SimCoef                package:simco                R Documentation

_A _f_u_n_c_t_i_o_n _t_o _c_a_r_r_y _o_u_t _t_h_e _c_a_l_c_u_l_a_t_i_o_n _o_f _s_i_m_i_l_a_r_i_t_y _c_o_e_f_f_i_c_i_e_n_t_s _f_r_o_m _m_u_l_t_i_p_l_e _S_t_r_u_c_t_u_r_e _o_u_t_p_u_t _f_i_l_e_s.

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

     This function takes multiple Structure files that have already
     been imported using the '"SimCoImport()"' function and calculates
     similarity coefficients for them.

     The output is printed to the screen and includes the number of
     populations (K) that are assumed, the number of individuals (I),
     the number of Structure runs that have been analysed, the range,
     median, mean similariy coefficient, and standard error of the
     mean. Lastly, the output displays the similarity coefficients and
     the pairs of runs that were compared.

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

     SimCoef(mydata)

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

  mydata: mydata is a dataframe generated using '"SimCoImport()"' which
          is the Structure output files, appended and labelled with a
          capital letter. 

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

     An accompanying PDF is given with this package with further
     details of use.

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

Number of populations (K): The number of populations that were assumed
          when generating the Strucure files

Number of individuals (I): The number of individuals/samples in the
          datafile

Number of Structure runs: The number of Structure runs that have been
          compared

   Range: The range of similarity coefficients

Median Similarity Coefficient: The median similarity coefficient

Mean Similarity Coefficient: The mean similarity coefficient

SEM of Similarity Coefficient: The standard error of the mean
          similarity coefficient

The similarity coefficients: a list of the similarity coefficients

 Summary: A table showing the pairs of runs that were compared (matches
          up with the list of similarity coeffiencts).

_N_o_t_e:

_A_u_t_h_o_r(_s):

     Owen R. Jones (owen.jones@imperial.ac.uk)

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

     Rebbeck, CA, Jones, OR, & Tsai, IJ  (Submitted to
     _Bioinformatics_) SimCo: A program to automate the comparison of
     multiple structure runs (available from owen.jones@imperial.ac.uk)

     Pritchard, J. K. et al. (2000) Inference of population structure
     using multilocus genotype data. _Genetics_. 155, 945-959.

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

     'SimCoImport' 'structureexample'

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

     #You should import the files you want to use first using the SimCoImport() command.
     #In this example it is assumed that you are using a pre-imported dataset called "structureexample"

     data(structureexample)
     SimCoef(structureexample)

