moveHMM - Animal Movement Modelling using Hidden Markov Models
Provides tools for animal movement modelling using hidden Markov models. These include processing of tracking data, fitting hidden Markov models to movement data, visualization of data and fitted model, decoding of the state process, etc. <doi:10.1111/2041-210X.12578>.
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animal-movementhidden-markov-modelhmmmovement-ecologyopenblascpp
9.61 score 44 stars 153 scripts 723 downloads
aniMotum - Fit Continuous-Time State-Space and Latent Variable Models for Quality Control of Argos Satellite (and Other) Telemetry Data and for Estimating Changes in Animal Movement
Fits continuous-time random walk, correlated random walk and move persistence state-space models for location estimation and behavioural inference from animal tracking data ('Argos', processed light-level 'geolocation', 'GPS'). Template Model Builder ('TMB') is used for fast random-effects estimation. The 'Argos' data can be: (older) least squares-based locations; (newer) Kalman filter-based locations with error ellipse information; or a mixture of both. The models estimate two sets of location states corresponding to: 1) each observation, which are (usually) irregularly timed; and 2) user-specified time intervals (regular or irregular). A track re-routing function is provided to adjust location estimates for known movement barriers. Track simulation functions are provided. Latent variable models are also provided to estimate move persistence from track data not requiring state-space model filtering.
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animal-movementanimal-trackingrandom-effects-modelstate-space-modelstmbcpp
8.00 score 49 stars 1 dependents 65 scriptsglatos - A package for the Great Lakes Acoustic Telemetry Observation System
Functions useful to members of the Great Lakes Acoustic Telemetry Observation System https://glatos.org; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.
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acoustic-telemetryanimal-movement-tracking
5.63 score 13 stars 1 dependents 152 scriptsnichetools - Complementary Package to 'nicheROVER' and 'SIBER'
Provides functions complementary to packages 'nicheROVER' and 'SIBER' allowing the user to extract Bayesian estimates from data objects created by the packages 'nicheROVER' and 'SIBER'. Please see the following publications for detailed methods on 'nicheROVER' and 'SIBER' Hansen et al. (2015) <doi:10.1890/14-0235.1>, Jackson et al. (2011) <do i:10.1111/j.1365-2656.2011.01806.x>, and Layman et al. (2007) <doi:10.1890/0012-9658(2007)88[42:CSIRPF]2.0.CO;2>, respectfully.
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jagscpp
5.41 score 2 stars 16 scripts 520 downloads
mort - Identifying Potential Mortalities and Expelled Tags in Aquatic Acoustic Telemetry Arrays
A toolkit for identifying potential mortalities and expelled tags in aquatic acoustic telemetry arrays. Designed for arrays with non-overlapping receivers.
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acoustic-telemetryaquaticmortality-estimation
5.35 score 4 stars 16 scripts 174 downloadspathroutr - An R Package for (Re-)Routing Paths Around Barriers
The `pathroutr` package aims to provide a set of tools for routing marine animal tracks around land barriers based on the shortest path through a visibility graph network. The foundation of the package is a graph network created from a Delaunay Triangle mesh created from the vertices of land polygons within the study area. Any network edges that cross or fall completely within the land (barrier) polygons are removed.
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5.21 score 17 stars 1 dependents 16 scriptsecotox - Analysis of Ecotoxicology
A simple approach to using a probit or logit analysis to calculate lethal concentration (LC) or time (LT) and the appropriate fiducial confidence limits desired for selected LC or LT for ecotoxicology studies (Finney 1971; Wheeler et al. 2006; Robertson et al. 2007). The simplicity of 'ecotox' comes from the syntax it implies within its functions which are similar to functions like glm() and lm(). In addition to the simplicity of the syntax, a comprehensive data frame is produced which gives the user a predicted LC or LT value for the desired level and a suite of important parameters such as fiducial confidence limits and slope. Finney, D.J. (1971, ISBN: 052108041X); Wheeler, M.W., Park, R.M., and Bailer, A.J. (2006) <doi:10.1897/05-320R.1>; Robertson, J.L., Savin, N.E., Russell, R.M., and Preisler, H.K. (2007, ISBN: 0849323312).
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biologydose-response-modelinglogitprobittoxicology
4.47 score 4 stars 21 scripts 369 downloads
trps - Bayesian Trophic Position Models using 'Stan'
Bayesian trophic position models using 'stan' by leveraging 'brms' for stable isotope data. Trophic position models are derived by using equations from Post (2002) <doi:10.1890/0012-9658(2002)083[0703:USITET]2.0.CO;2>, Vander Zanden and Vadeboncoeur (2002) <doi:10.1890/0012-9658(2002)083[2152:FAIOBA]2.0.CO;2>, and Heuvel et al. (2024) <doi:10.1139/cjfas-2024-0028>.
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4.30 score 7 scripts 186 downloadsmatos - Interface with the Mid-Atlantic Acoustic Telemetry Observing System (MATOS)
This package provides HTML-scaping functions to interact with the MATOS website (https://matos.asascience.com/), allowing aggregation of data and the downloading and posting of files.
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animal-trackingapiapi-wrapperbiotelemetryfishfisheriesfisheries-research
4.08 score 4 stars 9 scripts