diff --git a/src/DSMH_initialization.m b/src/DSMH_initialization.m new file mode 100644 index 000000000..38e16da4e --- /dev/null +++ b/src/DSMH_initialization.m @@ -0,0 +1,118 @@ +function [ ix2, temperedlogpost, loglik, ModelName, MetropolisFolder, npar, NumberOfParticles, bayestopt_] = ... + DSMH_initialization(TargetFun, xparam1, mh_bounds,dataset_,dataset_info,options_,M_,estim_params_,bayestopt_,oo_) +% function [ ix2, ilogpo2, ModelName, MetropolisFolder, FirstBlock, FirstLine, npar, NumberOfParticles, bayestopt_] = ... +% DSMH_initialization(TargetFun, xparam1, mh_bounds,dataset_,dataset_info,options_,M_,estim_params_,bayestopt_,oo_) +% Dynamic Striated Metropolis-Hastings initialization. +% +% INPUTS +% o TargetFun [char] string specifying the name of the objective +% function (tempered posterior kernel and likelihood). +% o xparam1 [double] (p*1) vector of parameters to be estimated (initial values). +% o mh_bounds [double] (p*2) matrix defining lower and upper bounds for the parameters. +% o dataset_ data structure +% o dataset_info dataset info structure +% o options_ options structure +% o M_ model structure +% o estim_params_ estimated parameters structure +% o bayestopt_ estimation options structure +% o oo_ outputs structure +% +% OUTPUTS +% o ix2 [double] (NumberOfParticles*npar) vector of starting points for different chains +% o ilogpo2 [double] (NumberOfParticles*1) vector of initial posterior values for different chains +% o iloglik2 [double] (NumberOfParticles*1) vector of initial likelihood values for different chains +% o ModelName [string] name of the mod-file +% o MetropolisFolder [string] path to the Metropolis subfolder +% o npar [scalar] number of parameters estimated +% o NumberOfParticles [scalar] Number of particles requested for the parameters distributions +% o bayestopt_ [structure] estimation options structure +% +% SPECIAL REQUIREMENTS +% None. + +% Copyright (C) 2006-2017 Dynare Team +% +% This file is part of Dynare. +% +% Dynare is free software: you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation, either version 3 of the License, or +% (at your option) any later version. +% +% Dynare is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License for more details. +% +% You should have received a copy of the GNU General Public License +% along with Dynare. If not, see . + +%Initialize outputs +ix2 = []; +ilogpo2 = []; +iloglik2 = []; +ModelName = []; +MetropolisFolder = []; +npar = []; +NumberOfParticles = []; + +ModelName = M_.fname; +if ~isempty(M_.bvar) + ModelName = [ModelName '_bvar']; +end + +MetropolisFolder = CheckPath('dsmh',M_.dname); +BaseName = [MetropolisFolder filesep ModelName]; + +NumberOfParticles = options_.dsmh.number_of_particles; %Number of particles for the parameters +npar = length(xparam1); + +% Here we start a new DS Metropolis-Hastings, previous draws are discarded. +disp('Estimation::dsmh: Initialization...') +% Delete old dsmh files if any... +files = dir([BaseName '_dsmh*_blck*.mat']); +%if length(files) +% delete([BaseName '_dsmh*_blck*.mat']); +% disp('Estimation::smc: Old dsmh-files successfully erased!') +%end +% Delete old log file. +file = dir([ MetropolisFolder '/dsmh.log']); +%if length(file) +% delete([ MetropolisFolder '/dsmh.log']); +% disp('Estimation::dsmh: Old dsmh.log file successfully erased!') +% disp('Estimation::dsmh: Creation of a new dsmh.log file.') +%end +fidlog = fopen([MetropolisFolder '/dsmh.log'],'w'); +fprintf(fidlog,'%% DSMH log file (Dynare).\n'); +fprintf(fidlog,['%% ' datestr(now,0) '.\n']); +fprintf(fidlog,' \n\n'); +fprintf(fidlog,'%% Session 1.\n'); +fprintf(fidlog,' \n'); +prior_draw(bayestopt_,options_.prior_trunc); +% Find initial values for the NumberOfParticles chains... +set_dynare_seed('default'); +fprintf(fidlog,[' Initial values of the parameters:\n']); +disp('Estimation::dsmh: Searching for initial values...'); +ix2 = zeros(npar,NumberOfParticles); +temperedlogpost = zeros(NumberOfParticles,1); +loglik = zeros(NumberOfParticles,1); +%stderr = sqrt(bsxfun(@power,mh_bounds.ub-mh_bounds.lb,2)/12)/10; +for j=1:NumberOfParticles + validate = 0; + while validate == 0 + candidate = prior_draw()'; +% candidate = xparam1(:) + 0.001*randn(npar,1);%bsxfun(@times,stderr,randn(npar,1)) ; + if all(candidate(:) >= mh_bounds.lb) && all(candidate(:) <= mh_bounds.ub) + ix2(:,j) = candidate ; + [temperedlogpost(j),loglik(j)] = tempered_likelihood(TargetFun,candidate,0.0,dataset_,dataset_info,options_,M_,estim_params_,bayestopt_,mh_bounds,oo_); + if isfinite(loglik(j)) % if returned log-density is Inf or Nan (penalized value) + validate = 1; + end + end + end +end +fprintf(fidlog,' \n'); +disp('Estimation::dsmh: Initial values found!') +skipline() + + diff --git a/src/DSMH_sampler.m b/src/DSMH_sampler.m new file mode 100644 index 000000000..56c9185a0 --- /dev/null +++ b/src/DSMH_sampler.m @@ -0,0 +1,303 @@ +function DSMH_sampler(TargetFun,xparam1,mh_bounds,dataset_,dataset_info,options_,M_,estim_params_,bayestopt_,oo_) +% function DSMH_sampler(TargetFun,ProposalFun,xparam1,sampler_options,mh_bounds,dataset_,dataset_info,options_,M_,estim_params_,bayestopt_,oo_) +% Dynamic Striated Metropolis-Hastings algorithm. +% +% INPUTS +% o TargetFun [char] string specifying the name of the objective +% function (posterior kernel). +% o ProposalFun [char] string specifying the name of the proposal +% density +% o xparam1 [double] (p*1) vector of parameters to be estimated (initial values). +% o sampler_options structure +% .invhess [double] (p*p) matrix, posterior covariance matrix (at the mode). +% o mh_bounds [double] (p*2) matrix defining lower and upper bounds for the parameters. +% o dataset_ data structure +% o dataset_info dataset info structure +% o options_ options structure +% o M_ model structure +% o estim_params_ estimated parameters structure +% o bayestopt_ estimation options structure +% o oo_ outputs structure +% +% SPECIAL REQUIREMENTS +% None. +% +% PARALLEL CONTEXT +% The most computationally intensive part of this function may be executed +% in parallel. The code suitable to be executed in +% parallel on multi core or cluster machine (in general a 'for' cycle) +% has been removed from this function and been placed in the posterior_sampler_core.m funtion. +% +% The DYNARE parallel packages comprise a i) set of pairs of Matlab functions that can be executed in +% parallel and called name_function.m and name_function_core.m and ii) a second set of functions used +% to manage the parallel computations. +% +% This function was the first function to be parallelized. Later, other +% functions have been parallelized using the same methodology. +% Then the comments write here can be used for all the other pairs of +% parallel functions and also for management functions. + +% Copyright (C) 2006-2017 Dynare Team +% +% This file is part of Dynare. +% +% Dynare is free software: you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation, either version 3 of the License, or +% (at your option) any later version. +% +% Dynare is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License for more details. +% +% You should have received a copy of the GNU General Public License +% along with Dynare. If not, see . + + +lambda = exp(bsxfun(@minus,options_.dsmh.H,1:1:options_.dsmh.H)/(options_.dsmh.H-1)*log(options_.dsmh.lambda1)); +c = 55 ; + +% Step 0: Initialization of the sampler +[ param, tlogpost_iminus1, loglik, ~, ~, npar, nparticles, bayestopt_] = ... + DSMH_initialization(TargetFun, xparam1, mh_bounds, dataset_,dataset_info,options_,M_,estim_params_,bayestopt_,oo_); + +ESS = zeros(options_.dsmh.H,1) ; +zhat = 1 ; + +% The DSMH starts here + for i=1:options_.dsmh.H + disp(''); + disp('Tempered iteration'); + disp(i) ; + % Step 1: sort the densities and compute IS weigths + [tlogpost_iminus1,loglik,param] = sort_matrices(tlogpost_iminus1,loglik,param) ; + [tlogpost_i,weights,zhat,ESS,mu,Omegachol] = compute_IS_weights_and_moments(param,tlogpost_iminus1,loglik,lambda,i,zhat,ESS) ; + % Step 2: tune c_i + c = tune_c(TargetFun,param,tlogpost_i,lambda,i,c,Omegachol,weights,dataset_,dataset_info,options_,M_,estim_params_,bayestopt_,mh_bounds,oo_); + % Step 3: Metropolis step + [param,tlogpost_iminus1,loglik] = mutation_DSMH(TargetFun,param,tlogpost_i,tlogpost_iminus1,loglik,lambda,i,c,Omegachol,weights,dataset_,dataset_info,options_,M_,estim_params_,bayestopt_,mh_bounds,oo_); + end + +weights = exp(loglik*(lambda(end)-lambda(end-1))); +weights = weights/sum(weights); +indx_resmpl = DSMH_resampling(weights,rand(1,1),nparticles); +distrib_param = param(:,indx_resmpl); + +%% Plot parameters densities +TeX = options_.TeX; + +[nbplt,nr,nc,lr,lc,nstar] = pltorg(npar); + +if TeX + fidTeX = fopen([M_.fname '_param_density.tex'],'w'); + fprintf(fidTeX,'%% TeX eps-loader file generated by DSMH.m (Dynare).\n'); + fprintf(fidTeX,['%% ' datestr(now,0) '\n']); + fprintf(fidTeX,' \n'); +end + +number_of_grid_points = 2^9; % 2^9 = 512 !... Must be a power of two. +bandwidth = 0; % Rule of thumb optimal bandwidth parameter. +kernel_function = 'gaussian'; % Gaussian kernel for Fast Fourier Transform approximation. +for plt = 1:nbplt, + if TeX + NAMES = []; + TeXNAMES = []; + end + hh = dyn_figure(options_.nodisplay,'Name','Parameters Densities'); + for k=1:min(nstar,npar-(plt-1)*nstar) + subplot(nr,nc,k) + kk = (plt-1)*nstar+k; + [name,texname] = get_the_name(kk,TeX,M_,estim_params_,options_); + if TeX + if isempty(NAMES) + NAMES = name; + TeXNAMES = texname; + else + NAMES = char(NAMES,name); + TeXNAMES = char(TeXNAMES,texname); + end + end + optimal_bandwidth = mh_optimal_bandwidth(distrib_param(kk,:)',nparticles,bandwidth,kernel_function); + [density(:,1),density(:,2)] = kernel_density_estimate(distrib_param(kk,:)',number_of_grid_points,... + nparticles,optimal_bandwidth,kernel_function); + plot(density(:,1),density(:,2)); + hold on + title(name,'interpreter','none') + hold off + axis tight + drawnow + end + dyn_saveas(hh,[ M_.fname '_param_density' int2str(plt) ],options_.nodisplay,options_.graph_format); + if TeX + % TeX eps loader file + fprintf(fidTeX,'\\begin{figure}[H]\n'); + for jj = 1:min(nstar,length(x)-(plt-1)*nstar) + fprintf(fidTeX,'\\psfrag{%s}[1][][0.5][0]{%s}\n',deblank(NAMES(jj,:)),deblank(TeXNAMES(jj,:))); + end + fprintf(fidTeX,'\\centering \n'); + fprintf(fidTeX,'\\includegraphics[scale=0.5]{%s_ParametersDensities%s}\n',M_.fname,int2str(plt)); + fprintf(fidTeX,'\\caption{ParametersDensities.}'); + fprintf(fidTeX,'\\label{Fig:ParametersDensities:%s}\n',int2str(plt)); + fprintf(fidTeX,'\\end{figure}\n'); + fprintf(fidTeX,' \n'); + end +end + +function indx = DSMH_resampling(weights,noise,number) + indx = zeros(number,1); + cumweights = cumsum(weights); + randvec = (transpose(1:number)-1+noise(:))/number; + j = 1; + for i=1:number + while (randvec(i)>cumweights(j)) + j = j+1; + end + indx(i) = j; + end + +function [tlogpost_iminus1,loglik,param] = sort_matrices(tlogpost_iminus1,loglik,param) + [~,indx_ord] = sortrows(tlogpost_iminus1); + tlogpost_iminus1 = tlogpost_iminus1(indx_ord); + param = param(:,indx_ord); + loglik = loglik(indx_ord); + +function [tlogpost_i,weights,zhat,ESS,mu,Omegachol] = compute_IS_weights_and_moments(param,tlogpost_iminus1,loglik,lambda,i,zhat,ESS) + if i==1 + tlogpost_i = tlogpost_iminus1 + loglik*lambda(i); + else + tlogpost_i = tlogpost_iminus1 + loglik*(lambda(i)-lambda(i-1)); + end + weights = exp(tlogpost_i-tlogpost_iminus1); + zhat = (mean(weights))*zhat ; + weights = weights/sum(weights); + ESS(i) = 1/sum(weights.^2); + % estimates of mean and variance + mu = param*weights; + z = bsxfun(@minus,param,mu); + Omega = z*diag(weights)*z'; + Omegachol = chol(Omega)'; + +function c = tune_c(TargetFun,param,tlogpost_i,lambda,i,c,Omegachol,weights,dataset_,dataset_info,options_,M_,estim_params_,bayestopt_,mh_bounds,oo_) + disp('tuning c_i...'); + disp('Initial value ='); + disp(c) ; + npar = size(param,1); + lower_prob = (.5*(options_.dsmh.alpha0+options_.dsmh.alpha1))^5; + upper_prob = (.5*(options_.dsmh.alpha0+options_.dsmh.alpha1))^(1/5); + stop=0 ; + while stop==0 + acpt = 0.0; + indx_resmpl = DSMH_resampling(weights,rand(1,1),options_.dsmh.G); + param0 = param(:,indx_resmpl); + tlogpost0 = tlogpost_i(indx_resmpl); + for j=1:options_.dsmh.G + for l=1:options_.dsmh.K + validate = 0; + while validate == 0 + candidate = param0(:,j) + sqrt(c)*Omegachol*randn(npar,1); + if all(candidate >= mh_bounds.lb) && all(candidate <= mh_bounds.ub) + [tlogpostx,loglikx] = tempered_likelihood(TargetFun,candidate,lambda(i),dataset_,dataset_info,options_,M_,estim_params_,bayestopt_,mh_bounds,oo_); + if isfinite(loglikx) % if returned log-density is not Inf or Nan (penalized value) + validate = 1; + if rand(1,1)= mh_bounds.lb) && all(candidate(:) <= mh_bounds.ub) + [tlogpostx,loglikx] = tempered_likelihood(TargetFun,candidate,lambda(i),dataset_,dataset_info,options_,M_,estim_params_,bayestopt_,mh_bounds,oo_); + if isfinite(loglikx) % if returned log-density is not Inf or Nan (penalized value) + validate = 1; + if u2