diff --git a/matlab/PlotPosteriorDistributions.m b/matlab/PlotPosteriorDistributions.m index d96d6178cacecbe45bbc66c7b369e688bbdeba07..e280eee710dea9872ac236af834601d1d98a79ef 100644 --- a/matlab/PlotPosteriorDistributions.m +++ b/matlab/PlotPosteriorDistributions.m @@ -1,6 +1,5 @@ function oo_ = PlotPosteriorDistributions(estim_params_, M_, options_, bayestopt_, oo_) - -% function PlotPosteriorDistributions() +% oo_ = PlotPosteriorDistributions(estim_params_, M_, options_, bayestopt_, oo_) % plots posterior distributions % % INPUTS @@ -36,7 +35,6 @@ latexDirectoryName = CheckPath('latex',M_.dname); graphDirectoryName = CheckPath('graphs',M_.dname); TeX = options_.TeX; -nblck = options_.mh_nblck; nvx = estim_params_.nvx; nvn = estim_params_.nvn; ncx = estim_params_.ncx; @@ -66,7 +64,7 @@ for i=1:npar hh_fig=dyn_figure(options_.nodisplay, 'Name', figurename); end [nam,texnam] = get_the_name(i, TeX, M_, estim_params_, options_.varobs); - [x2, f2, abscissa, dens, binf2, bsup2] = draw_prior_density(i, bayestopt_); + [x2, f2, ~, ~, binf2, bsup2] = draw_prior_density(i, bayestopt_); top2 = max(f2); if i <= nvx name = M_.exo_names{estim_params_.var_exo(i,1)}; diff --git a/matlab/check_prior_bounds.m b/matlab/check_prior_bounds.m index 14d93cfd67b547ad80b52aeadec68e43d1fd05f7..bf77952d6325d60bd6031be733a278ce2e08263d 100644 --- a/matlab/check_prior_bounds.m +++ b/matlab/check_prior_bounds.m @@ -1,10 +1,9 @@ function check_prior_bounds(xparam1,bounds,M_,estim_params_,options_,bayestopt_) -% function check_prior_bounds(xparam1,bounds,M_,estim_params_,options_) +% function check_prior_bounds(xparam1,bounds,M_,estim_params_,options_,bayestopt_) % checks the parameter vector of violations of the prior bounds % Inputs: % -xparam1 [double] vector of parameters to be estimated (initial values) -% -bounds [vector] vector containing the lower and upper -% bounds +% -bounds [vector] vector containing the lower and upper bounds % -M_ [structure] characterizing the model. % -estim_params_ [structure] characterizing parameters to be estimated % -options_ [structure] characterizing the options diff --git a/matlab/fjaco.m b/matlab/fjaco.m index e3a5e913e7b9b33cd8296024ad1af6e3d45d4549..3d41787b15eef7a0c59e1922325460fc137de514 100644 --- a/matlab/fjaco.m +++ b/matlab/fjaco.m @@ -1,5 +1,5 @@ function fjac = fjaco(f,x,varargin) - +% fjac = fjaco(f,x,varargin) % FJACO Computes two-sided finite difference Jacobian % USAGE % fjac = fjaco(f,x,P1,P2,...) diff --git a/matlab/mh_autocorrelation_function.m b/matlab/mh_autocorrelation_function.m index eb659f68653f879a8a43e64bf0136f634dff4e08..cf10a82798c58ac95d307820db9343524dd737c2 100644 --- a/matlab/mh_autocorrelation_function.m +++ b/matlab/mh_autocorrelation_function.m @@ -1,10 +1,9 @@ function mh_autocorrelation_function(options_,M_,estim_params_,type,blck,name1,name2) +% mh_autocorrelation_function(options_,M_,estim_params_,type,blck,name1,name2) % This function plots the autocorrelation of the sampled draws in the % posterior distribution. % -% % INPUTS -% % options_ [structure] Dynare structure. % M_ [structure] Dynare structure (related to model definition). % estim_params_ [structure] Dynare structure (related to estimation). @@ -63,7 +62,7 @@ clear record; PosteriorDraws = GetAllPosteriorDraws(M_.dname, M_.fname, column, FirstMhFile, FirstLine, TotalNumberOfMhFiles, NumberOfDraws, nblck, blck); % Compute the autocorrelation function: -[autocov,autocor] = sample_autocovariance(PosteriorDraws,options_.mh_autocorrelation_function_size); +[~,autocor] = sample_autocovariance(PosteriorDraws,options_.mh_autocorrelation_function_size); % Plot the posterior draws: @@ -101,7 +100,7 @@ axis tight if ~exist(M_.dname, 'dir') mkdir('.',M_.dname); end -if ~exist([M_.dname filesep 'graphs']) +if ~exist([M_.dname filesep 'graphs'],'dir') mkdir(M_.dname,'graphs'); end diff --git a/matlab/plot_priors.m b/matlab/plot_priors.m index 50b7b6a2b3a3ca913d985eab857627510eb31640..63b811fd8bf4f5c8e1e1dfd96f5720946506694d 100644 --- a/matlab/plot_priors.m +++ b/matlab/plot_priors.m @@ -1,5 +1,5 @@ function plot_priors(bayestopt_,M_,estim_params_,options_,optional_title) -% function plot_priors +% plot_priors(bayestopt_,M_,estim_params_,options_,optional_title) % plots prior density % % INPUTS @@ -41,7 +41,7 @@ else figurename = optional_title; end npar = length(bayestopt_.p1); -[nbplt,nr,nc,lr,lc,nstar] = pltorg(npar); +[nbplt,nr,nc,~,~,nstar] = pltorg(npar); if TeX && any(strcmp('eps',cellstr(options_.graph_format))) fidTeX = fopen([latexDirectoryName filesep M_.fname '_Priors.tex'],'w'); @@ -59,7 +59,7 @@ for plt = 1:nbplt for index=1:nstar0 names = []; i = (plt-1)*nstar + index; - [x,f,abscissa,dens,binf,bsup] = draw_prior_density(i,bayestopt_); + [x,f] = draw_prior_density(i,bayestopt_); [nam,texnam] = get_the_name(i,TeX,M_,estim_params_,options_.varobs); subplot(nr,nc,index) hh_plt = plot(x,f,'-k','linewidth',2); diff --git a/matlab/print_table_prior.m b/matlab/print_table_prior.m index 44096e5b2681d02b0c2acc6b81c355937301c977..b9253af4c7e9a2facb5d1bd6bbfd62dd078f9ae9 100644 --- a/matlab/print_table_prior.m +++ b/matlab/print_table_prior.m @@ -52,7 +52,7 @@ options_.prior_trunc = prior_trunc_backup ; RESIZE = false; for i=1:size(bayestopt_.name,1) - [Name,tmp] = get_the_name(i,1,M_,estim_params_,options_.varobs); + [Name,~] = get_the_name(i,1,M_,estim_params_,options_.varobs); if length(Name)>size(T1,2) resize = true; else diff --git a/matlab/set_prior.m b/matlab/set_prior.m index 635568dc861804863848ddc499ba25568e2b880e..e6739f4686f7433ef53e285cb02df6890626c5b1 100644 --- a/matlab/set_prior.m +++ b/matlab/set_prior.m @@ -133,7 +133,7 @@ if ncn bayestopt_.p4 = [ bayestopt_.p4; estim_params_.corrn(:,10)]; %take generalized distribution into account bayestopt_.jscale = [ bayestopt_.jscale; estim_params_.corrn(:,11)]; baseid = length(bayestopt_.name); - bayestopt_.name = [bayestopt_.name; cell(ncn, 1)];; + bayestopt_.name = [bayestopt_.name; cell(ncn, 1)]; for i=1:ncn k1 = estim_params_.corrn(i,1); k2 = estim_params_.corrn(i,2); @@ -163,8 +163,8 @@ bayestopt_.p7 = bayestopt_.p6 ; %% check for point priors and disallow them as they do not work with MCMC if any(bayestopt_.p2 ==0) - error(sprintf(['Error in prior for %s: you cannot use a point prior in estimation. Either increase the prior standard deviation',... - ' or fix the parameter completely.'], bayestopt_.name{bayestopt_.p2 ==0})) + error('Error in prior for %s: you cannot use a point prior in estimation. Either increase the prior standard deviation',... + ' or fix the parameter completely.', bayestopt_.name{bayestopt_.p2 ==0}) end % generalized location parameters by default for beta distribution @@ -285,7 +285,7 @@ end CheckPath('prior',M_.dname); % I save the prior definition if the prior has changed. -if exist([ M_.dname '/prior/definition.mat']) +if exist([ M_.dname '/prior/definition.mat'],'file') old = load([M_.dname '/prior/definition.mat'],'bayestopt_'); prior_has_changed = 0; if length(bayestopt_.p1)==length(old.bayestopt_.p1) diff --git a/matlab/write_latex_prior_table.m b/matlab/write_latex_prior_table.m index 51a003075682a63d8e18e3d8645d4913c787be3e..9dd0496d2acda9815ac4a23fd1e722f1d5da7764 100644 --- a/matlab/write_latex_prior_table.m +++ b/matlab/write_latex_prior_table.m @@ -28,7 +28,7 @@ function write_latex_prior_table % You should have received a copy of the GNU General Public License % along with Dynare. If not, see <https://www.gnu.org/licenses/>. -global M_ options_ bayestopt_ estim_params_ +global M_ options_ estim_params_ if ~isbayes(estim_params_) fprintf('\nwrite_latex_prior_table:: No prior distributions detected. Skipping table creation.\n') @@ -39,13 +39,13 @@ if (size(estim_params_.var_endo,1) || size(estim_params_.corrn,1)) % Prior over measurement errors are defined... if ((isfield(options_,'varobs') && isempty(options_.varobs)) || ~isfield(options_,'varobs')) % ... But the list of observed variabled is not yet defined. - fprintf(['\nwrite_latex_prior_table:: varobs should be declared before. Skipping table creation.\n']) + fprintf('\nwrite_latex_prior_table:: varobs should be declared before. Skipping table creation.\n') return end end % Fill or update bayestopt_ structure -[xparam1, estim_params_, BayesOptions, lb, ub, M_] = set_prior(estim_params_, M_, options_); +[~, estim_params_, BayesOptions, ~, ~, M_] = set_prior(estim_params_, M_, options_); % Get untruncated bounds bounds = prior_bounds(BayesOptions, options_.prior_trunc); @@ -112,7 +112,7 @@ fprintf(fidTeX,'\\endlastfoot\n'); % Column 8: the upper bound of the interval containing 90% of the prior mass. PriorIntervals = prior_bounds(BayesOptions,(1-options_.prior_interval)/2) ; for i=1:size(BayesOptions.name,1) - [tmp,TexName] = get_the_name(i, 1, M_, estim_params_, options_.varobs); + [~,TexName] = get_the_name(i, 1, M_, estim_params_, options_.varobs); PriorShape = PriorNames{ BayesOptions.pshape(i) }; PriorMean = BayesOptions.p1(i); PriorMode = BayesOptions.p5(i);