********************************************************************** * * * Input EMM parmfile * * * ********************************************************************** ESTIMATION DESCRIPTION (required) SpotRate Project name, pname, char* 2.5 EMM version, defines format of this file, emmver, float 0 Objfun type, 0 EMM, 1 MLE, 2 usr, type, int 0 Proposal type, 0 group_move, 1 cond_move, 2 usr, proptype, int 1 Write detailed output if print=1, int 457 Seed for simulations, iseed, int 1000 Number of MCMC simulations per file, lchain, int 5 Number of MCMC simulation files, nfile, int 1.0 Rescale parameter increments by this value, incfac, float 1.0 Rescale proposal scaling by this value, sclfac, float 1.0 Rescale objfun by this value, temperature, float 1 Sandwich variance not computed if kilse=1, int 1 The stride used to write MCMC simulations, stride, int 0 Max cache size, max_cache_size, int DATA DESCRIPTION (required) (mod and obj constructors see realmat data(M,n)) 1 Dimension of the data, M, int 834 Number of observations, n, int dmark.dat File name, any length, no embedded blanks, dsn, string 4 Read these white space separated fields, fields, intvec MODEL DESCRIPTION (required) 6 Number of model parameters, num_mod_parms, int 8 Number of model functionals, num_mod_funcs, int MODEL PARMFILE (required) (constructor sees as vector pfvec, alvec) __none__ File name, code __none__ if none, mod_parmfile, string #begin additional lines 5000 Number of observations in simulated data, slen (=N), int 500 Initial simulations to eliminate transients, spin, int #end additional lines OBJFUN PARMFILE (required) (constructor sees as vector pfvec, alvec) 11114000.fit File name, code __none__ if none, obj_parmfile, string #begin additional lines #end additional lines PARAMETER START VALUES (required) 0.05 1 0.0 1 1.5 1 0.0 1 0.1 1 0.0 1 PROPOSAL SCALING (required) 1.95312500000000000e-03 1.95312500000000000e-03 1.95312500000000000e-03 1.95312500000000000e-03 1.95312500000000000e-03 1.95312500000000000e-03 ********************************************************************** * * * EMM parmfile interpretation * * * ********************************************************************** ESTIMATION DESCRIPTION pname = SpotRate emmver = 2.5 objtype = 0 proptype = 0 print = true seed = 457 lchain = 1000 nfile = 5 incfac = 1 (should have exact binary representation) sclfac = 1 temperature = 1 kilse = true stride = 1 max_cache_size = 0 DATA DESCRIPTION M = 1 n = 834 dsn = dmark.dat fieldline: 4 Read these white space separated fields fields: 4 MODEL DESCRIPTION len_mod_parm = 6 len_mod_func = 8 MODEL PARMFILE is_mod_parmfile = false #begin additional lines 5000 Number of observations in simulated data, slen (=N), int 500 Initial simulations to eliminate transients, spin, int #end additional lines PARAMETER START VALUES rho = Col 1 Row 1 0.050000 Row 2 0.0 Row 3 1.50000 Row 4 0.0 Row 5 0.10000 Row 6 0.0 rho_mask = Row 1 1 Row 2 1 Row 3 1 Row 4 1 Row 5 1 Row 6 1 Number fixed = 0 Number active = 6 fixed = Null Vector active = Row 1 1 Row 2 2 Row 3 3 Row 4 4 Row 5 5 Row 6 6 PARAMETER INCREMENTS not found. Parameters are not put on a grid. Cache is ineffective. PROPOSAL SCALING (after multiplication by sclfac) (output parmfile this scale and sclfac=1.0) prop_scale = Col 1 Row 1 0.00195312 Row 2 0.00195312 Row 3 0.00195312 Row 4 0.00195312 Row 5 0.00195312 Row 6 0.00195312 OBJFUN PARMFILE is_obj_parmfile = true obj_parmfile = 11114000.fit #begin additional lines #end additional lines ********************************************************************** * * * Prop groups * * * ********************************************************************** Constructed from PROPOSAL GROUPING, if present; If not, move one at a time grouping is used. If rho has fixed elements, they are in Group 0 and not changed during the MCMC iterations. PROPOSAL GROUPING correlations have been converted to variances using the prop_scale vector above. Frequencies are relative, not absolute. Group 0 freq = 1 gvec = Row 1 1 ginc = Col 1 Row 1 9.5367e-07 mean = Col 1 Row 1 0.050000 Vmat = Col 1 Row 1 3.8147e-06 Group 1 freq = 1 gvec = Row 1 2 ginc = Col 1 Row 1 9.5367e-07 mean = Col 1 Row 1 0.0 Vmat = Col 1 Row 1 3.8147e-06 Group 2 freq = 1 gvec = Row 1 3 ginc = Col 1 Row 1 9.5367e-07 mean = Col 1 Row 1 1.50000 Vmat = Col 1 Row 1 3.8147e-06 Group 3 freq = 1 gvec = Row 1 4 ginc = Col 1 Row 1 9.5367e-07 mean = Col 1 Row 1 0.0 Vmat = Col 1 Row 1 3.8147e-06 Group 4 freq = 1 gvec = Row 1 5 ginc = Col 1 Row 1 9.5367e-07 mean = Col 1 Row 1 0.10000 Vmat = Col 1 Row 1 3.8147e-06 Group 5 freq = 1 gvec = Row 1 6 ginc = Col 1 Row 1 9.5367e-07 mean = Col 1 Row 1 0.0 Vmat = Col 1 Row 1 3.8147e-06 ********************************************************************** * * * First 12 observations * * * ********************************************************************** Col 1 Col 2 Col 3 Col 4 Col 5 Col 6 Row 1 0.25073 0.22636 2.47971 -0.60543 -0.89149 1.35755 Col 7 Col 8 Col 9 Col 10 Col 11 Col 12 Row 1 0.74114 1.18142 -2.45871 0.76837 0.0 -1.42493 ********************************************************************** * * * Last 12 observations * * * ********************************************************************** Col 1 Col 2 Col 3 Col 4 Col 5 Col 6 Row 1 0.94871 0.71252 -0.25128 1.00560 0.52506 0.84181 Col 7 Col 8 Col 9 Col 10 Col 11 Col 12 Row 1 -0.33758 -1.32905 1.27177 0.067385 -2.20009 0.46266 ********************************************************************** * * * SNP now controls print * * * ********************************************************************** ********************************************************************** * * * EMM now controls print * * * **********************************************************************