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ubms (version 1.2.7)

Bayesian Models for Data from Unmarked Animals using 'Stan'

Description

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) ; Fiske and Chandler (2011) .

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Version

Install

install.packages('ubms')

Monthly Downloads

324

Version

1.2.7

License

GPL (>= 3)

Maintainer

Ken Kellner

Last Published

October 1st, 2024

Functions in ubms (1.2.7)

plot_spatial

Plot A Map of the State Parameter Based on a Spatial ubms Model
names,ubmsFitList-method

Get Names of Models in a ubmsFitList
priors

Prior distributions
predict,ubmsFit-method

Predict parameter values from a fitted model
plot_residuals,ubmsFit-method

Plot Model Residuals
stan_occuRN

Fit the Occupancy Model of Royle and Nichols (2003)
projected

Projected Occupancy Trajectories
plot_posteriors,ubmsFit-method

Plot Posterior Distributions
stan_pcount

Fit the N-mixture model of Royle (2004)
posterior_predict,ubmsFit-method

Draw from the posterior predictive distribution
stan_occuTTD

Fit Time-to-detection Occupancy Models
ranef,ubmsFit-method

Extract Random Effects
posterior_linpred,ubmsFit-method

Posterior Distribution of the Linear Predictor
residuals,ubmsFit-method

Extract Model Residuals
[,ubmsFit,character,missing,missing-method

Extract a Submodel from a ubmsFit Model
nsamples,ubmsFit-method

Get number of Posterior Samples Stored in a ubmsFit Model
[,ubmsSubmodelList,character,missing,missing-method

Extract a ubmsSubmodel From a ubmsSubmodelList Object
stan_colext

Fit the MacKenzie et al. (2003) Dynamic Occupancy Model
stan_distsamp

Fit the Royle et al. (2004) Distance Sampling Model
turnover

Turnover Probability
traceplot,ubmsFit-method

Markov Chain Traceplots
stan_occu

Fit the MacKenzie et al. (2002) Occupancy Model
stan_multinomPois

Fit the Multinomial-Poisson Mixture Model
waic,ubmsFit-method

Widely Applicable Information Criterion (WAIC)
summary,ubmsFit-method

Extract Summary Statistics from a ubmsFit Model
ubms

ubms
ubmsFitList-extractors

Extractors for ubmsFitList objects Extract parts of ubmsFitList objects.
get_stancode,ubmsFit-method

Get Stan Code From Model
fitList,ubmsFit-method

Create a List of ubmsFit Models
fitted,ubmsFit-method

Extract Fitted Values
gof

Check model goodness-of-fit
extract,ubmsFit-method

Extract Samples From a ubmsFit Model
get_elapsed_time,ubmsFit-method

Get Model Runtime
getY,ubmsFit-method

Extract y, the Response Variable, From a ubmsFit Model
RSR

Get Information for a Restricted Spatial Regression Model
modSel,ubmsFitList-method

Model Selection For a List of ubmsFit Models
extract_log_lik

Extract Pointwise Log-likelihood From Model
coef,ubmsFit-method

Extract Coefficient Values From a ubmsFit Model
names,ubmsFit-method

Get Parameter Names From a ubmsFit Model
kfold,ubmsFit-method

K-fold Cross-validation of a ubmsFit Model
loo,ubmsFit-method

Leave-one-out Cross Validation
plot_effects,ubmsFit-method

Plot Marginal Effects of Covariates
plot,ubmsFit,ANY-method

Plot Residuals For All Submodels in a ubmsFit Model