Model Based Clustering of Binary Dissimilarity Measurements

Documentation for package ‘dmbc’ version 0.4.0

DESCRIPTION file.
Code demos. Use demo() to run them.

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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