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>.
Last updated 8 months ago
8.61 score 38 stars 107 scripts 624 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.
Last updated 14 days ago
animal-movementanimal-trackingrandom-effects-modelstate-space-modelstmb
7.01 score 38 stars 55 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.glos.us; many more broadly relevant to simulating, processing, analysing, and visualizing acoustic telemetry data.
Last updated 2 months ago
6.68 score 9 stars 113 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) <doi: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.
Last updated 1 months ago
6.21 score 2 stars 17 scripts 212 downloadstRophicPosition - Bayesian Trophic Position Estimation with Stable Isotopes
Estimates the trophic position of a consumer relative to a baseline species. It implements a Bayesian approach which combines an interface to the 'JAGS' MCMC library of 'rjags' and stable isotopes. Users are encouraged to test the package and send bugs and/or errors to [email protected].
Last updated 1 months ago
5.57 score 23 scripts 102 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.
Last updated 3 months ago
acoustic-telemetryaquaticmortality-estimation
5.53 score 3 stars 16 scripts 137 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.
Last updated 1 years ago
4.89 score 16 stars 1 packages 16 scriptsmatos - 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.
Last updated 7 months ago
animal-trackingapiapi-wrapperbiotelemetryfishfisheriesfisheries-research
4.69 score 3 stars 9 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).
Last updated 3 months ago
biologydose-response-modelinglogitprobittoxicology
4.50 score 3 stars 10 scripts 612 downloadssoapcheckr - Check knot locations used by soap film smoothers for GAMS
Soapcheckr allows users to easily check if the boundary used and supplied will work when using a soap-film smoother for Generalized Addtive Models (GAMs) supported by the package {mgcv}. The package also allows for users to assess if the knots and data points they want to supply the GAM will fit within the boundary.
Last updated 1 years ago
3.65 score 9 stars 10 scripts