# Model Based Clustering of Binary Dissimilarity Measurements

## Documentation for package ‘dmbc’ version 0.4.0

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

## Help Pages

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