Model Based Clustering of Binary Dissimilarity Measurements


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Documentation for package ‘dmbc’ version 0.4.0

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A B C D I K M P S U

dmbc-package Model-Based Clustering of Several Dissimilarity Matrices.

-- A --

adjust_x Adjustment of the center and orientation of a latent configuration.
animals List of binary dissimilarity matrices among 18 animals.

-- B --

bmds Bayesian multidimensional scaling (BMDS) using Markov Chain Monte Carlo (MCMC).
bmds_get_x_mode Posterior mode latent configuration in Bayesian multidimensional scaling (BMDS).

-- C --

check_control Auxiliary Function for Controlling DMBC Model Fitting
check_list_na Auxiliary function to recursively check NAs in a list.
check_prior Auxiliary Function for Setting DMBC Model Priors
clusters-method Extract the final cluster memberships from a 'dmbc_config' class instance.
comp_ssr Sum of squared residuals (SSR) from the observed distances and the given latent configuration.
control_dmbc Auxiliary Function for Controlling DMBC Model Fitting

-- D --

dmbc Estimation of a DMBC model.
dmbc-internal Internal functions for MCMC simulation.
dmbc-p Model-Based Clustering of Several Dissimilarity Matrices.
dmbc-pkg Model-Based Clustering of Several Dissimilarity Matrices.
dmbc_check_groups Auxiliary function for checking the grouping results of a fitted DMBC model.
dmbc_config An S4 class to represent the latent configuration estimate for a DMBC model.
dmbc_config-class An S4 class to represent the latent configuration estimate for a DMBC model.
dmbc_config-clusters Extract the final cluster memberships from a 'dmbc_config' class instance.
dmbc_config-initialize Create an instance of the 'dmbc_config' class using new/initialize.
dmbc_config-plot Provide a graphical summary of a 'dmbc_config' class instance.
dmbc_config-show Show an instance of the 'dmbc_config' class.
dmbc_config-summary Provide a summary of a 'dmbc_config' class instance.
dmbc_control Auxiliary Function for Controlling DMBC Model Fitting
dmbc_data An S4 class to represent the data to use in a DMBC model.
dmbc_data-class An S4 class to represent the data to use in a DMBC model.
dmbc_data-initialize Create an instance of the 'dmbc_data' class using new/initialize.
dmbc_data-plot Provide a graphical summary of a 'dmbc_data' class instance.
dmbc_data-show Show an instance of the 'dmbc_data' class.
dmbc_data-summary Provide a summary of a 'dmbc_data' class instance.
dmbc_fit Fitter function for DMBC models.
dmbc_fit-class An S4 class to represent the results of fitting DMBC model.
dmbc_fit-initialize Create an instance of the 'dmbc_fit' class using new/initialize.
dmbc_fit-plot Provide a graphical summary of a 'dmbc_fit' class instance.
dmbc_fit-show Show an instance of the 'dmbc_fit' class.
dmbc_fit-subset Subsetting a 'dmbc_fit' object.
dmbc_fit-summary Provide a summary of a 'dmbc_fit' class instance.
dmbc_fit_list An S4 class to represent the results of fitting DMBC model.
dmbc_fit_list-class An S4 class to represent the results of fitting DMBC model.
dmbc_fit_list-initialize Create an instance of the 'dmbc_fit_list' class using new/initialize.
dmbc_fit_list-plot Provide a graphical summary of a 'dmbc_fit_list' class instance.
dmbc_fit_list-show Show an instance of the 'dmbc_fit_list' class.
dmbc_fit_list-subset Subsetting a 'dmbc_fit_list' object.
dmbc_fit_list-summary Provide a summary of a 'dmbc_fit_list' class instance.
dmbc_fit_list_to_list Conversion of an 'dmbc_fit_list' object to a 'list'.
dmbc_fit_list_to_mcmc.list Conversion of an 'dmbc_fit_list' object to an object of class 'mcmc.list'.
dmbc_fit_to_mcmc Conversion of an 'dmbc_fit' object to an object of class 'mcmc'.
dmbc_get_configuration Extractor function for a fitted DMBC model.
dmbc_get_map Extractor function for a fitted DMBC model.
dmbc_get_ml Extractor function for a fitted DMBC model.
dmbc_get_postmean Extractor function for a fitted DMBC model.
dmbc_get_postmedian Extractor function for a fitted DMBC model.
dmbc_IC Model selection of DMBC models.
dmbc_ic An S4 class to represent the comparison of a set of DMBC models.
dmbc_ic-class An S4 class to represent the comparison of a set of DMBC models.
dmbc_ic-initialize Create an instance of the 'dmbc_ic' class using new/initialize.
dmbc_ic-plot Provide a graphical summary of a 'dmbc_ic' class instance.
dmbc_ic-show Show an instance of the 'dmbc_ic' class.
dmbc_ic-summary Provide a summary of a 'dmbc_ic' class instance.
dmbc_ic-update Provide an update of a 'dmbc_ic' class instance.
dmbc_init Function to compute the starting values before fitting a DMBC models.
dmbc_internal Internal functions for MCMC simulation.
dmbc_logLik Log-likelihood for DMBC models.
dmbc_logLik_rbmds Log-likelihood for DMBC models.
dmbc_match_groups Auxiliary function for realigning the grouping of a fitted DMBC model.
dmbc_mcmc Internal functions for MCMC simulation.
dmbc_model An S4 class to represent a DMBC model.
dmbc_model-class An S4 class to represent a DMBC model.
dmbc_model-initialize Create an instance of the 'dmbc_model' class using new/initialize.
dmbc_model-show Show an instance of the 'dmbc_model' class.
dmbc_pack_par Internal functions for MCMC simulation.
dmbc_prior Auxiliary Function for Setting DMBC Model Priors
dmbc_relabel Internal functions for MCMC simulation.

-- I --

initialize-method Create an instance of the 'dmbc_config' class using new/initialize.
initialize-method Create an instance of the 'dmbc_data' class using new/initialize.
initialize-method Create an instance of the 'dmbc_fit' class using new/initialize.
initialize-method Create an instance of the 'dmbc_fit_list' class using new/initialize.
initialize-method Create an instance of the 'dmbc_ic' class using new/initialize.
initialize-method Create an instance of the 'dmbc_model' class using new/initialize.

-- K --

kinship List of binary dissimilarity matrices among 15 kinship terms.

-- M --

mdsic Information criterion for Bayesian multidimensional scaling (BMDS).

-- P --

plot-method Provide a graphical summary of a 'dmbc_config' class instance.
plot-method Provide a graphical summary of a 'dmbc_data' class instance.
plot-method Provide a graphical summary of a 'dmbc_fit' class instance.
plot-method Provide a graphical summary of a 'dmbc_fit_list' class instance.
plot-method Provide a graphical summary of a 'dmbc_ic' class instance.
prior_dmbc Auxiliary Function for Setting DMBC Model Priors

-- S --

show-method Show an instance of the 'dmbc_config' class.
show-method Show an instance of the 'dmbc_data' class.
show-method Show an instance of the 'dmbc_fit' class.
show-method Show an instance of the 'dmbc_fit_list' class.
show-method Show an instance of the 'dmbc_ic' class.
show-method Show an instance of the 'dmbc_model' class.
simdiss Simulated binary dissimilarity matrices.
subset-method Subsetting a 'dmbc_fit' object.
subset-method Subsetting a 'dmbc_fit_list' object.
summary-method Provide a summary of a 'dmbc_config' class instance.
summary-method Provide a summary of a 'dmbc_data' class instance.
summary-method Provide a summary of a 'dmbc_fit' class instance.
summary-method Provide a summary of a 'dmbc_fit_list' class instance.
summary-method Provide a summary of a 'dmbc_ic' class instance.

-- U --

update-method Provide an update of a 'dmbc_ic' class instance.
update_prior Auxiliary Function for Setting DMBC Model Priors