# Bayesian Models for Data from Unmarked Animals using 'Stan'

## Documentation for package ‘ubms’ version 1.2.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ubms-package | ubms
$-method | Extractors for ubmsFitList objects Extract parts of ubmsFitList objects.
cauchy | Prior distributions
coef-method | Extract Coefficient Values From a ubmsFit Model
extract-method | Extract Samples From a ubmsFit Model
extract_log_lik | Extract Pointwise Log-likelihood From Model
extract_log_lik-method | Extract Pointwise Log-likelihood From Model
fitList | Create a List of ubmsFit Models
fitList-method | Create a List of ubmsFit Models
fitted-method | Extract Fitted Values
gamma | Prior distributions
getY-method | Extract y, the Response Variable, From a ubmsFit Model
get_elapsed_time-method | Get Model Runtime
get_stancode-method | Get Stan Code From Model
gof | Check model goodness-of-fit
gof-method | Check model goodness-of-fit
kfold-method | K-fold Cross-validation of a ubmsFit Model
laplace | Prior distributions
logistic | Prior distributions
loo-method | Leave-one-out Cross Validation
modSel-method | Model Selection For a List of ubmsFit Models
names-method | Get Parameter Names From a ubmsFit Model
names-method | Get Names of Models in a ubmsFitList
normal | Prior distributions
nsamples-method | Get number of Posterior Samples Stored in a ubmsFit Model
plot-method | Check model goodness-of-fit
plot-method | Plot Residuals For All Submodels in a ubmsFit Model
plot_effects | Plot Marginal Effects of Covariates
plot_effects-method | Plot Marginal Effects of Covariates
plot_marginal | Plot Marginal Effects of Covariates
plot_marginal-method | Plot Marginal Effects of Covariates
plot_posteriors | Plot Posterior Distributions
plot_posteriors-method | Plot Posterior Distributions
plot_residuals | Plot Model Residuals
plot_residuals-method | Plot Model Residuals
plot_spatial | Plot A Map of the State Parameter Based on a Spatial ubms Model
posterior_linpred | Posterior Distribution of the Linear Predictor
posterior_linpred-method | Posterior Distribution of the Linear Predictor
posterior_predict | Draw from the posterior predictive distribution
posterior_predict-method | Draw from the posterior predictive distribution
predict | Predict parameter values from a fitted model
predict-method | Predict parameter values from a fitted model
priors | Prior distributions
projected | Projected Occupancy Trajectories
projected-method | Projected Occupancy Trajectories
ranef | Extract Random Effects
ranef-method | Extract Random Effects
residuals-method | Extract Model Residuals
RSR | Get Information for a Restricted Spatial Regression Model
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)
student_t | Prior distributions
summary-method | Extract Summary Statistics from a ubmsFit Model
traceplot-method | Markov Chain Traceplots
turnover | Turnover Probability
turnover-method | Turnover Probability
ubms | ubms
ubmsFitList-extractors | Extractors for ubmsFitList objects Extract parts of ubmsFitList objects.
uniform | Prior distributions
waic-method | Widely Applicable Information Criterion (WAIC)
[-method | Extract a Submodel from a ubmsFit Model
[-method | Extract a ubmsSubmodel From a ubmsSubmodelList Object
[-method | Extractors for ubmsFitList objects Extract parts of ubmsFitList objects.
[[-method | Extractors for ubmsFitList objects Extract parts of ubmsFitList objects.