mclustOptions             package:mclust             R Documentation

_S_e_t _d_e_f_a_u_l_t _v_a_l_u_e_s _f_o_r _u_s_e _w_i_t_h _M_C_L_U_S_T.

_D_e_s_c_r_i_p_t_i_o_n:

     Supplies a list of values an enumeration of models for use with
     _MCLUST_.

_U_s_a_g_e:

     mclustOptions(emModelNames=NULL, hcModelNames=NULL, 
                   bicPlotSymbols=NULL, bicPlotColors=NULL, 
                   classPlotSymbols=NULL, classPlotColors=NULL, warn=TRUE) 

_A_r_g_u_m_e_n_t_s:

emModelNames: A vector of 3-character strings that are associated with
          multivariate  models for which EM estimation is available in
          MCLUST. 
           The current default is  all of the multivariate mixture
          models supported in 'MCLUST'. The help file for
          'mclustModelNames' describes the available models. 

hcModelNames: A vector of character strings associated with
          multivariate models for which model-based hierarchical
          clustering is available in MCLUST. 
           The current default is the following list:

           "EII": spherical, equal volume 
           "VII": spherical, unequal volume 
           "EEE": ellipsoidal, equal volume, shape, and orientation 
           "VVV": ellipsoidal, varying volume, shape, and orientation  

bicPlotSymbols: A vector whose entries are either integers
          corresponding to graphics symbols or single characters for
          plotting BIC curves. The default is 
           'c(EII=17,VII=2,EEI=16,EVI=10,VEI=13,VVI=1, 
           EEE=15,EEV=12,VEV=7,VVV=0,E=17,V=2)'. 

bicPlotColors: A vector whose entries are either integers corresponding
          to colors to BIC curves. 'c(EII="gray",VII="black",
           EEI="orange",EVI="brown",VEI="red",VVI="magenta", 
           EEE="forestgreen",EEV="green",VEV="cyan",VVV="blue",
           E="gray",V="black")'. 

classPlotSymbols: A vector whose entries are either integers
          corresponding to graphics symbols or single characters for
          plotting for classifications. Classes are assigned symbols in
          the given order. The default is
          'c(17,0,10,4,11,18,6,7,3,16,2,12,8,15,1,9,14,13,5)'.  

classPlotColors: A vector whose entries are either integers
          corresponding to graphics symbols or single characters for
          plotting for classifications. Classes are assigned symbols in
          the given order. The default is
           ' "blue", "red", "green", "cyan", "magenta", 
             "forestgreen", "purple", "orange", "gray", "brown",
          "black")' 

    warn: A logical value allowing some types of warnings to be turned
          on or off globally. Most of these warnings have to do with  
          situations in which singularities are encountered.  The
          default is 'warn = TRUE'.  

_D_e_t_a_i_l_s:

     'mclustOptions' is provided for assigning values to the '.Mclust'
     list, which is used to supply default values to various functions
     in MCLUST.

     Calls to 'mclustOptions' do not in themselves affect the outcome
     of computations.

_V_a_l_u_e:

     A named list in which the names are the names of the arguments and
     the values are the values supplied to the arguments.

_R_e_f_e_r_e_n_c_e_s:

     C. Fraley and A. E. Raftery (2002). Model-based clustering,
     discriminant analysis, and density estimation. _Journal of the
     American Statistical Association 97:611-631_. 

     C. Fraley and A. E. Raftery (2006). MCLUST Version 3 for R: Normal
     Mixture Modeling and Model-Based Clustering,  Technical Report no.
     504, Department of Statistics, University of Washington.

_S_e_e _A_l_s_o:

     '.Mclust', 'emControl'

_E_x_a_m_p_l_e_s:

     irisBIC <- mclustBIC(iris[,-5])
     summary(irisBIC, iris[,-5])

     .Mclust
     .Mclust <- mclustOptions(emModelNames = c("VII", "VVI", "VVV"))
     .Mclust

     irisBIC <- mclustBIC(iris[,-5])
     summary(irisBIC, iris[,-5])

     .Mclust <- mclustOptions() # restore default values
     .Mclust

