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Simulation Data & R scripts for: "Introducing recurrent events analyses to assess species interactions based on camera trap data: a comparison with time-to-first-event approaches"
<p><strong>Files descriptions:</strong></p> <p>All csv files refer to results from the different models (PAMM, AARs, Linear models, MRPPs) on each iteration of the simulation. One row being one iteration. <br>"results_perfect_detection.csv" refers to the results from the first simulation part with all the observations.<br>"results_imperfect_detection.csv" refers to the results from the first simulation part with randomly thinned observations to mimick imperfect detection.</p> <p>ID_run: identified of the iteration (N: number of sites, D_AB: duration of the effect of A on B, D_BA: duration of the effect of B on A, AB: effect of A on B, BA: effect of B on A, Se: seed number of the iteration).<br>PAMM30: p-value of the PAMM running on the 30-days survey.<br>PAMM7: p-value of the PAMM running on the 7-days survey.<br>AAR1: ratio value for the Avoidance-Attraction-Ratio calculating AB/BA.<br>AAR2: ratio value for the Avoidance-Attraction-Ratio calculating BAB/BB.<br>Harmsen_P: p-value from the linear model with interaction Species1*Species2 from Harmsen et al. (2009).<br>Niedballa_P: p-value from the linear model comparing AB to BA (Niedballa et al. 2021).<br>Karanth_permA: rank of the observed interval duration median (AB and BA undifferenciated) compared to the randomized median distribution, when permuting on species A (Karanth et al. 2017).<br>MurphyAB_permA: rank of the observed AB interval duration median compared to the randomized median distribution, when permuting on species A (Murphy et al. 2021). <br>MurphyBA_permA: rank of the observed BA interval duration median compared to the randomized median distribution, when permuting on species A (Murphy et al. 2021). <br>Karanth_permB: rank of the observed interval duration median (AB and BA undifferenciated) compared to the randomized median distribution, when permuting on species B (Karanth et al. 2017).<br>MurphyAB_permB: rank of the observed AB interval duration median compared to the randomized median distribution, when permuting on species B (Murphy et al. 2021). <br>MurphyBA_permB: rank of the observed BA interval duration median compared to the randomized median distribution, when permuting on species B (Murphy et al. 2021). <br> </p> <p>"results_int_dir_perf_det.csv" refers to the results from the second simulation part, with all the observations.<br>"results_int_dir_imperf_det.csv" refers to the results from the second simulation part, with randomly thinned observations to mimick imperfect detection.<br>ID_run: identified of the iteration (N: number of sites, D_AB: duration of the effect of A on B, D_BA: duration of the effect of B on A, AB: effect of A on B, BA: effect of B on A, Se: seed number of the iteration).<br>p_pamm7_AB: p-value of the PAMM running on the 7-days survey testing for the effect of A on B.<br>p_pamm7_AB: p-value of the PAMM running on the 7-days survey testing for the effect of B on A.<br>AAR1: ratio value for the Avoidance-Attraction-Ratio calculating AB/BA.<br>AAR2_BAB: ratio value for the Avoidance-Attraction-Ratio calculating BAB/BB.<br>AAR2_ABA: ratio value for the Avoidance-Attraction-Ratio calculating ABA/AA.<br>Harmsen_P: p-value from the linear model with interaction Species1*Species2 from Harmsen et al. (2009).<br>Niedballa_P: p-value from the linear model comparing AB to BA (Niedballa et al. 2021).<br>Karanth_permA: rank of the observed interval duration median (AB and BA undifferenciated) compared to the randomized median distribution, when permuting on species A (Karanth et al. 2017).<br>MurphyAB_permA: rank of the observed AB interval duration median compared to the randomized median distribution, when permuting on species A (Murphy et al. 2021). <br>MurphyBA_permA: rank of the observed BA interval duration median compared to the randomized median distribution, when permuting on species A (Murphy et al. 2021). <br>Karanth_permB: rank of the observed interval duration median (AB and BA undifferenciated) compared to the randomized median distribution, when permuting on species B (Karanth et al. 2017).<br>MurphyAB_permB: rank of the observed AB interval duration median compared to the randomized median distribution, when permuting on species B (Murphy et al. 2021). <br>MurphyBA_permB: rank of the observed BA interval duration median compared to the randomized median distribution, when permuting on species B (Murphy et al. 2021). <br> </p> <p><strong>Scripts files description:</strong><br>1_Functions: R script containing the functions:<br> - MRPP from Karanth et al. (2017) adapted here for time efficiency.<br> - MRPP from Murphy et al. (2021) adapted here for time efficiency.<br> - Version of the ct_to_recurrent() function from the recurrent package adapted to process parallized on the simulation datasets.<br> - The simulation() function used to simulate two species observations with reciprocal effect on each other.<br>2_Simulations: R script containing the parameters definitions for all iterations (for the two parts of the simulations), the simulation paralellization and the random thinning mimicking imperfect detection.<br>3_Approaches comparison: R script containing the fit of the different models tested on the simulated data.<br>3_1_Real data comparison: R script containing the fit of the different models tested on the real data example from Murphy et al. 2021.<br>4_Graphs: R script containing the code for plotting results from the simulation part and appendices.<br>5_1_Appendix - Check for similarity between codes for Karanth et al 2017 method: R script containing Karanth et al. (2017) and Murphy et al. (2021) codes lines and the adapted version for time-efficiency matter and a comparison to verify similarity of results.<br>5_2_Appendix - Multi-response procedure permutation difference: R script containing R code to test for difference of the MRPPs approaches according to the species on which permutation are done.</p>
Fig. 1 in A preliminary camera trapping study of mammals of Monti Lepini (Central Italy)
Fig. 1 - Geographical location of the Lepini Mountains area and positions of the camera traps (the different colours group the two arrays of cameras). / Collocazione geografica dei Monti Lepini e schema di posizionamento delle fototrappole (i colori differenti sono per le due disposizioni consecutive di ogni sessione).
Fig. 2 in On the activity of two medium-sized canids: the Golden Jackal (Canis aureus) and the Red Fox (Vulpes vulpes) in the Natural Bark "Sinite Kamani" (Bulgaria) revealed by camera traps
Fig. 2. Number of all pictures of Red Fox (Vulpes vulpes) taken during 24h (expressed for one hour time interval) during seasons.
Fig. 4 in On the activity of two medium-sized canids: the Golden Jackal (Canis aureus) and the Red Fox (Vulpes vulpes) in the Natural Bark "Sinite Kamani" (Bulgaria) revealed by camera traps
Fig. 4. Daytime activity (feeding on dog food) of the Red Fox and the Golden Jackal registered by camera traps at the Sinite Kamani Natural Park.
Fig. 1 in On the activity of two medium-sized canids: the Golden Jackal (Canis aureus) and the Red Fox (Vulpes vulpes) in the Natural Bark "Sinite Kamani" (Bulgaria) revealed by camera traps
Fig. 1. Location of Sinite Kamani Natural Park and schematic position of the camera traps through the park (black circles).
Fig. 3 in On the activity of two medium-sized canids: the Golden Jackal (Canis aureus) and the Red Fox (Vulpes vulpes) in the Natural Bark "Sinite Kamani" (Bulgaria) revealed by camera traps
Fig. 3. Number of all pictures of Golden Jackal (Canis aureus) taken during 24h (expressed for one hour time interval) during seasons.
Рис. 2. Черношапочные сурки и их местообитания на хребте КоΑар: A — виΑ на ЦентраΛьный КоΑар и ΑоΛину р. СреΑний Сакукан; B — местообитание сурков поΑ переваΛом; C — местообитание сурков по берегам р. Того; D — местообитание сурков на вершине гребня, каΑр с фотоΛовушки; E — сурки; F — черношапочный сурок обΛизывает пΛасты каменного угΛя, каΑр из виΑеосъемки Fig. 2. Black-capped marmots and their habitats on the Kodar Ridge: A — view of the Central Kodar and the valley of the Middle Sakukan River; B — habitat of marmots under the mountain pass; C — habitat of marmots along the banks of the Togo River; D — marmot habitat at the top of the mountain ridge, camera trap frame; E — marmots; F — the black-capped marmot licks coal, freeze frame from video in On the ecology of the Doppelmayer`s Black-capped marmot (Marmota camtschatica doppelmayeri Birula, 1922): Kodar Mountain Ridge, Transbaikalia, Russia
Рис. 2. Черношапочные сурки и их местообитания на хребте КоΑар: A — виΑ на ЦентраΛьный КоΑар и ΑоΛину р. СреΑний Сакукан; B — местообитание сурков поΑ переваΛом; C — местообитание сурков по берегам р. Того; D — местообитание сурков на вершине гребня, каΑр с фотоΛовушки; E — сурки; F — черношапочный сурок обΛизывает пΛасты каменного угΛя, каΑр из виΑеосъемки Fig. 2. Black-capped marmots and their habitats on the Kodar Ridge: A — view of the Central Kodar and the valley of the Middle Sakukan River; B — habitat of marmots under the mountain pass; C — habitat of marmots along the banks of the Togo River; D — marmot habitat at the top of the mountain ridge, camera trap frame; E — marmots; F — the black-capped marmot licks coal, freeze frame from video
Рис. 5. Пятнистый оΛень неоΑнократно снят фотоΛовушками в бассейнах рек Обор и Àурмин. 15.10.2020. 14.49. Фото А. С. БатаΛова Fig. 5. Sika deer repeatedly photographed by camera traps in the basins of the rivers Obor and Durmin; 15.10.2020. 14:49. Photo by A. S. Batalova in New data on the distribution of sika deer Cervus nippon Temminck, 1838 in the Lower Amur Region
Рис. 5. Пятнистый оΛень неоΑнократно снят фотоΛовушками в бассейнах рек Обор и Àурмин. 15.10.2020. 14.49. Фото А. С. БатаΛова Fig. 5. Sika deer repeatedly photographed by camera traps in the basins of the rivers Obor and Durmin; 15.10.2020. 14:49. Photo by A. S. Batalova
Рис. 1. Карта-схема заповеΔника «БоΛьшехехцирский» и распоΛожение фотоΛовушек на территории. ЛегенΔа: спΛошная черная Λиния — границы заповеΔника; пунктирная Λиния — границы заказника «Хехцирский»; красный кружок — место установки фотоΛовушки Fig. 1. The map of the Bolshekhekhtsirsky State Nature Reserve and the location of camera traps. Legend: solid black line boundaries of the reserve; dotted line — bou in New data on the mammalian fauna of the Bolshekhekhtsirsky Nature Reserve
Рис. 1. Карта-схема заповеΔника «БоΛьшехехцирский» и распоΛожение фотоΛовушек на территории. ЛегенΔа: спΛошная черная Λиния — границы заповеΔника; пунктирная Λиния — границы заказника «Хехцирский»; красный кружок — место установки фотоΛовушки Fig. 1. The map of the Bolshekhekhtsirsky State Nature Reserve and the location of camera traps. Legend: solid black line boundaries of the reserve; dotted line — bou
Supporting data for "Snap happy: camera traps are an effective sampling tool when compared to alternative methods"
<p>Author recommendations and response ratios extracted from studies comparing camera traps to another survey method. These data underlie the analyses in a the journal article 'Snap happy: camera traps are an effective sampling tool when compared to alternative methods', published in the journal Royal Society Open Science (https://doi.org/10.1098/rsos.181748). </p>
Camera trap fauna survey in Talissieu (France) 2016-2018
<p>Mammals and birds presence identified from a camera trap survey in a mixed forest and fields environment in the Lavours marsh (France). This dataset gathers observations from April 2016 to November 2018 (with some missing days) from a single camera trap (2 successive models) placed in different locations in Talissieu (Ain, France).</p> <p>See <a href="https://doi.org/10.5281/zenodo.2533381">doi:10.5281/zenodo.2533381</a> for more information.</p> <p>location : 5.7211 45.8625 (WGS84)</p> <p>fields :</p> <pre>id_obs <int> identifier date_heure <dttm> UTC date time of observation (%Y-%m-%dT%H:%M:%SZ) cd_nom_taxref <int> TAXREF taxon identifier see https://inpn.mnhn.fr/programme/referentiel-taxonomique-taxref taxref_cd_ref <int> TAXREF valid taxon identifier taxon <chr> taxon name (binomial) espece <chr> taxon name (vernacular, french) nom_complet <chr> taxon name (binomial with author) nom_complet_html <chr> taxon name (binomial italicized, with author) classe <chr> class ordre <chr> order famille <chr> family rang <chr> rank (ES : species, GN : genus, FM : family, OR : order, CL : class) effectif <int> number of individuals sexe <chr> sex type <chr> V: visual direction <chr> direction of travel (mostly blank) temperature <int> ambiant temperature (°C) duree_estimee_min <int> duration in frame (min) rem_obs <chr> observation note id_session <int> session identifier debut_session <dttm> session date time start UTC (%Y-%m-%dT%H:%M:%SZ) fin_session <dttm> session date time end UTC (%Y-%m-%dT%H:%M:%SZ) duree_session_h <int> session duration (h) rem_session <chr> session note id_localisation <int> camera trap location identifier lieu <chr> camera trap location name x_wgs84 <dbl> camera trap longitude (decimal degrees WGS84) y_wgs84 <dbl> camera trap latitude (decimal degrees WGS84) alti <int> camera trap altitude (m, NGF) azimuth <int> camera trap azimuth (°) habitat <chr> habitat type environnement <chr> local environment type cible <chr> target camera <chr> camera model id_etude <int> study identifier nom_etude <chr> study name date <date> observation date (%Y-%m-%d) heure <dbl> observation hour (%I, UTC)</pre> <p> </p>
Fig. 2 in Camera Trapping The Indochinese Tiger, Panthera Tigris Corbetti, In A Secondary Forest In Peninsular Malaysia
Fig. 2. Cumulative number of individual tiger captured per month around FELDA Jerangau Barat, Terengganu between April 2000 to September 2000.
Fig. 3 in Camera Trapping The Indochinese Tiger, Panthera Tigris Corbetti, In A Secondary Forest In Peninsular Malaysia
Fig. 3. Identification of tiger individuals from infra-red sensor camera traps. Example of individual identification of tiger cubs (a, b) and adults (c, d) based on stripe patterns.
Fig. 2 in Camera-Trapping Survey Of Mammals In And Around Imbak Canyon Conservation Area In Sabah, Malaysian Borneo
Fig. 2. The observed species accumulation curve (-o-) and 95% CIs (---) for mammalian species in and around Imbak Canyon Conservation Area. The curve was constructed using abundancebased rarefaction approach (i.e., by using the number of independent photographs captured) with 100 randomisation runs in EstimateS (Colwell, 2009).
Fig. 3. Activity patterns for 14 in Camera-Trapping Survey Of Mammals In And Around Imbak Canyon Conservation Area In Sabah, Malaysian Borneo
Fig. 3. Activity patterns for 14 mammal species (with n ≥ 8) photocaptured in and around Imbak Canyon Conservation Area in central Sabah, Malaysian Borneo. Dotted bar indicates percent frequency of independent photographs taken during the day time (0600–1800 hours); Black bar indicates percent frequency of independent photographs taken during night time (1800–0600 hours). Species are listed in order of decreasing frequency of diurnal activity. Numbers in parentheses indicate sample size.
Fig. 1 in Camera-Trapping Survey Of Mammals In And Around Imbak Canyon Conservation Area In Sabah, Malaysian Borneo
Fig. 1. Imbak Canyon Conservation Area (ICCA) in central Sabah, northern part of Malaysian Borneo. Circles show the localities of 13 plots (P1–P13) where camera traps were placed (+). Each plot is approximately 3.5 km in radius.
Figs 2-5 in Accessing camera trap survey feasibility for estimating Blastocerus dichotomus (Cetartiodactyla, Cervidae) demographic parameters
Figs 2-5. Individual discrimination of marsh deer males (Blastocerus dichotomus Illiger, 1815) using antler morphology: a spike-antlered male (2) and two different branched antlers (3 and 4). The arrows indicate the different horn tips. Marsh deer female accompanied by a fawn (5).
Fig. 1 in Accessing camera trap survey feasibility for estimating Blastocerus dichotomus (Cetartiodactyla, Cervidae) demographic parameters
Fig. 1. Map outlining the aerial and camera trap surveys conducted at the Jataí Ecological Station, state of SÃo Paulo, Brazil in order to obtain marsh deer demographic parameters.
Fig. 2 in A Camera Trapping Inventory For Mammals In A Mixed Use Planted Forest In Sarawak
Fig. 2. Some of the photographs taken by camera during the study period showing how animals respond to a lure. A, Helarctos malayanus, Malayan Sun Bear; B, Sus barbatus, Bearded Pig; C, Viverra tangalunga, Malay Civet / Tangalung.
Fig. 1 in A Camera Trapping Inventory For Mammals In A Mixed Use Planted Forest In Sarawak
Fig. 1. Location of Planted Forest Zone within Bintulu Division in Sarawak, Malaysia. Planted Forest Zone is indicated in dark striped areas in center of map.
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