chooseCN           package:adegenet           R Documentation(utf8)

_F_u_n_c_t_i_o_n _t_o _c_h_o_o_s_e _a _c_o_n_n_e_c_t_i_o_n _n_e_t_w_o_r_k

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

     The function 'chooseCN' is a simple interface to build a
     connection network (CN) from xy coordinates. The user chooses from
     6 types of graph and one additional weighting scheme. 'chooseCN'
     calls functions from appropriate packages, handles non-unique
     coordinates and returns a connection network either with classe
     'nb' or 'listw'.

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

     chooseCN(xy, ask = TRUE, type = NULL, result.type = "nb", d1 = NULL, 
         d2 = NULL, k = NULL,  a=NULL, dmin=NULL, plot.nb = TRUE, edit.nb = FALSE) 

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

      xy: an matrix or data.frame with two columns for x and y
          coordinates.

     ask: a logical stating whether graph should be chosen
          interactively (TRUE,default) or not (FALSE). Set to FALSE if
          'type' is provided.

    type: an integer giving the type of graph (see details).

result.type: a character giving the class of the returned object.
          Either "nb" (default) or "listw", both from 'spdep' package.
          See details.

      d1: the minimum distance between any two neighbours. Used if
          'type=5.'

      d2: the maximum distance between any two neighbours. Used if
          'type=5'. Can also be a character: "dmin" for the minimum
          distance so that each site has at least one connection, or
          "dmax" to have all sites connected (despite the later has no
          sense).

       k: the number of neighbours per point. Used if 'type=6'.

       a: the exponent of the inverse distance matrix. Used if
          'type=7'.

    dmin: the minimum distance between any two distinct points. Used to
          avoid infinite spatial proximities (defined as the inversed
          spatial distances). Used if 'type=7'.

 plot.nb: a logical stating whether the resulting graph should be
          plotted (TRUE, default) or not  (FALSE).

 edit.nb: a logical stating whether the resulting graph should be
          edited manually for corrections (TRUE) or not  (FALSE,
          default).

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

     There are 7 kinds of graphs proposed: 
      Delaunay triangulation (type 1)
      Gabriel graph (type 2)
      Relative neighbours (type 3)
      Minimum spanning tree (type 4)
      Neighbourhood by distance (type 5)
      K nearests neighbours (type 6)
      Inverse distances (type 7)

     The last option (type=7) is not a true neighbouring graph: all
     sites are neighbours, but the spatial weights are directly
     proportional to the inversed spatial distances.
      Also not that in this case, the output of the function is always
     a 'listw' object, even if 'nb' was requested.

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

     Returns a connection network having the class 'nb' or 'listw'. The
     xy coordinates are passed as attribute to the created object.

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

     Thibaut Jombart t.jombart@imperial.ac.uk

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

     'spca'

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

     data(nancycats)
     if(require(spdep) & require(ade4)){

     par(mfrow=c(2,2))
     cn1 <- chooseCN(nancycats@other$xy,ask=FALSE,type=1)
     cn2 <- chooseCN(nancycats@other$xy,ask=FALSE,type=2)
     cn3 <- chooseCN(nancycats@other$xy,ask=FALSE,type=3)
     cn4 <- chooseCN(nancycats@other$xy,ask=FALSE,type=4)
     par(mfrow=c(1,1))
     }

