unmarked - Models for Data from Unmarked Animals

Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.

Last updated 25 days ago

openblascppopenmp

12.88 score 4 stars 12 dependents 652 scripts 7.1k downloads

jagsUI - A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses

A set of wrappers around 'rjags' functions to run Bayesian analyses in 'JAGS' (specifically, via 'libjags'). A single function call can control adaptive, burn-in, and sampling MCMC phases, with MCMC chains run in sequence or in parallel. Posterior distributions are automatically summarized (with the ability to exclude some monitored nodes if desired) and functions are available to generate figures based on the posteriors (e.g., predictive check plots, traceplots). Function inputs, argument syntax, and output format are nearly identical to the 'R2WinBUGS'/'R2OpenBUGS' packages to allow easy switching between MCMC samplers.

Last updated 25 days ago

jagscpp

10.02 score 35 stars 7 dependents 1.4k scripts 2.0k downloads

ubms - Bayesian Models for Data from Unmarked Animals using 'Stan'

Fit Bayesian hierarchical models of animal abundance and occurrence via the 'rstan' package, the R interface to the 'Stan' C++ library. Supported models include single-season occupancy, dynamic occupancy, and N-mixture abundance models. Covariates on model parameters are specified using a formula-based interface similar to package 'unmarked', while also allowing for estimation of random slope and intercept terms. References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.

Last updated 10 days ago

distance-samplinghierarchical-modelsn-mixture-modeloccupancystanopenblascpp

7.88 score 35 stars 73 scripts 412 downloads

IPMbook - Functions and Data for the Book 'Integrated Population Models'

Provides functions and data sets to accompany the book 'Integrated Population Models: Theory and Ecological Applications with R and JAGS' by Michael Schaub and Marc Kéry (ISBN: 9780128205648).

Last updated 24 days ago

3.95 score 1 stars 177 scripts 399 downloads

ASMbook - Functions for the Book "Applied Statistical Modeling for Ecologists"

Provides functions to accompany the book "Applied Statistical Modeling for Ecologists" by Marc Kéry and Kenneth F. Kellner (2024, ISBN: 9780443137150). Included are functions for simulating and customizing the datasets used for the example models in each chapter, summarizing output from model fitting engines, and running custom Markov Chain Monte Carlo.

Last updated 7 months ago

3.90 score 2 stars 10 scripts 277 downloads