Bayesian Models for Data from Unmarked Animals using 'Stan'

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Documentation for package ‘ubms’ version 1.2.6

• 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.