ontario, CanadaNigel E. HusseyCape Research and Diver Development, Simon’s Town, South AfricaDylan T. IrionInstitute of Zoology, Zoological Society of London, London, UKDavid M. P. JacobyCentre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Perth, Western Australia, AustraliaOliver J. D. JewellDyer Island Conservation Trust, Western Cape, South AfricaOliver J. D. Jewell & Alison TownerBlue Wilderness Research Unit, Scottburgh, South AfricaRyan JohnsonUniversity of California Davis, Davis, CA, USAA. Peter KlimleyCape Research Centre, South African National Parks, Steenberg, South AfricaAlison A. KockShark Spotters, Fish Hoek, South AfricaAlison A. KockInstitute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, South AfricaAlison A. KockWestern Cape Department of Agriculture, Veterinary Services, Elsenburg, South AfricaPieter KoenDepartamento de Biologia Marinha, Universidade Federal Fluminense (UFF), Niterói, BrazilFernanda O. LanaDepartment of Zoology, University of Cambridge, Cambridge, UKJames S. E. LeaAtlantic White Shark Conservancy, Chatham, MA, USAHeather MarshallFisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, AustraliaJaime D. McAllister, Jayson M. Semmens, German Soler & Kilian M. StehfestPontificia Universidad Católica del Ecuador Sede Manabi, Portoviejo, EcuadorCesar Peñaherrera-PalmaMarine Megafauna Foundation, Truckee, CA, USASimon J. Pierce & Christoph A. RohnerConservation and Fisheries Department, Ascension Island Government, Georgetown, Ascension Island, UKAndrew J. RichardsonMarine Conservation Society Seychelles, Victoria, SeychellesDavid R. L. RowatCORDIO, East Africa, Mombasa, KenyaMelita SamoilysUpwell, Monterey, CA, USAGeorge ShillingerDepartment of Zoology and Institute for Coastal and Marine Research, Nelson Mandela University, Port Elizabeth, South AfricaMalcolm J. SmaleNational Institute of Polar Research, Tachikawa, Tokyo, JapanYuuki Y. WatanabeSOKENDAI (The Graduate University for Advanced Studies), Tachikawa, Tokyo, JapanYuuki Y. WatanabeCentre for Ecology and Conservation, University of Exeter, Penryn, UKSam B. WeberDepartment of Biological Sciences, University of Rhode Island, Kingston, RI, USABradley M. WetherbeeDepartment of Oceanography and Environment, Fisheries Research Division, Instituto de Fomento Pesquero (IFOP), Valparaíso, ChilePatricia M. ZárateDepartment of Biological Sciences, Macquarie University, Sydney, New South Wales, AustraliaRobert HarcourtSchool of Life and Environmental Sciences, Deakin University, Geelong, Victoria, AustraliaGraeme C. HaysAZTI – BRTA, Pasaia, SpainXabier IrigoienIKERBASQUE, Basque Foundation for Science, Bilbao, SpainXabier IrigoienInstituto de Fisica Interdisciplinar y Sistemas Complejos, Consejo Superior de Investigaciones Cientificas, University of the Balearic Islands, Palma de Mallorca, SpainVictor M. EguiluzWildlife Conservation Research Unit, Department of Zoology, University of Oxford, Tubney, UKLara L. SousaOcean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UKSamantha J. Simpson & David W. SimsCentre for Biological Sciences, University of Southampton, Southampton, UKDavid W. SimsN.Q. and D.W.S. planned the data analysis. N.Q. led the data analysis with contributions from M.V. and D.W.S. N.E.H. contributed analysis tools. D.W.S. led the manuscript writing with contributions from N.Q., N.E.H. and all authors. Seven of the original authors were not included in the Reply authorship; two authors retired from science and the remaining five, although supportive of our Reply, declined to join the authorship due to potential conflicts of interest with the authors of the Comment and/or their institutions. More

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A simple methodological framework was established for testing the BCR model using empirical datasets, consisting of the GPS data of 5 animals. For each of these 5 animals, the three parameters were accordingly tuned using a straightforward estimation procedure. This procedure uses the empirical datasets to infer the parameters’values (Fig. 1). We also used the datasets to assess the model’s reliability—or performance-. We also detail other analyzes that were carried out to ensure the robustness and consistency of the approach, including the deterministic nature of the 5 statistics and a sensitivity analysis. This analysis consists in evaluating the performance of the BCR using a sweep method that produce arbitrary values of the parameters instead of using data-driven estimations. All BCR simulations and the five statistics were performed using MATLAB Version 7.13.0.564 (R2011b).Figure 1Framework used for testing the BCR model performance, for one animal. Black lines detail the two operations processed from the GPS dataset. The 3 parameters are estimated from the GPS data and—using these parameters—1000 simulations of the BCR model are computed. No particular operations are associated with the dotted black lines, but they show how the BCR and the GPS dataset are evaluated and compared using the statistics.Full size imageDataThe locations of 5 GPS-collared red deer (Cervus elaphus) were gathered at La Petite Pierre National Hunting and Wildlife Reserve (NHWR), in north-eastern of France (48.8321 (Lat.) / 7.3514 (Lon.)). The reserve is an unfenced 2670 ha forest area characteristics by deciduous trees (mostly Fagus sylvatica) in the western part and by coniferous species (mostly Pinus sylvestris and Abies alba) in the eastern part in nature reserve surrounded by crops and pastures. It is located at a low elevation area of the Vosges mountain range, which rises up to 400 m a. s. l. The climate is continental with cool summers and mild winters (mean January and July temperatures of 1.4 and 19.6 (^{circ })C, respectively, data from Phalsbourg weather station, Meteo France, from 2004 to 2017). Three ungulate species are present and mainly managed through hunting in the NHWR: wild boar, red deer and roe deer. The present study focuses on female red deer for test model. A detailed overview of the landscape and surroundings is given in40. The GPS data had regular observation frequencies with high frequency sampling (Table 1). In the following text, we note (X_i = [X_i^{(1)}, X_i^{(2)}]) the locations of the individual with (X_i in {mathbb {R}}^{2}), (i=1,2,ldots ,n) and where (X_i^{(1)}), (X_i^{(2)}) represent the longitude and latitude respectively. We use (t_{i}) ((t_1=0)) as the time elapsed between two successive locations (X_{i-1}), (X_{i}) and$$begin{aligned} {overline{T}}= dfrac{1}{n} sum _{i=1}^{n} t_i end{aligned}$$
(1)
as the average sampling time. The trajectory of the animal, or ‘path’, was interpolated using linear interpolation between each pair of recorded observations (Fig. 2 and detailed in Supplementary Methods (Eq. 21) and associated Graphic 2). It approximates the animal travels in straight lines at constant velocity between each pair of locations41. The attractor (X_F) of one individual was estimated as the isobarycenter of all recorded locations:$$begin{aligned} X_F = left[ frac{1}{n}sum _{i=1}^{n} X_i^{(1)}, frac{1}{n}sum _{i=1}^{n} X_i^{(2)} right] end{aligned}$$
(2)
Table 1 Data summary. For each animal, the total number of observations n is given along with the period of collection (date and time), the sampling rate ({overline{T}}) (i.e. the average time between 2 observations) (in min.) and corresponding standard deviation, total distance (in kilometers), total recording time (in days) and average speed s (in (10^{-2}) m.s-1).Full size tableFigure 2Individual paths of the five red deer. Individual paths of the five red deer. The individual paths are plotted for the five red deer (left panel, a) along with the distribution of the relative turning angles (degrees) in polar plots (right panel, b). An angular value of 0 consists in a straight motion from the previous location, while a relative turning angle of 180 (^{circ }) c corresponds to a turn back.Full size image
BCR modelThe model aims at estimating the location at the next time step, given the actual location X at step i:$$begin{aligned} X_{i+1} = f left( X_i right) end{aligned}$$
(3)
such that the function (f(cdot )) is assumed to be representative of the behavior of the animal on sufficiently large time scales. We considered one individual of a given species with no interaction and simulated its movement in continuous space and discrete time in 2 dimensions. The BCR includes 3 parameters coupled with isotropic diffusion:

Diffusion: A random direction with uniform spatial distribution in a 2D plane,

Bias ((p_F)): An increased probability to go to a fixed point named attractor42. This attractor was estimated as the isobarycenter of all recorded locations, defined as (X_F) (Eq. 2). This yields a bias or advection parameter in the direction of (X_F). We use the term ’attraction’ for the bias component of the BCR and the term ’den’ for the attractor. In the data set we study, the den is equivalent to the deer’s bunk.

Correlated component ((p_I)): This parameter increases the probability to move forward, i.e. to perform one step in the direction of the previous step. This is equivalent to a short term bias in movement, when the animal has inertia. We refers to ’inertia’ for the correlated component,

Immobility ((p_s)): We included this as a specific parameter and the movement is stopped for one step. This takes into account the absence of movement between a pair of locations. It can be accredited to technological limitations with the satellite telemetry due to a weak GPS signal strength, possibly due to natural elements: such as when the animal was standing underneath a rock or due to dense clouds, dust particles, mountains or flying objects, such as airplanes). However, this can also be part of the behavior of the animals, during specific times: sleep cycles or foraging for instance. We use (d_{min }) to denote this distance cutoff and set (d_{min }=10)m which corresponds to the magnitude of the error typically found in GPS locations43. We also use (d_{min }) to encapsulate GPS error and peculiar ecological behavior, not associated with (p_I) or (p_F), that are beyond the scope of this study.

The effect of each parameter is detailed in Fig. 3. The typical model contains all three parameters: (p_I), (p_s) and (p_F) for describing animal motion while offering a trade-off between the number of parameters and the description of animal motion.Figure 3Simulated animal motions over arbitrary parameter values. Fifty motions of length (n_s=100) steps are simulated and originate from a common centroid (downward-pointing triangle) with increased levels of correlation ((p_I)), immobility ((p_s)) and bias ((p_F)). Both the location of the attractor (X_F) (black dot) and the log-normal parameters controlling the step size distribution are fixed ((mu =3), (sigma ^2 = 1)).Full size imageEstimation of the parametersThe estimation of the three parameters for each animal is based on the empirical datasets. We distinguished between the states, where one state is described by the pair (left{ X_{i-1}, X_iright} ) and the situations, where one situation is described by the past ((X_{i-1})), current ((X_i)) and future ((X_{i+1})) locations. Knowing both the state of the animal at a given time step i and its situation—the realization of movement at the next time step (i+1)—allowed for collecting the occurrences of inertia, immobilism and attraction. This could be done provided we account for the variability of the movement: the animal may not be heading exactly toward the den, or performing inertia with an exact angular value of (pi ). Thus we discretized the space around the animal in 8 quadrants at each time step i. For example, if the animal was heading straight forward with a margin of (pm pi /8) then it was considered in the situation of inertia. In other words, the state could fall in a situation of inertia with a margin of (pm pi /8). Such a discretization can be represented as a matrix, depending on the state of the animal, its location and the location of the den at each time step (see Supplementary methods, Eq. 19). In order to gather enough data samples per situation, we arbitrary used angular thresholds of (pi /8) as a convenient trade-off between data scarcity and precision loss. Using smaller threshold values (say (pi /10)) may result in too few samples per situations. Using larger threshold values such as (pi /4) may result in a loss of precision while capturing additional movement samples that may not correspond to the situation.We first needed to define in which state is the animal at each step i. A state is the 2-tuple containing the previous and actual observation ({X_{i-1}, X_i}). We wanted to distinguish between non-conflicting and conflicting states, where a non-conflicting state is when the animal is in one state only, while a conflicting state is when the animal is in two states at once. We defined two conflicting states:$$begin{aligned} {mathscr {H}}_{IF}:={i : widehat{ left| X_{i-1} X_i X_F right| } le pi /8} end{aligned}$$
(4)
when the animal was already heading toward the den (X_F), and:$$begin{aligned} {mathscr {H}}_{Is}:={i : dleft( X_{i-1}, X_iright) le d_{min }} end{aligned}$$
(5)
when the distance between two consecutive observations was too small ((le d_{min }) m.), describing an individual that was already immobile. Such that the subset of non-conflicting states is:$$begin{aligned} {mathscr {H}}:={1,cdots ,n} – {mathscr {H}}_{IF} – {mathscr {H}}_{Is} end{aligned}$$
(6)
We then needed to assess in which situation the animal was for each corresponding state. A situation is the 3-tuple (left{ X_{i-1}, X_i, X_{i+1}right} ). We defined three subsets of situations corresponding to a straight forward motion (I), no motion (s) and a motion toward the den (F):$$begin{aligned} I:= {i: pi – pi /8 < widehat{(X_{i-1} X_i X_{i+1})} le pi + pi /8} end{aligned}$$ (7) $$begin{aligned} s:= {i: dleft( X_i, X_{i+1} right) le d_{min }} end{aligned}$$ (8) $$begin{aligned} F:= {i: mid widehat{X_{i-1} X_t X_{i+1}} - widehat{X_{i-1} X_i X_F} mid le pi /8} end{aligned}$$ (9) With (d(cdot ,cdot )) the Euclidean distance between two locations. For the situations in s, we considered that the animal is not performing a motion if the Euclidean distance between two successive locations was (le d_{min })m.We counted the number of states falling in each situation, for states in ({mathscr {H}}) (Eq. 6). We defined (x_{1}), (x_{2}), (x_{3}) as the empirical proportion of cases corresponding to each situation:$$begin{aligned} {left{ begin{array}{ll} x_1 = dfrac{# I cap {mathscr {H}}}{# {mathscr {H}}} ; qquad x_1:=dfrac{1+p_I}{chi } \[16pt] x_2 =dfrac{# s cap {mathscr {H}}}{# {mathscr {H}}} ; qquad x_2:=dfrac{p_s}{chi }\[16pt] x_3 = dfrac{# F cap {mathscr {H}}}{# {mathscr {H}}} ; qquad x_3:=dfrac{1+p_F}{chi } end{array}right. } end{aligned}$$ (10) with (chi = 8+p_{I}+p_{s}+p_{F}). The values of (x_1), (x_2) and (x_3) were then gathered for each animal. We did not use immobile locations (i.e. distances separating two successive observations must be ( > d_{min }) m) for the estimations of (x_1) and (x_3). Solving Eq. (10) for (chi ) with respect to (x_1), (x_2), (x_3) yields:$$begin{aligned} chi = dfrac{6}{1-(x_{1} + x_{2} + x_{3})} end{aligned}$$
(11)
Plugging in Eq. 10:$$begin{aligned} {left{ begin{array}{ll} p_{I} = x_1 chi -1\ p_{s} = x_2 chi \ p_{F} = x_3 chi -1 end{array}right. } end{aligned}$$
(12)
Note that we assumed that (p_{IF} = p_I + p_F) in ({mathscr {H}}_{IF}) and (p_{Is} = p_I + p_s) in ({mathscr {H}}_{Is}) as a convenient arrangement and ignoring higher order conflicting cases. Investigating the step-size distribution in the 5 deers, we found a log-normal step size distribution (Supplementary Fig. S1). We then set a log-normal distribution (ln {mathscr {N}}(mu , sigma ^2)) for the step size distribution for the step size in the BCR.The same estimation procedure was used for configurations using a different number of parameters and quantity (chi ) is accordingly calculated depending on the number of parameters used. It is possible to obtain negative values using this inference method. A parameter with a negative values reflects a direction that is not favored by the animal. In such a case, one should rethink the design of the BCR by changing the parameters (see Supplementary methods, section “negative parameters”). In the subsequent sections, we only consider parameters with positives values.BCR dynamicsThe BCR dynamics for each animal are completely determined by the three parameters (p_F), (p_I), (p_s), taking values in ({mathbb {R}}^{+}), and the step-size distribution. If (p_F = p_I = p_s = 0), the BCR resumes to a typical two-dimensional random walk with a log-normal step size distribution (ln {mathscr {N}}(mu , sigma ^2)). The dynamics can be visualized in Fig. 3 for different values of each parameter. When simulating a step in the model, the motion in ({mathscr {H}}) is described by:$$begin{aligned} f left( X_i right) = {left{ begin{array}{ll} left{ X_i^{(1)} + d cos (alpha _1) ; X_i^{(2)} + d sin (alpha _1) right} &{} qquad text {if } x in [0,8[ \ left{ X_i^{(1)} + d cos (alpha _2) ; X_i^{(2)} + d sin (alpha _2) right} &{} qquad text {if } x in [8,8+p_I[ \ X_i &{} qquad text {if } x in [8+p_I, 8+p_I+p_s[ \ left{ X_i^{(1)} + d cos (alpha _3) ; X_i^{(2)} + d sin (alpha _3) right} &{} qquad text {else} end{array}right. } end{aligned}$$
(13)
with x, d, (alpha _1) random variables defined as (x sim {mathscr {U}} in [0, chi ]), (d sim ln {mathscr {N}}(mu , sigma )), (alpha _1 sim {mathscr {U}} in [0,2pi ]). Variables (alpha _2), (alpha _3) are related to the angular values (alpha _2 = {{,{mathrm{atan2}},}}(X_{i}^2 – X_{i-1}^2, X_{i}^1 – X_{i-1}^1)), (alpha _3 = {{,{mathrm{atan2}},}}(X_{F}^{(2)} – X_{i}^{(2)}, X_{F}^{(1)} – X_{i}^{(1)})) with ({{,{mathrm{atan2}},}}(y, x)) the four quadrant inverse tangent function (14):$$begin{aligned} {{,{mathrm{atan2}},}}(y, x) = {left{ begin{array}{ll} arctan left( {frac{y}{x}}right) &{} x > 0,\ arctan left( {frac{y}{x}}right) +pi &{} x< 0{text {, }}y ge 0,\ arctan left( {frac{y}{x}}right) -pi &{} x< 0{text {, }}y< 0,\ +{frac{pi }{2}} &{} x=0{text {, }}y > 0,\ -{frac{pi }{2}} &{} x=0{text {, }}y < 0,\ 0 &{} x=0{text {, }}y=0text {.} end{array}right. } end{aligned}$$ (14) The motion in ({mathscr {H}}_{Is}) is:$$begin{aligned} f left( X_i right) = {left{ begin{array}{ll} left{ X_i^{(1)} + d cos (alpha _1) ; X_i^{(2)} + d sin (alpha _1) right} &{} qquad text {if } x in [0,8[ \ X_i &{} qquad text {if } x in [8, 8+p_I+p_s[ \ left{ X_i^{(1)} + d cos (alpha _3) ; X_i^{(2)} + d sin (alpha _3) right} &{} qquad text {else} end{array}right. } end{aligned}$$ (15) The motion in ({mathscr {H}}_{IF}) is:$$begin{aligned} f left( X_t right) = {left{ begin{array}{ll} left{ X_i^{(1)} + d cos (alpha _1) ; X_i^{(2)} + d sin (alpha _1) right} &{} qquad text {if } x in [0,8[ \ X_t &{} qquad text {if } x in [8, 8+p_s[ \ left{ X_i^{(1)} + d cos (alpha _2) ; X_i^{(2)} + d sin (alpha _2) right} &{} qquad text {else} end{array}right. } end{aligned}$$ (16) Statistics for describing animal movementWe simulated (N=1000) BCR and used 5 statistics to assess the model reliability on spatial features including: (i) the distribution of relative turning angles which provides information about the movement of the animal, (ii) the home range which provides information about the spatial density of observations and (iii) observation counts using still and mobile transects, providing information on absolute observation abundance44. A detailed description of each statistic is provided in Supplementary Methods and Fig. S2. The reliability—or performance—was assessed in each animal and studied statistic using two error terms (e_1) and (e_2). Error (e_1) is the (L^1) norm to compare the differences between the statistic ({tilde{mathscr {S}}}) computed over a simulated path, and the statistic (smash {{mathscr {S}}}) computed over the data-set:$$begin{aligned} e_1 mathrel {mathop :}= sum {text {errors}} = sum _{k=1}^N |smash {{mathscr {S}}}- {tilde{mathscr {S}}}_k| end{aligned}$$ (17) With (k = 1,ldots , N) the number of simulations of the BCR. Error (e_1) is the sum of absolute differences in the given statistic, and is a natural way of measuring the distance between the statistics computed on the data set and the trajectories generated using the BCR. We also focused on the average relative error (e_2) as an indicator of the sensitivity:$$begin{aligned} e_2 mathrel {mathop :}= dfrac{1}{N} sum _{k=1}^N dfrac{{tilde{mathscr {S}}}_k}{smash {{mathscr {S}}}} end{aligned}$$ (18) Distribution of turning anglesFor each individual, the distribution of counter-clockwise relative turning angles (widehat{(X_{i-1} X_i X_{i+1})}) was gathered, provided (d(X_{i-1}, X_{i}) > d_{min }) and (d(X_{i}, X_{i+1}) > d_{min }). This means that we only kept the angles from observations that were separated by an Euclidean distance greater than (d_{min }).Home rangeWe used an adaptive kernel density estimator (matlab package kde2d—kernel density estimation version 1.3.0.0) as an estimator of the utilization distribution45 to represent the home range of the animal. The approach of Z.I. Botev provided an estimate of observation density using a bivariate (Gaussian) kernel with diagonal bandwidth matrix46. The density was estimated over a grid of (210 times 210) nodes and we computed the home range area (in m2) for various values: 100, 99, 95, 90, 80, …, 20, 10% of the estimated density. Similarly to the distribution of turning angles, we compared each value of the data’s home range against the simulated one.DilationDilation is generally used to account for the spatial attributes of an object such as to measure an area around the path or the volume of a brownian motion (see Wiener sausage47 and Gromov–Hausdorff distance). In our approach, we use dilation of both simulated and GPS paths for two reasons: to have a real—and comparable—number that accounts for how a trajectory has explored space and because it is natural tool from a census point of view (the dilated path corresponds to the area where the animal can be detected). Each simulated or real path was plotted in binary format in a window and dilated with a disk shape. The window size was set to a huge value in order to encapsulate the dilated path while preventing boundary effects, i.e. the convex envelope of the dilated area did not collide with any window border. We then estimated the surface covered by the dilated path for 100 different sizes of the disk, from disk size 1 to disk size 100. We compared each value of the data’s estimated surface against the simulated one.Immobile transectsWe used still transects that counted the number of times the animal was seen in their line of sight. We arbitrary set the line-of-sight value at 200 m. The number of sightings of each transect was gathered and ordered in decreasing order, thus breaking the spatial dependence. We then compared the bins of the resulting histogram in the data and in the simulated path.Mobile transectsFirst, the movement of the animal was linearly interpolated from the GPS data, meaning that between two recorded locations the individual followed a linear path. The speed of the animal between two locations was accordingly reconstructed using the recorded times (t_i) between each location. Second, we used mobile transects as the ecological sampling method, where each transect ‘count’ the intersection between its path and the animal’s one. The mobile transects followed a predefined path at a given constant speed as time increased. The area of vision of each transect was defined as a circle of a given radius. Each time the path of an individual collided with an area of vision, the count of the corresponding transect increased by 1. Two types of movements were used: linear and clockwise rotational transects. The initial locations of both types of transects are (X_1) and (X_F). Both the animal and mobile transects started to move at the same time. At each of the two locations (X_1), (X_F), 8 linear transects moved in the 8 cardinal directions, totalizing 16 transects. For the linear transects, every 10,000 time steps, we set (2 times 8) new transects starting at the same locations and following the same directions. Clockwise rotational transects were rotated around (X_1) and (X_F) using a 500 m radius. When we reached (t_n), we gathered the total count (i.e. the count of all transects). For the two types of transects, we gathered the total count for 6 different lines of sight: 50, 100, 200, 400, 500, 1000 m. and 4 speeds: s/4, s/2, s, 2 s with s the average speed of the animal. We then aggregated the overall count in each of the two types of transects, and compared the results from the data and the simulated path (Supplementary Methods and Fig. S2).Scale invarianceSeveral authors pointed out that the temporal resolution of the discretization is of importance: it should be relevant to the considered behavioral mechanisms5,48,49,50. Schlägel and Lewis focused on the quantification of movement models’ robustness under subsampled movement paths49. They found that increased subsampling leads to a strong deviation of the central parameter in resource selection models49,51. They underlined that important quantities derived from empirical data (e.g. parameters estimates, travel distance or sinuosity) can differ based on the temporal resolution of the data49,51. Moreover, Postlethwaite and Dennis highlighted the difficulty of comparing model results amongst tracking-datasets that vary substantially in temporal grain50). Each of the studied dataset has a relatively high sampling rate (roughly 10 m) and a period of study that is appropriate to the analysis of animal movement at the year scale (Table 1). In order to investigate such a possible effect on the BCR dynamic, we changed the sampling rate of the movement path to ensure that the three parameters (p_I), (p_s) and (p_F) are scale invariant. The movement path formed by the GPS observations (X_i) was subsampled (decimated) for each individual. We only kept every (k^{text {th}}) observation starting with the first one and (k in left[ 1,10right] ). For (k=1) the path corresponded to the original one. The time spent between each successive observation was also accordingly reconstructed in order to keep track of ({overline{T}}) in subsampled movement paths. The time between two locations (X_i) and (X_{i+k}) was reconstructed as:$$begin{aligned} t_{j}’ = sum _{i=j}^{i+(k-1)} t_i end{aligned}$$
(19)
with (j in left[ 1, 1+k, 1+2k, ldots , n-left( k-1 right) right] ). We did not change the value of (d_{min }) as we subsampled the movement path because we designed (p_s) for capturing GPS noise and movements that are associated with peculiar ecological behaviors that are beyond the scope of this study in terms of time and spatial scales (foraging for instance). We then compared the resulting parameters (p_I), (p_F) and (p_s) as the resampling rate k increased.FluctuationsWhereas the BCR is a stochastic process, the deterministic aspects of the 5 statistics were tested with an increasing number of steps (n_s). The statistic associated with each realization of the model (a simulated path) is a random variable. If the distribution of these random variables has low concentration (high variance) then it is not a convenient statistic as it cannot be used as a reference for assessing the model’s performance, even when averaging over multiples realizations. On the opposite, if the statistic is deterministic (no fluctuations) it can provide a reliable tool to assess the model’s performance. This was numerically tested over a range of increasing (n_s) values with (n_s = 10^4, 2times 10^4, ldots , 4 times 10^5). For each of those step values, a set of 100 BCR was simulated with parameters (p_I), (p_F) and (p_s) estimated from the first deer (see Table 2) and we studied the variance of the statistics.Sensitivity analysisIn order to assess whether the estimated parameters are optimal (i.e. providing the best possible performance) and to study parameter scarcity, we also evaluated the performance of the model using arbitrary weight values. We first started by evaluating how using one parameter instead of the three could alter the performance of the model. We then extended this sensitivity analyse by drawing arbitrary values for each parameter from a multi-dimensional square mesh, whose center corresponds to the estimated values of (p_I), (p_s), (p_F), estimated using GPS data (Fig. 1). We additionally used values that are distant from the estimated ones, up to (p_I=3), (p_F=3) and (p_s=5). We tested a total of 151 new configurations with these arbitrary values. For each configuration, we ran 150 simulations and evaluated them using the 5 statistics. The mean error of (|smash {{mathscr {S}}}- {tilde{mathscr {S}}}_k|) and its standard deviation are gathered and plotted for each arbitrary configuration. As a resume, we replicate the framework described in Fig. 1 but we inject arbitrary parameters instead of using data-driven parameterisations.ApplicationThe proposed model could be used to infer environmental and behavior information from the dataset. We chose to illustrate such an application by trying to detect anomalous voids (or holes) in the spatial territory of the individual using the GPS dataset and Monte-Carlo simulations of the model. Anomalous means that the observed void is not related to the randomness of the movement, but rather related to a geographical artifact. The parameters (p_I), (p_F), (p_s), (mu ) and (sigma ^2) of the BCR were accordingly estimated from the data of each individual, similarly to previous experiments (Fig. 1). A simple heuristic was used to find voids in empirical and simulated paths for each individual: we computed the alpha shape of all locations using a fixed alpha radius of 60 m. This allowed for determining the surface covered by all locations while preserving the voids. We then collected the area of each void provided they had an area of at least 100 m2. We focused on voids near the center of the alpha shape in order to avoid artificial voids, generated by the weak density of locations at the boundaries. We ran 10,000 iterations of the model for each animal and estimated the probability (p_{varnothing }) of finding voids of different sizes in the simulated paths. This probability was then compared to voids found in the GPS datasets and available environmental information was used to determine whether any geographical element(s) could explain the unexpected voids. More

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NEWS AND VIEWS
07 July 2021

How to buffer against an urban food shortage

There is widespread concern that the risk of food shocks — sudden disruptions to food supply — is increasing. It emerges that a city’s vulnerability to food shocks can be reduced by diversifying its supply chains.

Zia Mehrabi

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Zia Mehrabi

Zia Mehrabi is at the Sustainability Innovation Lab at Colorado and at the Environmental Studies Program, University of Colorado Boulder, Boulder, Colorado 80303, USA.

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More than half of the world’s population lives in urban areas, a proportion that is set to increase1 to 68% by 2050. These urban residents depend on supply chains to produce, procure, prepare and deliver food, and they are exposed to potential supply-chain disruptions and food shortages from changes in human activity and natural processes. There is growing recognition that food-system resilience needs to be improved, but how best to buffer against urban food shortages remains an open question for both research and policy. Writing in Nature, Gomez et al.2 assess how the flow of agricultural products to a city depends on the diversity of the city’s trading partners. The authors apply ideas from engineering — such as those used when ensuring infrastructure is protected from flooding — to inform the design of food systems that can buffer cities against food shortfalls.For decades, scientists and industry have been warning governments and consumers about the risks of food shortages. Such shortages have a range of possible causes, including droughts and heatwaves, pest and disease outbreaks, financial downturns and trade policies3. More recently, the COVID-19 pandemic has led academics, and society more generally, to revisit the question of how fragile urban food supplies really are (Fig. 1).

Figure 1 | Empty supermarket shelves during the COVID-19 pandemic. Many city dwellers around the world experienced such scenes, which were largely driven by panic buying and changing consumer behaviour. Gomez et al.2 demonstrate that the resilience of food supply chains can be increased by boosting their diversity.Credit: Oli Scarff/AFP/Getty

There have been many proposed solutions to deal with the dangers of food shortages, from climate-resilient agricultural management practices to promoting local food systems and self-sufficiency4. One solution that is gaining attention is to increase the number and variety of agricultural products, farms and companies procuring and delivering food. Diverse food supply chains might buffer cities against food shortages — in the same way that, in finance, a varied portfolio of stocks limits investment risk and, in ecology, a diverse mixture of species maintains ecosystem functions.
Read the paper: Supply chain diversity buffers cities against food shocks
Gomez et al. used data on the origin and destination of different agricultural commodities for 284 cities and 45 non-city geographical areas in the United States. They identified domestic food systems for each city — that is, all of the geographical areas that supply crops, meat, live animals or animal feed to that city. The authors then determined how many cities faced different thresholds of abrupt food-supply disruptions, known as food shocks, using the percentage difference between the minimum and mean of supply amounts for each food sector over four years for each city. More specifically, they counted the number of cities in which the minimum was more than a particular percentage (ranging from 3% to 15%) smaller than the mean in any one of those four years.Next, Gomez and colleagues combined those data with simple indicators of geographical similarity — such as the physical distance and difference in climate between each city and the geographical areas in that city’s supply network. With this information in hand, the authors tested the idea that groups of cities with more-diverse supply chains are better able to buffer against food shocks than are groups whose supply chains are less diverse. Indeed, they found that cities importing food from suppliers that are more dissimilar from themselves are less likely to face shocks than are cities whose supply-chain partners are less diverse. Such supply-chain benefits would not be reaped from having solely local food systems.Gomez et al. then considered design concepts from engineering, where infrastructure systems should be planned to withstand shocks — such as extreme flooding — of a given frequency and magnitude. The authors undertook some bold extrapolations, in which they estimated the size of food shocks that would be faced by different US cities given their current supply-chain diversity. They found that a rare shock, such as one occurring once in 100 years, would cause a food-supply loss of about 22–32% across different cities.
Transforming the global food system
The other implicit finding from Gomez and colleagues’ model is that even moderate supply-chain diversity is effective at reducing the probability of extremely large shocks. The authors also applied their analysis to shocks happening in multiple food sectors simultaneously. They obtained similar results to those for single-sector shocks — with supply-chain diversity also providing a buffering effect for these even rarer occurrences.Gomez and colleagues’ work has major implications for the way in which resilient food systems should be built, but it also has a few caveats. First, the authors used only four years of data for each city, posing problems for characterizing the distribution of shocks at each city. This limited time series makes it difficult to define the baseline variation in food supply — that is, what is considered normal — for consumers and retailers alike. It also makes it hard to see to what extent diversified supply chains buffer against food shortages under normal conditions compared with years marked by extreme events, and whether the net benefits are large enough to trigger a change in food-procurement policies.Second, the food-flow data used by Gomez et al. do not represent actual flows for each year, but instead are simply annual production quantities proportionally distributed according to observed flows5 in 2012. Therefore, the authors’ analysis does not capture, or allow for, rerouting or other social responses at the onset of extreme events. Such social responses within and after shock years would result in changing food flows across the supply network.
Rural areas drive increases in global obesity
Third, Gomez and colleagues did not validate the predictive worth of their model beyond the four years considered, or outside the United States. This lack of verification is perhaps most limiting for applying the findings in practice — partly because the stability of food supply is itself dynamic, and will change with increasing volumes and types of food consumed, as well as with production technology. Although the observed phenomenon and general patterns might hold in other years and geographical regions, no data or analyses exist to validate whether the authors’ design suggestions will protect against future shocks to the degree claimed.Designing urban food systems to specification is not as easy as engineering a bridge or dam that won’t fail in 100 years. The major global concern with respect to urban food shortages and food security is for populations of middle- to low-income countries, particularly those that are dependent on imports6. Theoretically, supply-chain diversity will also have a buffering effect for these populations when the number of urban dwellers starts to drastically increase in the coming years, especially in Africa. However, such nations are probably not accurately described by the model presented. Moreover, they have different policy options and capacities for producing diverse supply chains compared with those possible in the United States. Nevertheless, Gomez and colleagues’ work provides a timely and refreshing reminder that building diverse supply chains offers a crucial mechanism for protecting urban dwellers from food shortages.

Nature 595, 175-176 (2021)
doi: https://doi.org/10.1038/d41586-021-01758-6

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Competing Interests
The author declares no competing interests.

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