autoconst              package:prabclus              R Documentation

_S_p_a_t_i_a_l _a_u_t_o_c_o_r_r_e_l_a_t_i_o_n _p_a_r_a_m_e_t_e_r _e_s_t_i_m_a_t_i_o_n

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

     Monte Carlo estimation of the disjunction/spatial autocorrelation
     parameter 'pd' for the simulation model used in 'randpop.nb', used
     for tests for clustering of presence-absence data.

     'autoconst' is the main function; 'autoreg' performs the
     simulation and is executed within 'autoconst'.

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

     autoconst(x, prange = c(0, 1), twostep = TRUE, step1 = 0.1,
     step2 = 0.01, plot = TRUE, nperp = 4, ejprob = NA,
     species.fixed = TRUE, pdfnb=FALSE)

     autoreg(x, probs, ejprob, plot = TRUE, nperp = 4, species.fixed = TRUE,
     pdfnb=FALSE)

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

       x: object of class 'prab' as generated by 'prabinit'.
          Presence-absence data to be analyzed.

  prange: numerical range vector, lower value not smaller than 0,
          larger value not larger than 1. Range where the parameter is
          to be found.

 twostep: logical. If 'TRUE', a first estimation step is carried out in
          the whole 'prange', and then the final estimation is
          determined between the preliminary estimator '-5*step2' and
          {+5*step2}. Else, the first simulation determines the final
          estimator.

   step1: numerical between 0 and 1. Interval length between subsequent
          choices of 'pd' for the first simulation.

   step2: numerical between 0 and 1. Interval length between subsequent
          choices of 'pd' for the second simulation in case of
          'twostep=TRUE'.

    plot: logical. If 'TRUE', a scatterplot of 'pd'-values against
          resulting 'ejprob' values (see below), with regression line
          and data value of 'ejprob' is shown.

   nperp: integer. Number of simulations per 'pd'-value.

  ejprob: numerical between 0 and 1. Observed disjunction probability
          for data 'x'; if not specified in advance, it will be
          computed by 'autoconst'.

species.fixed: logical. If 'TRUE', sizes of generated species match the
          species sizes in 'x', else they are generated from the
          empirical distribution of species sizes in 'x'.

   probs: vector of numericals between 0 and 1. 'pd' values for the
          simulation.

   pdfnb: logical. If 'TRUE', the probabilities of the regions are
          modified according to the number of neighboring regions in
          'randpop.nb', see Hennig and Hausdorf (2002), p. 5.

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

     The spatial autocorrelation parameter 'pd' of the model for the
     generation of presence-absence data sets used by 'randpop.nb' can
     be estimated by use of the observed disjuction probability
     'ejprob' which is the sum of all species' connectivity components
     minus the number of species divided by the number of "presence"
     entries minus the number of species. This is done by a simulation
     of artificial data sets with characteristics of 'x' and different
     'pd'-values, governed by 'prange, step1, step2' and 'nperp'.
     'ejprob' is then calculated for all simulated populations. A
     linear regression of 'ejprob' on 'pd' is performed and the
     estimator of 'pd' is determined by computing the inverse of the
     regression function for the 'ejprob'-value of 'x'.

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

     'autoconst' produces the same list as 'autoreg' with additional
     component 'ejprob'. The components are  

      pd: (eventually) estimated parameter 'pd'.

    coef: (eventually) estimated regression coefficients.

  ejprob: see above.

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

     Christian Hennig hennig@math.uni-hamburg.de <URL:
     http://www.math.uni-hamburg.de/home/hennig/>

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

     Hennig, C. and Hausdorf, B. (2002) Distance-based parametric
     bootstrap tests for clustering of species ranges, submitted, <URL:
     http://stat.ethz.ch/Research-Reports/110.html>.

     Hausdorf, B. and Hennig, C. (2003)  Biotic Element Analysis in
     Biogeography. To appear in  _Systematic Biology_.

     Hausdorf, B. and Hennig, C. (2003) Nestedness of nerth-west
     European land snail ranges as a consequence of differential
     immigration from Pleistocene glacial refuges. _Oecologia_ 135,
     102-109.

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

     'randpop.nb', 'prabinit', 'con.comp'

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

     data(kykladspecreg)
     # Note: If you do not use the installed package, replace this by
     # kykladspecreg <- read.table("(path/)kykladspecreg.dat")
     data(nb)
     # Note: If you do not use the installed package, replace this by
     # nb <- list()
     # for (i in 1:34)
     #   nb <- c(nb,list(scan(file="(path/)nb.dat",
     #                   skip=i-1,nlines=1)))
     set.seed(1234)
     x <- prabinit(prabmatrix=kykladspecreg, neighborhood=nb)
     ax <- autoconst(x,nperp=2)

