nancycats           package:adegenet           R Documentation(utf8)

_M_i_c_r_o_s_a_t_e_l_l_i_t_e_s _g_e_n_o_t_y_p_e_s _o_f _2_3_7 _c_a_t_s _f_r_o_m _1_7 _c_o_l_o_n_i_e_s _o_f _N_a_n_c_y (_F_r_a_n_c_e)

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

     This data set gives the genotypes of 237 cats (Felis catus L.) for
     9 microsatellites markers. The individuals are divided into 17
     colonies whose spatial coordinates are also provided.

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

     data(nancycats)

_F_o_r_m_a_t:

     'nancycats' is a genind object with spatial coordinates of the
     colonies as a supplementary components (@xy). Beware: these
     coordinates are given for the true names (stored in @pop.names)
     and not for the generic names (used in @pop).

_S_o_u_r_c_e:

     Dominique Pontier (UMR CNRS 5558, University Lyon1, France)

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

     Devillard, S.; Jombart, T. & Pontier, D. Disentangling spatial and
     genetic structure of stray cat (Felis catus L.) colonies in urban
     habitat using: not all colonies are equal. submitted to _Molecular
     Ecology_

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

     data(nancycats)
     nancycats

     # summary's results are stored in x
     x <- summary(nancycats)

     # some useful graphics
     barplot(x$loc.nall,ylab="Alleles numbers",main="Alleles numbers
     per locus")

     plot(x$pop.eff,x$pop.nall,type="n",xlab="Sample size",ylab="Number of alleles")
     text(x$pop.eff,y=x$pop.nall,lab=names(x$pop.nall))

     par(las=3)
     barplot(table(nancycats@pop),ylab="Number of genotypes",main="Number of genotypes per colony")

     # are cats structured among colonies ?
     if(require(hierfstat)){

     if(require(ade4)){
     gtest <- gstat.randtest(nancycats,nsim=99)
     gtest
     plot(gtest)
     }

     dat <- genind2hierfstat(nancycats)

     Fstat <- varcomp.glob(dat$pop,dat[,-1])
     Fstat
     }

