propTyped-methods          package:adegenet          R Documentation

_C_o_m_p_u_t_e _t_h_e _p_r_o_p_o_r_t_i_o_n _o_f _t_y_p_e_d _e_l_e_m_e_n_t_s

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

     The generic function 'propTyped' is devoted to investigating the
     structure of missing data in adegenet objects.

     Methods are defined for genind and genpop objects. They can return
     the proportion of available (i.e. non-missing) data per
     individual/population, locus, or the combination of both in with
     case the matrix indicates which entity (individual or population)
     was typed on which locus.

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

     ## S4 method for signature 'genind':
     propTyped(x,  by=c("ind","loc","both"))
     ## S4 method for signature 'genpop':
     propTyped(x,  by=c("pop","loc","both"))

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

       x: a genind and genpop object

      by: a character being "ind","loc", or "both" for genind object
          and "pop","loc", or "both" for genpop object. It specifies
          whether proportion of typed data are provided by entity
          ("ind"/"pop"), by locus ("loc") or both ("both"). See
          details.

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

     When 'by' is set to "both", the result is a matrix of binary data
     with entities in rows (individuals or populations) and markers in
     columns. The values of the matrix are 1 for typed data, and 0 for
     NA.

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

     A vector of proportion (when 'by' equals "ind", "pop", or "loc"),
     or a matrix of binary data (when 'by' equals "both")

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

     Thibaut Jombart t.jombart@imperial.ac.uk

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

     data(nancycats)
     propTyped(nancycats,by="loc")
     propTyped(genind2genpop(nancycats),by="both")

