srd            package:MarkedPointProcess            R Documentation

_S_i_m_u_l_a_t_i_o_n _s_t_u_d_y _f_o_r _m_a_r_k_e_d _p_o_i_n_t _p_r_o_c_e_s_s_e_s

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

     The function reproduces the simulation study published by
     Schlather, Ribeiro and Diggle (2004)

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

     srd.jrssb(input=NULL, repet=500, dev=2, PrintLevel=2, readlines=TRUE,
               ps.path="ps/", data.save.path="data/", simu.path="simu/",
               tex.path="tex/", biondi.etal=NULL, final=TRUE)

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

   input: vector of values for automatic choice of the submenues

   repet: number of realisations investigated for each parameter set. 2
          * 'repet' gives also roughly the number of hours needed to do
          all the simulations! 

     dev: device, see 'Dev'

PrintLevel: If 'PrintLevel'>1 some information on the course of the
          algorithm is printed 

readlines: logical. Only used if 'is.numeric(dev)'. If the operating
          system is unix and 'readlines=FALSE' then the system waits a
          second before the next plot is calculated or shown. Otherwise
          the system waits for return. 

 ps.path: path used for all postscript files in 'srd.jrssb' 

data.save.path: directory where intermediate results in the analysis of
          the data are stored

simu.path: directory used to store intermediate results for the
          simulations 

tex.path: path used for all created tex files containing tables

biondi.etal: list of two components:

        _c_o_o_r_d: a matrix of two columns for the coordinates and

        _d_i_a_m_e_t_e_r: a vector for the marks

          The data set by Biondi et al., used in Schlather, Ribeiro and
          Diggle (2004), is not freely available. 

   final: logical. If 'FALSE' then several parameters are changed so
          that the algorithms run faster. Especially 'repet' is limited
          to 3, 'optim' is very sloppy, and the parameter sets for the
          simulation study are remarkably reduced. 'final=FALSE' is
          used for debugging or demonstration, but the results are not
          reliable. 

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

     The simulation study is written in a way that 'srd.jrssb()' might
     be called several times on a parallel CPU system or PVD from the
     same directory. The non-interaction of the different instances is
     managed by means of lock files.  It is ensured that no simulation
     study for a specific parameter set is performed twice. However,
     the programming has been kept simple so that a lock files might be
     created but the simulation is not performed by any process because
     of strange interaction. In this case all remaining lock files have
     to be deleted after the first run of the simulation study, and the
     study has to be re-run. Then, 'srd.jrssb()' does the simulation
     study only for remaining cases.

     For both the simulation studies and the data analyses,
     intermediate stored results are re-used if run again.

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

     'NULL'. Side effect is the creation of postscript files and tex
     files.

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

     Martin Schlather, schlath@hsu-hh.de <URL:
     http://www.unibw-hamburg.de/WWEB/math/schlath/schlather.html>

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

     Schlather, M., Ribeiro, P. and Diggle, P. (2004) Detecting
     Dependence Between Marks and Locations of Marked Point Processes.
     _J. R. Statist. Soc., Ser. B_ *66*, 79-83.

     Biondi, F., Myers, D.E., and Avery, C.C. (1994) Geostatistically
     modeling stem size and increment in an old-growth forest. _Can. J.
     Forest Res._ *24*, 1354-1368.

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

     'rfm.test', 'simulateMPP', 'MarkedPointProcess'

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

     # repet=2 is for demonstration of functionality
     # repet=50 gives more reliable results
     # repet=500 and final=TRUE have been used in the simulation study
       
     printlevel <- 1 + !interactive()
     srd.jrssb(input=if(!interactive()) c(1:2,0), repet=2, dev=TRUE,
               final=FALSE, Pr=printlevel)

