1 /*------------------------------------------------------ 2 Maximum likelihood estimation 3 of migration rate and effectice population size 4 using a Metropolis-Hastings Monte Carlo algorithm 5 ------------------------------------------------------- 6 P R O F I L E L I K E L I H O O D R O U T I N E S 7 8 Peter Beerli 1997, Seattle 9 beerli@fsu.edu 10 11 Copyright 1996-2002 Peter Beerli and Joseph Felsenstein, Seattle WA 12 Copyright 2003-2004 Peter Beerli, Tallahassee FL 13 14 Permission is hereby granted, free of charge, to any person obtaining 15 a copy of this software and associated documentation files (the 16 "Software"), to deal in the Software without restriction, including 17 without limitation the rights to use, copy, modify, merge, publish, 18 distribute, sublicense, and/or sell copies of the Software, and to 19 permit persons to whom the Software is furnished to do so, subject 20 to the following conditions: 21 22 The above copyright notice and this permission notice shall be 23 included in all copies or substantial portions of the Software. 24 25 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 26 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 27 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 28 IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR 29 ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF 30 CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION 31 WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 32 33 $Id: profile.h 2157 2013-04-16 22:27:40Z beerli $ 34 -------------------------------------------------------*/ 35 extern boolean print_profile_likelihood_driver (long which, world_fmt * world, 36 long *gmaxptr); 37 extern void print_profile_likelihood (long which, world_fmt * world, long *gmaxptr); 38 extern long print_profile_percentile (world_fmt * world); 39 extern void allocate_profile_percentiles (world_fmt * world); 40 extern void destroy_profile_percentiles (world_fmt * world); 41 extern void print_profile_title (world_fmt * world); 42 extern long warp (long ii); 43 extern long choose_profile_parameters (world_fmt * world, long *profilelist); 44 45 #define GRIDSIZE 9 46 #define GRIDMIDDLE 5 47 #define GRID {0.01,0.05,0.10,0.50,0.99,0.95,0.90,0.50,1.0} 48 #define SHOWGRID {0.005,0.025,0.05,0.25,0.995,0.975,0.95,0.75,0.50} 49 #define GRID2 {0.005,0.025,0.05,0.25,0.5, 0.75,0.95,0.975,0.995} 50 #define INDEX {0,1,2,3,8,7,6,5,4} 51 #define DEVIATE {0.02,0.10,0.20, 0.5, 50.,10., 5., 2., 1.} 52 #define DEVIATE2 {0.02,0.10,0.20, 0.5, 1., 2., 5., 10., 50. } 53 //#define DEVIATE {0.002,0.010,0.020, 0.05, 5000.,1000., 500., 200., 1.} 54 //#define ABSOLUTE {1e-100,1e100} 55