Package index
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AIC(<s4t_ageclass_model>) - Compute and return AIC of fitted model objects
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AIC(<s4t_cjs_ml>) - Compute AIC of fitted model objects
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abundance_estimates() - Calculate abundance estimates
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add_covariates() - Add covariates to a space4time capture history object
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anova(<s4t_ageclass_model>) - Compute likelihood ratio tests of two fitted model objects
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anova(<s4t_cjs_ml>) - Compute likelihood ratio tests of two fitted model objects
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clean_s4t_ch_obs() - Clean the capture history of a space4time capture history object
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coef(<s4t_ageclass_model>)coefficients(<s4t_ageclass_model>) - Extract fitted model coefficients
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coef(<s4t_cjs_ml>)coefficients(<s4t_cjs_ml>) - Extract fitted model coefficients
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confint(<s4t_ageclass_model>) - Confidence intervals for fitted model parameters for s4t_ageclass_model
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confint(<s4t_cjs_ml>) - Confidence intervals for fitted model parameters for s4t_cjs_ml
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extract_ageclass_fit() - Extract
s4t_ageclass_modelobject from as4t_cjs_rstanors4t_cjs_mlobject -
extract_covariates() - Extract indices and covariates from space4time capture history objects
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extract_log_lik_s4t() - Extract pointwise log-likelihood from a fitted s4t_cjs_rstan model
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fit_ageclass() - Fit age-class model using ordinal regression
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fit_s4t_cjs_ml() - Fit space-for-time mark-recapture model in likelihood framework
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fit_s4t_cjs_rstan() - Fit space-for-time mark-recapture model in Bayesian framework
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linear_s4t_config() - Create site configuration for simple linear arrangement
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loo(<s4t_cjs_rstan>) - Efficient approximate leave-one-out cross-validation (LOO)
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plot(<s4t_ageclass_model>) - Plot confusion matrix for fit_ageclass objects
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plotCH() - Plot summary of s4t_cjs_ch object
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plotCov() - Effect plot for s4t_cjs_rstan object
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plotSurvival() - Plot apparent survival estimates from fitted
s4t_cjs_mlors4t_cjs_rstanobjects -
plotTransitions() - Plot transition probability estimates from fitted
s4t_cjs_mlors4t_cjs_rstanobjects -
predict(<s4t_ageclass_model>) - Model predictions from fitted
fit_ageclassobjects -
print(<clean_s4t_ch>) - Print summary of
clean_s4t_chobject -
print(<cov_s4t_ch>) - Print summary of
cov_s4t_chobject -
print(<s4t_ch>) - Print summary of
s4t_chobject -
print(<s4t_cjs_ml>) - Print
s4t_cjs_ml -
print(<s4t_cjs_rstan>) - Print summary of
s4t_cjs_rstan -
print(<s4t_config>) - Print summary of
s4t_configobject -
print(<summary.s4t_cjs_ml>) - Print summary of
s4t_cjs_ml -
read_DART_file() - Read DART Basin TribPit observation files and combine with auxiliary age data
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remove_kelt_obs() - Remove observations of kelts
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s4t_ch() - Create space-for-time mark-recapture capture history object
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s4t_config() - Create space4time site configuration object (
s4t_config) -
sim_simple_s4t_ch() - Simulate simple capture history
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simplebranch_s4t_config() - Create site configuration for simple branching site arrangement
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space4time - space4time
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summary(<s4t_ageclass_model>) - Summarize a fitted model object
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summary(<s4t_cjs_ml>) - Summarize a fitted model object
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summary(<s4t_cjs_rstan>) - Summary method for
s4t_cjs_rstanobjects -
traceplot.s4t_cjs_rstan() - Markov chain traceplots
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vcov(<s4t_ageclass_model>) - Calculate variance-covariance matrix for a fitted model object
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vcov(<s4t_cjs_ml>) - Calculate variance-covariance matrix for a fitted model object
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waic(<s4t_cjs_rstan>) - Widely applicable information criterion (WAIC)