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 5 months ago

fortrancpp

6.56 score 9 stars 1 dependents 85 scripts 850 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 4 months ago

openblascpp

6.26 score 18 stars 3 dependents 63 scripts 672 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 4 days ago

3.26 score 3 stars 4 scripts

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 5 months ago

2.78 score 2 stars 1 scripts

walk - Model Animal Movement With Continuous-Time Markov Chains

Model animal movement using continuous-time Markov chain models.

Last updated 9 months ago

openblascpp

2.60 score 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 2 years ago

openblascppopenmp

2.48 score 2 dependents

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 months ago

2.40 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 3 years ago

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 8 years ago

1.90 score 16 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 5 months ago

1.70 score 1 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 11 months ago

1.70 score 1 stars

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

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

Last updated 3 years ago

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 3 years ago

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 9 months ago

openblascpp

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 2 years ago

1.18 score 1 stars 15 scripts 156 downloads