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crawl - Fit Continuous-Time Correlated Random Walk Models to Animal Movement Data

Fit continuous-time correlated random walk models with time indexed covariates to animal telemetry data. The model is fit using the Kalman-filter on a state space version of the continuous-time stochastic movement process.

Last updated

openblascpp

7.70 score 21 stars 3 dependents 74 scripts 735 downloads

crawl - Fit Continuous-Time Correlated Random Walk Models to Animal Movement Data

Fit continuous-time correlated random walk models with time indexed covariates to animal telemetry data. The model is fit using the Kalman-filter on a state space version of the continuous-time stochastic movement process.

Last updated

openblascpp

7.69 score 21 stars 3 dependents 72 scripts 753 downloads

marked - Mark-Recapture Analysis for Survival and Abundance Estimation

Functions for fitting various models to capture-recapture data including mixed-effects Cormack-Jolly-Seber(CJS) and multistate models and the multi-variate state model structure for survival estimation and POPAN structured Jolly-Seber models for abundance estimation. There are also Hidden Markov model (HMM) implementations of CJS and multistate models with and without state uncertainty and a simulation capability for HMM models.

Last updated

cpp

6.11 score 11 stars 1 dependents 98 scripts 591 downloads

picMaps - Mapping Utilities for The Pacific Ocean

This package provides objects and functions for making plots and maps easier to create in the Pacific Ocean.

Last updated

3.68 score 4 stars 24 scripts

nimbleJSextras - Aadditional Functions and Distributions For Bayesian Inference Of Jolly-Seber Models For The NIMBLE Package

More about what it does (maybe more than one line). Continuation lines should be indented.

Last updated

3.21 score 19 scripts

walk - Model Animal Movement With Continuous-Time Markov Chains

Model animal movement using continuous-time Markov chain models.

Last updated

openblascppopenmp

2.70 score 1 stars 1 scripts

expQ2 - Non-negative vector * exp of rate matrix

Calculate `v'exp(Q)` by uniformisation or scaling and squaring, or exp(Q) by scaling and squaring. This is a duplicate of the `expQ` package written by Chris Sherlock hosted at "https://github.com/ChrisGSherlock/expQ" with changes made to pass R CRAN checks.

Last updated

openblascppopenmp

2.48 score 2 dependents

distanceMCMC - Functions to Fit Distance Sampling Models Via MCMC Using Nimble

Functions for Bayesian distance sampling models for use within nimble.

Last updated

2.30 score

multAbund - Model Multivariate Abundance and Occurence Using the Dirichlet Process Prior

This package provides RJMCMC samplers to make Bayesian inference for Joint Species Distribution models (JSDM) using a Dirichlet Process clustering method. The DP clustering method allows species to be grouped into functional guilds for modeling between species associations in abundance or occurence values at surveyed sites.

Last updated

openblascpp

2.18 score 3 stars 4 scripts

pupR - Model-Based Estimation of Northern Fur Seal Pup Production

Provide a set of models for estimation of northern fur seal pup production.

Last updated

2.02 score 21 scripts

dmnormLR - Custom nimble distributions for multivariate normal models that are not full rank

Custom, non-full rank multivariate normal distributions for nimble. Used for penalized splines, etc.

Last updated

2.00 score

ctmmUtils - Auxillary functions for using the {ctmm} package efficiently

Utility functions to augment the the {ctmm} package. The additional function are targeted toward analysis of marine mammal telemetry, but can be used or easily modified for other situations.

Last updated

2.00 score 1 stars

crawlUtils - Enhance And Integrate the {crawl} Package For Spatial Analysis Of Telemetry Output

Utility functions to augment the the {crawl} package and integrate it with the {sf} package for spatial analysis of telemetry model output. The additional function are targeted toward analysis of marine mammal telemetry, but can be used or easily modified for other situations.

Last updated

2.00 score 2 stars 1 scripts

agTrend.ssl - Aggregated Abundance Trends using GAMs

The package supplies a set of functions for stochastically imputing missing site-level abundance measurements so sites can be aggregated to regional abundance for trend estimation. This package is specifically intended for trend estimation for the NMFS Alaska Fisheries Science Center's assessment of Steller sea lion trends in Alaska and the U.S. west coast. Although the methodology is applicable to other applications, there are aspects of sea lion surveys hard coded into the analysis.

Last updated

1.70 score 1 stars

dsmextraLite - A Toolkit for Extrapolation Assessments in Density Surface Models

This is a user-friendly tools for the detection and assessment of extrapolation in multivariate environmental space (Bouchet et al. 2019), with applications to density surface models of line transect data. It provides convenience functions for summarising and visualising extrapolation in prediction areas. This is a streamlined version of the dsmextras package (https://github.com/densitymodelling/dsmextra) that uses update spatial data packages.

Last updated

1.70 score 3 scripts

dsmextraLite - A Toolkit for Extrapolation Assessments in Density Surface Models

This is a user-friendly tools for the detection and assessment of extrapolation in multivariate environmental space (Bouchet et al. 2019), with applications to density surface models of line transect data. It provides convenience functions for summarising and visualising extrapolation in prediction areas. This is a streamlined version of the dsmextras package (https://github.com/densitymodelling/dsmextra) that uses update spatial data packages.

Last updated

1.70 score 3 scripts

markedTMB - Mark-Recapture Analysis for Survival Estimation

Functions for fitting various models to capture-recapture data including mixed-effects multistate models, multi-variate state models and multistate live and dead recovery structure for survival estimation. All models are implemented with TMB.

Last updated

1.70 score 1 stars 1 scripts

mbpp - Model-based estimation of northern fur seal pup production

Impliments methods for model-based estimation of northern fur seal pup production.

Last updated

jagscpp

1.70 score

cmpR - Conway-Maxwell-Poisson Distribution Function

Provides functions for calculating the Conway-Maxwell-Poisson distribution function and variable simulation

Last updated

cpp

1.70 score

moveMMPP - Fit Continuous-Time Markov Modulated Poisson Process Movement Models to Animal Resight Data

Using animal resight data, the package functions allow the user to estimate movement rates and resource selection using a continuous-time Markov chain movement model.

Last updated

openblascppopenmp

1.48 score

stocc - Fit a Spatial Occupancy Model via Gibbs Sampling

Fit a spatial-temporal occupancy models using a probit formulation instead of a traditional logit model.

Last updated

1.20 score 1 stars 16 scripts 184 downloads