Modeling functions

stan_colext()

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

stan_distsamp()

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

stan_multinomPois()

Fit the Multinomial-Poisson Mixture Model

stan_occu()

Fit the MacKenzie et al. (2002) Occupancy Model

stan_occuRN()

Fit the Occupancy Model of Royle and Nichols (2003)

stan_occuTTD()

Fit Time-to-detection Occupancy Models

stan_pcount()

Fit the N-mixture model of Royle (2004)

normal() uniform() student_t() logistic() cauchy() gamma() laplace()

Prior distributions

RSR()

Get Information for a Restricted Spatial Regression Model

Model diagnostics

fitted(<ubmsFit>)

Extract Fitted Values

gof()

Check model goodness-of-fit

plot(<ubmsFit>,<ANY>)

Plot Residuals For All Submodels in a ubmsFit Model

plot_residuals(<ubmsFit>)

Plot Model Residuals

plot_posteriors(<ubmsFit>)

Plot Posterior Distributions

residuals(<ubmsFit>)

Extract Model Residuals

traceplot(<ubmsFit>)

Markov Chain Traceplots

Model selection

extract_log_lik()

Extract Pointwise Log-likelihood From Model

fitList(<ubmsFit>)

Create a List of ubmsFit Models

kfold(<ubmsFit>)

K-fold Cross-validation of a ubmsFit Model

loo(<ubmsFit>)

Leave-one-out Cross Validation

modSel(<ubmsFitList>)

Model Selection For a List of ubmsFit Models

waic(<ubmsFit>)

Widely Applicable Information Criterion (WAIC)

Inference

coef(<ubmsFit>)

Extract Coefficient Values From a ubmsFit Model

extract(<ubmsFit>)

Extract Samples From a ubmsFit Model

plot_effects(<ubmsFit>) plot_marginal(<ubmsFit>)

Plot Marginal Effects of Covariates

plot_spatial()

Plot A Map of the State Parameter Based on a Spatial ubms Model

posterior_linpred(<ubmsFit>)

Posterior Distribution of the Linear Predictor

posterior_predict(<ubmsFit>)

Draw from the posterior predictive distribution

predict(<ubmsFit>)

Predict parameter values from a fitted model

projected()

Projected Occupancy Trajectories

ranef(<ubmsFit>)

Extract Random Effects

summary(<ubmsFit>)

Extract Summary Statistics from a ubmsFit Model

turnover()

Turnover Probability

Utility

get_elapsed_time(<ubmsFit>)

Get Model Runtime

get_stancode(<ubmsFit>)

Get Stan Code From Model