DOI: 10.5061/dryad.xwdbrv1g2
title: A comparison of density estimation methods for monitoring marked and unmarked animal populations

description: These data were generated to compare different methods of estimating
 population density from marked and unmarked animal populations. We compare
 conventional live trapping with two more modern, non-invasive field
 methods of population estimation: genetic fingerprinting from hair-tube
 sampling and camera trapping for the European pine marten (Martes martes).
 We used arrays of camera traps, live traps, and hair tubes to collect the
 relevant data in the Ring of Gullion in Northern Ireland. We apply marked
 spatial capture-recapture models to the genetic and live trapping data
 where individuals were identifiable, and unmarked spatial
 capture-recapture (uSCR), distance sampling (CT-DS), and random encounter
 models (REM) to the camera trap data where individual ID was not possible.
 All five approaches produced plausible and relatively consistent point
 estimates (0.41 – 0.99 animals per km2), despite differences in precision,
 cost, and effort being apparent. In addition to the data, we provide novel
 code for running unmarked spatial capture-recapture (uSCR) and random
 encounter models (REM) to the camera trap data where individual ID was not
 possible. 
description: All fieldwork was carried out in the Ring of Gullion, Northern
 Ireland, UK. 
 <strong>Cameras</strong> Thirty
 Bushnell HD Trophy Cam 8MP camera traps (model number: 119577) with 8GB SD
 cards were deployed during June and July 2019. Thirty Bushnell HD Trophy
 Cam 8MP camera traps (model number: 119577) with 8GB SD cards were
 deployed during June and July 2019. At the end of the survey period,
 camera traps were checked and for each detection (the first image in a
 trigger sequence of an individual pine marten) distance to animal (m) and
 angle of detection (°) were measured <em>in
 situ</em>. <strong>Noninvasive genetic
 sampling</strong> Twenty hair tubes based on
 those developed by Mullins <em>et al</em>. (2010), were
 deployed across the study site between June and July 2019. Hair-tubes were
 checked weekly and sticky patches and bait were replaced on each visit.
 Hair samples were frozen at -20oC prior to DNA extraction. Microsatellite
 analysis to identify individual pine marten was carried out using up to 11
 microsatellite markers. Each sample was analysed in duplicate and only
 samples giving identical results in the replicates were scored.
 <strong>Live traps</strong> Twelve
 Tomahawk 205 live cage traps were deployed along two perpendicular
 transects spaced approximately 400m apart. Trapping was conducted from
 August - October 2019 with daily trap checks. Trapped animals were
 anaesthetised with an intramuscular injection of ketamine (25mg per kg)
 and midazolam (0.2mg per kg) and scanned for a microchip. 
 <strong>Statistical analyses</strong>
 Spatially explicit capture-recapture (SECR) models were used to
 estimate density for both live trapping and gNIS (Efford &
 Boulanger, 2019). Occasion lengths for live trapping were one day, whilst
 for gNIS were one week. For live trapping, we specified a single-use
 detector type, whilst for gNIS we specified a proximity-based detector
 type. Density was calculated from camera traps using REM (Rowcliffe
 <em>et al</em>. 2008), CT-DS (Howe <em>et al</em>.
 2017) and uSCR (Chandler & Royle, 2013).
description: Please refer to the README file.