benaug Goto Github PK

2-flank-spim

2-flank SPIM from Augustine et al. (2018) implemented in Nimble.

acoustic-scr

Acoustic SCR MCMC samplers

benaug.github.io

capture-recapture-classify-genotype

Capture-Recapture-Classify-Genotype

categorical-spim

Nimble sampler for categorical SPIM from "Spatial capture–recapture for categorically marked populations with an application to genetic capture–recapture"

coupled-classification-occupancy

Coupled Classification Occupancy

edna-latent-copies

Models for an eDNA release experiment that treat copy number as latent count variables

genotype-spim

Spatial capture-recapture accouting for genotyping error

group-scr

Group SCR sampler from Emmett et al. (2021) implemented in Nimble.

jolly-seber

Jolly Seber MCMC samplers in nimble, computationally efficient, Poisson recruitment process.

mbmisscap

Simulates hair snare mark recapture scenarios under various subsampling and DNA amplification models and asses bias introduced in Mb due to first captures being lost

move.hmm

Flexible, user-friendly Hidden (Semi) Markov Models for animal movement data (Langrock et al. 2012). This package was developed in part for van de Kirk (2013; http://onlinelibrary.wiley.com/doi/10.1111/1365-2656.12290/full). Since I wrote this package, Theo Michelot, Roland Langrock and others have written a better package for fitting HMMs to animal movement data, named moveHMM (sorry for the confusion!). To my knowlege, though, this package is the only one that fits hidden semi-Markov models.

multiscale-occupancy

Basic multiscale occupancy model that samples latent states from marginal distributions

openpopscr

Functions to simulate from and fit open population spatial capture recapture models.

random-thin-mvhyper

randomthinidcov

SCR Random thinning model with individual covariates (random thinning + categorical SCR)

royleyoung

Royle Young models for area or transect searches where you detect individuals (not their sign). Density and resource selection. Data simulators and files to fit models in nimble. Known ID versions only.

scr-bd

scr-biasedclassobs

Spatial Capture Recapture for class-structured populations where class observation probabilities depend on class level

scr-classify-pairwise

MCMC samplers for latent identity spatial capture-recapture models that use pairwise scores between samples

scr-dcov

Nimble MCMC samplers for Spatial Capture Recapture with density covariates.

scr-multisession

Minimal multisession SCR MCMC sampler in nimble using RJMCMC instead of data augmentation

spatial-mark-resight

Various spatial mark resight MCMC samplers allowing for all sample types including "unknown marked status"

spatial-mark-resight-idcov

Spatial Mark Resight samplers in nimble that allows for individual ID covariates (SMR + categorical SCR)

spim

Models fit: 2-Flank spatial partial identity model (SPIM), categorical SPIM, conventional and generalized categorical SMR.

unmarkedscr

Various unmarked SCR MCMC samplers in nimble