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get_the_name.m: do not pass full options structure as input

new-samplers
Johannes Pfeifer 2023-11-30 13:31:51 +01:00 committed by Sébastien Villemot
parent 0ba91259d8
commit 709ef9230f
No known key found for this signature in database
GPG Key ID: 2CECE9350ECEBE4A
26 changed files with 76 additions and 97 deletions
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4
matlab/+mom/standard_errors.m
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@ -62,7 +62,7 @@ if strcmp(options_mom_.mom.mom_method,'GMM') && options_mom_.mom.analytic_standa
idx_nan = find(any(isnan(D)));
if any(idx_nan)
for i = idx_nan
fprintf('No standard errors available for parameter %s\n',get_the_name(i,options_mom_.TeX, M_, estim_params_, options_mom_))
fprintf('No standard errors available for parameter %s\n',get_the_name(i,options_mom_.TeX, M_, estim_params_, options_mom_.varobs))
end
warning('There are NaN in the analytical Jacobian of Moments. Check your bounds and/or priors, or use a different optimizer.')
Asympt_Var = NaN(length(xparam),length(xparam));
@ -86,7 +86,7 @@ else
if nnz(info_p)==0 && nnz(info_m)==0
D(:,i) = (oo__p.mom.model_moments - oo__m.mom.model_moments)/(2*eps_value);
else
problpar = get_the_name(i,options_mom_.TeX, M_, estim_params_, options_mom_);
problpar = get_the_name(i,options_mom_.TeX, M_, estim_params_, options_mom_.varobs);
if info_p(1)==42
warning('method_of_moments:info','Cannot compute the Jacobian using finite differences for parameter %s due to hitting the upper bound - no standard errors available.\n',problpar)
else

4
matlab/DSMH_sampler.m
View File

@ -98,7 +98,7 @@ TeX = options_.TeX;
str = sprintf(' Param. \t Lower Bound (95%%) \t Mean \t Upper Bound (95%%)');
for l=1:npar
[name,~] = get_the_name(l,TeX,M_,estim_params_,options_);
[name,~] = get_the_name(l,TeX,M_,estim_params_,options_.varobs);
str = sprintf('%s\n %s \t\t %5.4f \t\t %7.5f \t\t %5.4f', str, name, lb95_xparam(l), mean_xparam(l), ub95_xparam(l));
end
disp([str])
@ -129,7 +129,7 @@ hh_fig = dyn_figure(options_.nodisplay,'Name','Parameters Densities');
for k=1:npar %min(nstar,npar-(plt-1)*nstar)
subplot(ceil(sqrt(npar)),floor(sqrt(npar)),k)
%kk = (plt-1)*nstar+k;
[name,texname] = get_the_name(k,TeX,M_,estim_params_,options_);
[name,texname] = get_the_name(k,TeX,M_,estim_params_,options_.varobs);
optimal_bandwidth = mh_optimal_bandwidth(distrib_param(k,:)',options_.posterior_sampler_options.dsmh.nparticles,bandwidth,kernel_function);
[density(:,1),density(:,2)] = kernel_density_estimate(distrib_param(k,:)',number_of_grid_points,...
options_.posterior_sampler_options.dsmh.nparticles,optimal_bandwidth,kernel_function);

4
matlab/Herbst_Schorfheide_sampler.m
View File

@ -126,7 +126,7 @@ TeX = options_.TeX;
str = sprintf(' Param. \t Lower Bound (95%%) \t Mean \t Upper Bound (95%%)');
for l=1:npar
[name,~] = get_the_name(l,TeX,M_,estim_params_,options_);
[name,~] = get_the_name(l,TeX,M_,estim_params_,options_.varobs);
str = sprintf('%s\n %s \t\t %5.4f \t\t %7.5f \t\t %5.4f', str, name, lb95_xparam(l), mean_xparam(l), ub95_xparam(l));
end
disp([str])
@ -156,7 +156,7 @@ hh_fig = dyn_figure(options_.nodisplay,'Name','Parameters Densities');
for k=1:npar %min(nstar,npar-(plt-1)*nstar)
subplot(ceil(sqrt(npar)),floor(sqrt(npar)),k)
%kk = (plt-1)*nstar+k;
[name,texname] = get_the_name(k,TeX,M_,estim_params_,options_);
[name,texname] = get_the_name(k,TeX,M_,estim_params_,options_.varobs);
optimal_bandwidth = mh_optimal_bandwidth(distrib_param(k,:)',options_.posterior_sampler_options.HSsmc.nparticles,bandwidth,kernel_function);
[density(:,1),density(:,2)] = kernel_density_estimate(distrib_param(k,:)',number_of_grid_points,...
options_.posterior_sampler_options.HSsmc.nparticles,optimal_bandwidth,kernel_function);

2
matlab/PlotPosteriorDistributions.m
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@ -65,7 +65,7 @@ for i=1:npar
figunumber = figunumber+1;
hh_fig=dyn_figure(options_.nodisplay, 'Name', figurename);
end
[nam,texnam] = get_the_name(i, TeX, M_, estim_params_, options_);
[nam,texnam] = get_the_name(i, TeX, M_, estim_params_, options_.varobs);
[x2, f2, abscissa, dens, binf2, bsup2] = draw_prior_density(i, bayestopt_);
top2 = max(f2);
if i <= nvx

4
matlab/check_prior_bounds.m
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@ -30,7 +30,7 @@ function check_prior_bounds(xparam1,bounds,M_,estim_params_,options_,bayestopt_)
outside_bound_pars=find(xparam1 < bounds.lb | xparam1 > bounds.ub);
if ~isempty(outside_bound_pars)
for ii=1:length(outside_bound_pars)
outside_bound_par_names{ii,1}=get_the_name(outside_bound_pars(ii),0,M_,estim_params_,options_);
outside_bound_par_names{ii,1}=get_the_name(outside_bound_pars(ii),0,M_,estim_params_,options_.varobs);
end
disp_string=[outside_bound_par_names{1,:}];
for ii=2:size(outside_bound_par_names,1)
@ -41,7 +41,7 @@ end
inadmissible_inverse_gamma_values=find(bayestopt_.pshape==4 & xparam1 == 0);
if ~isempty(inadmissible_inverse_gamma_values)
for ii=1:length(inadmissible_inverse_gamma_values)
inadmissible_inverse_gamma_par_names{ii,1}=get_the_name(inadmissible_inverse_gamma_values(ii),0,M_,estim_params_,options_);
inadmissible_inverse_gamma_par_names{ii,1}=get_the_name(inadmissible_inverse_gamma_values(ii),0,M_,estim_params_,options_.varobs);
end
disp_string=[inadmissible_inverse_gamma_par_names{1,:}];
for ii=2:size(inadmissible_inverse_gamma_par_names,1)

12
matlab/convergence_diagnostics/mcmc_diagnostics.m
View File

@ -71,12 +71,12 @@ param_name_tex = {};
Ifac=NaN(nblck,npar);
for jj = 1:npar
if options_.TeX
[par_name_temp, par_name_tex_temp] = get_the_name(jj, options_.TeX, M_,estim_params_, options_);
[par_name_temp, par_name_tex_temp] = get_the_name(jj, options_.TeX, M_,estim_params_, options_.varobs);
param_name = vertcat(param_name, par_name_temp);
par_name_tex_temp = strrep(par_name_tex_temp,'$','');
param_name_tex = vertcat(param_name_tex, par_name_tex_temp);
else
par_name_temp = get_the_name(jj, options_.TeX, M_, estim_params_, options_);
par_name_temp = get_the_name(jj, options_.TeX, M_, estim_params_, options_.varobs);
param_name = vertcat(param_name, par_name_temp);
end
Draws = GetAllPosteriorDraws(M_.dname, M_.fname, jj, FirstMhFile, FirstLine, TotalNumberOfMhFiles, NumberOfDraws, nblck);
@ -130,11 +130,11 @@ if options_.TeX
end
for jj=1:npar
if options_.TeX
[param_name_temp, param_name_tex_temp] = get_the_name(jj, options_.TeX, M_, estim_params_, options_);
[param_name_temp, param_name_tex_temp] = get_the_name(jj, options_.TeX, M_, estim_params_, options_.varobs);
param_name_tex = vertcat(param_name_tex, strrep(param_name_tex_temp, '$',''));
param_name = vertcat(param_name, param_name_temp);
else
param_name_temp = get_the_name(jj, options_.TeX, M_,estim_params_, options_);
param_name_temp = get_the_name(jj, options_.TeX, M_,estim_params_, options_.varobs);
param_name = vertcat(param_name, param_name_temp);
end
end
@ -290,7 +290,7 @@ for i = 1:pages
boxplot = 1;
for j = 1:npardisp % Loop over parameters %npardisp instead of 3
k = k+1;
[nam,namtex] = get_the_name(k,TeX,M_,estim_params_,options_);
[nam,namtex] = get_the_name(k,TeX,M_,estim_params_,options_.varobs);
for crit = 1:3% Loop over criteria
if crit == 1
plt1 = UDIAG(:,1,k);
@ -346,7 +346,7 @@ if reste
boxplot = 1;
for j = 1:reste
k = k+1;
[nam,namtex] = get_the_name(k,TeX,M_,estim_params_,options_);
[nam,namtex] = get_the_name(k,TeX,M_,estim_params_,options_.varobs);
for crit = 1:3
if crit == 1
plt1 = UDIAG(:,1,k);

4
matlab/dynare_identification.m
View File

@ -363,11 +363,11 @@ if prior_exist % use estimated_params block
name_tex = cell(totparam_nbr,1); %initialize cell for TeX parameter names
for jj=1:totparam_nbr
if options_.TeX
[param_name_temp, param_name_tex_temp]= get_the_name(jj,options_.TeX,M_,estim_params_,options_);
[param_name_temp, param_name_tex_temp]= get_the_name(jj,options_.TeX,M_,estim_params_,options_.varobs);
name_tex{jj,1} =param_name_tex_temp;
name{jj,1} = param_name_temp; %ordering corresponds to estimated_params
else
param_name_temp = get_the_name(jj,options_.TeX,M_,estim_params_,options_);
param_name_temp = get_the_name(jj,options_.TeX,M_,estim_params_,options_.varobs);
name{jj,1} = param_name_temp; %ordering corresponds to estimated_params
end
end

2
matlab/fjaco.m
View File

@ -57,7 +57,7 @@ feval(f,x,varargin{:});
%Auxiliary functions
function disp_info_error_identification_perturbation(info,j)
% there are errors in the solution algorithm
probl_par = get_the_name(j,varargin{4}.TeX,varargin{3},varargin{2},varargin{4});
probl_par = get_the_name(j,varargin{4}.TeX,varargin{3},varargin{2},varargin{4}.varobs);
skipline()
message = get_error_message(info,varargin{4});
fprintf('Parameter error in numerical two-sided difference method:\n')

67
matlab/get_the_name.m
View File

@ -1,46 +1,26 @@
function [nam, texnam] = get_the_name(k, TeX, M_, estim_params_, options_)
function [nam, texnam] = get_the_name(k, TeX, M_, estim_params_, varobs)
% [nam, texnam] = get_the_name(k, TeX, M_, estim_params_, varobs)
% Returns name of estimated parameter number k, following the internal ordering of
% the estimated parameters.
% Inputs:
% - k [integer] parameter number.
% - TeX [bool] if false, texnam is not returned (empty matrix)
% - M_ [structure] model
% - estim_params_ [structure] describing the estimated parameters
% - varobs [cell] name of observed variables
%
% Outputs
% - nam [char] internal name of the variable
% - texnam [char] TeX name of the same variable (if defined in the mod file)
%
% This function is called by:
% get_prior_info, mcmc_diagnostics, mode_check, PlotPosteriorDistributions, plot_priors
%
% This function calls:
% None.
%
%@info:
%! @deftypefn {Function File} {[@var{nam},@var{texnam}] =} get_the_name (@var{k},@var{TeX},@var{M_},@var{estim_params_},@var{options_})
%! @anchor{get_the_name}
%! @sp 1
%! Returns the name of the estimated parameter number @var{k}, following the internal ordering of the estimated parameters.
%! @sp 2
%! @strong{Inputs}
%! @sp 1
%! @table @ @var
%! @item k
%! Integer scalar, parameter number.
%! @item TeX
%! Integer scalar, if @var{TeX}==0 then @var{texnam} is not returned (empty matrix).
%! @item M_
%! Matlab's structure describing the model (initialized by @code{dynare}).
%! @item estim_params_
%! Matlab's structure describing the estimated parameters (initialized by @code{dynare}).
%! @item options_
%! Matlab's structure describing the options (initialized by @code{dynare}).
%! @end table
%! @sp 2
%! @strong{Outputs}
%! @sp 1
%! @table @ @var
%! @item nam
%! String, internal name of the variable
%! @item texnam
%! String, TeX name of the same variable (if defined in the mod file).
%! @end table
%! @sp 2
%! @strong{This function is called by:}
%! @sp 1
%! @ref{get_prior_info}, @ref{mcmc_diagnostics}, @ref{mode_check}, @ref{PlotPosteriorDistributions}, @ref{plot_priors}
%! @sp 2
%! @strong{This function calls:}
%! @sp 1
%! None.
%! @end deftypefn
%@eod:
% Copyright © 2004-2018 Dynare Team
% Copyright © 2004-2023 Dynare Team
%
% This file is part of Dynare.
%
@ -57,7 +37,6 @@ function [nam, texnam] = get_the_name(k, TeX, M_, estim_params_, options_)
% You should have received a copy of the GNU General Public License
% along with Dynare. If not, see <https://www.gnu.org/licenses/>.
nam = [];
texnam = [];
nvx = estim_params_.nvx;
@ -73,7 +52,7 @@ if k <= nvx
texnam = sprintf('$ \\sigma_{%s} $', tname);
end
elseif k <= (nvx+nvn)
vname = options_.varobs{estim_params_.nvn_observable_correspondence(k-estim_params_.nvx,1)};
vname = varobs{estim_params_.nvn_observable_correspondence(k-estim_params_.nvx,1)};
nam = sprintf('SE_EOBS_%s', vname);
if TeX
tname = M_.endo_names_tex{estim_params_.var_endo(k-estim_params_.nvx,1)};

4
matlab/gsa/filt_mc_.m
View File

@ -885,11 +885,11 @@ pnames=cell(np,1);
pnames_tex=cell(np,1);
for ii=1:length(bayestopt_.name)
if options_.TeX
[param_name_temp, param_name_tex_temp]= get_the_name(ii,options_.TeX,M_,estim_params_,options_);
[param_name_temp, param_name_tex_temp]= get_the_name(ii,options_.TeX,M_,estim_params_,options_.varobs);
pnames_tex{ii,1} = param_name_tex_temp;
pnames{ii,1} = param_name_temp;
else
param_name_temp = get_the_name(ii,options_.TeX,M_,estim_params_,options_);
param_name_temp = get_the_name(ii,options_.TeX,M_,estim_params_,options_.varobs);
pnames{ii,1} = param_name_temp;
end
end

8
matlab/gsa/map_calibration.m
View File

@ -38,11 +38,11 @@ pnames=cell(np,1);
pnames_tex=cell(np,1);
for jj=1:np
if options_.TeX
[param_name_temp, param_name_tex_temp]= get_the_name(nshock+jj, options_.TeX, M_, estim_params_, options_);
[param_name_temp, param_name_tex_temp]= get_the_name(nshock+jj, options_.TeX, M_, estim_params_, options_.varobs);
pnames_tex{jj,1} = param_name_tex_temp;
pnames{jj,1} = param_name_temp;
else
param_name_temp = get_the_name(nshock+jj, options_.TeX, M_, estim_params_, options_);
param_name_temp = get_the_name(nshock+jj, options_.TeX, M_, estim_params_, options_.varobs);
pnames{jj,1} = param_name_temp;
end
end
@ -353,11 +353,11 @@ if ~isempty(indx_moment)
name_tex=cell(np,1);
for jj=1:np
if options_.TeX
[param_name_temp, param_name_tex_temp]= get_the_name(jj,options_.TeX,M_,estim_params_,options_);
[param_name_temp, param_name_tex_temp]= get_the_name(jj,options_.TeX,M_,estim_params_,options_.varobs);
name_tex{jj,1} = param_name_tex_temp;
name{jj,1} = param_name_temp;
else
param_name_temp = get_the_name(jj,options_.TeX,M_,estim_params_,options_);
param_name_temp = get_the_name(jj,options_.TeX,M_,estim_params_,options_.varobs);
name{jj,1} = param_name_temp;
end
end

6
matlab/gsa/map_ident_.m
View File

@ -172,7 +172,7 @@ if opt_gsa.morris==1
set(gca,'position',[0.13 0.2 0.775 0.7])
for ip=1:npT
if options_.TeX
[~, param_name_tex_temp]= get_the_name(ip,options_.TeX,M_,estim_params_,options_);
[~, param_name_tex_temp]= get_the_name(ip,options_.TeX,M_,estim_params_,options_.varobs);
text(ip,-2,param_name_tex_temp,'rotation',90,'HorizontalAlignment','right','interpreter','latex')
else
text(ip,-2,bayestopt_.name{ip},'rotation',90,'HorizontalAlignment','right','interpreter','none')
@ -209,7 +209,7 @@ if opt_gsa.morris==1
set(gca,'position',[0.13 0.2 0.775 0.7])
for ip=1:npT
if options_.TeX
[~, param_name_tex_temp]= get_the_name(ip,options_.TeX,M_,estim_params_,options_);
[~, param_name_tex_temp]= get_the_name(ip,options_.TeX,M_,estim_params_,options_.varobs);
text(ip,-0.02,param_name_tex_temp,'rotation',90,'HorizontalAlignment','right','interpreter','latex')
else
text(ip,-0.02,bayestopt_.name{ip},'rotation',90,'HorizontalAlignment','right','interpreter','none')
@ -257,7 +257,7 @@ if opt_gsa.morris==1
xlabel(' ')
for ip=1:npT
if options_.TeX
[~, param_name_tex_temp]= get_the_name(ip,options_.TeX,M_,estim_params_,options_);
[~, param_name_tex_temp]= get_the_name(ip,options_.TeX,M_,estim_params_,options_.varobs);
text(ip,-0.02,param_name_tex_temp,'rotation',90,'HorizontalAlignment','right','interpreter','latex')
else
text(ip,-0.02,bayestopt_.name{ip},'rotation',90,'HorizontalAlignment','right','interpreter','none')

4
matlab/gsa/redform_map.m
View File

@ -45,11 +45,11 @@ pnames=cell(np,1);
pnames_tex=cell(np,1);
for jj=1:np
if options_.TeX
[param_name_temp, param_name_tex_temp]= get_the_name(nshock+jj,options_.TeX,M_,estim_params_,options_);
[param_name_temp, param_name_tex_temp]= get_the_name(nshock+jj,options_.TeX,M_,estim_params_,options_.varobs);
pnames_tex{jj,1} = param_name_tex_temp;
pnames{jj,1} = param_name_temp;
else
param_name_temp = get_the_name(nshock+jj,options_.TeX,M_,estim_params_,options_);
param_name_temp = get_the_name(nshock+jj,options_.TeX,M_,estim_params_,options_.varobs);
pnames{jj,1} = param_name_temp;
end
end

2
matlab/gsa/redform_screen.m
View File

@ -40,7 +40,7 @@ nliv = options_gsa_.morris_nliv;
pnames = M_.param_names(estim_params_.param_vals(:,1));
if options_.TeX
for par_iter=1:size(estim_params_.param_vals(:,1),1)
[~,tex_names{par_iter,1}]=get_the_name(estim_params_.param_vals(par_iter,1),options_.TeX, M_, estim_params_, options_);
[~,tex_names{par_iter,1}]=get_the_name(estim_params_.param_vals(par_iter,1),options_.TeX, M_, estim_params_, options_.varobs);
end
end
if nargin==0

8
matlab/gsa/stab_map_.m
View File

@ -119,11 +119,11 @@ name=cell(np,1);
name_tex=cell(np,1);
for jj=1:np
if options_.TeX
[param_name_temp, param_name_tex_temp]= get_the_name(nshock+jj,options_.TeX,M_,estim_params_,options_);
[param_name_temp, param_name_tex_temp]= get_the_name(nshock+jj,options_.TeX,M_,estim_params_,options_.varobs);
name_tex{jj,1} = param_name_tex_temp;
name{jj,1} = param_name_temp;
else
param_name_temp = get_the_name(nshock+jj,options_.TeX,M_,estim_params_,options_);
param_name_temp = get_the_name(nshock+jj,options_.TeX,M_,estim_params_,options_.varobs);
name{jj,1} = param_name_temp;
end
end
@ -535,11 +535,11 @@ if ~isempty(iunstable) || ~isempty(iwrong)
name_tex=cell(np,1);
for jj=1:np
if options_.TeX
[param_name_temp, param_name_tex_temp]= get_the_name(jj,options_.TeX,M_,estim_params_,options_);
[param_name_temp, param_name_tex_temp]= get_the_name(jj,options_.TeX,M_,estim_params_,options_.varobs);
name_tex{jj,1} = param_name_tex_temp;
name{jj,1} = param_name_temp;
else
param_name_temp = get_the_name(jj,options_.TeX,M_,estim_params_,options_);
param_name_temp = get_the_name(jj,options_.TeX,M_,estim_params_,options_.varobs);
name{jj,1} = param_name_temp;
end
end

16
matlab/gsa/stab_map_2.m
View File

@ -89,29 +89,29 @@ for j=1:npar
j2=j2+1;
if ishock
if options_.TeX
[param_name_temp1, param_name_tex_temp1]= get_the_name(j,options_.TeX,M_,estim_params_,options_);
[param_name_temp2, param_name_tex_temp2]= get_the_name(i2(jx),options_.TeX,M_,estim_params_,options_);
[param_name_temp1, param_name_tex_temp1]= get_the_name(j,options_.TeX,M_,estim_params_,options_.varobs);
[param_name_temp2, param_name_tex_temp2]= get_the_name(i2(jx),options_.TeX,M_,estim_params_,options_.varobs);
tmp_name=(['[',param_name_temp1,',',param_name_temp2,']']);
tmp_name_tex=(['[',param_name_tex_temp1,',',param_name_tex_temp2,']']);
name{entry_iter,1}=tmp_name;
name_tex{entry_iter,1}=tmp_name_tex;
else
[param_name_temp1]= get_the_name(j,options_.TeX,M_,estim_params_,options_);
[param_name_temp2]= get_the_name(i2(jx),options_.TeX,M_,estim_params_,options_);
[param_name_temp1]= get_the_name(j,options_.TeX,M_,estim_params_,options_.varobs);
[param_name_temp2]= get_the_name(i2(jx),options_.TeX,M_,estim_params_,options_.varobs);
tmp_name=(['[',param_name_temp1,',',param_name_temp2,']']);
name{entry_iter,1}=tmp_name;
end
else
if options_.TeX
[param_name_temp1, param_name_tex_temp1]= get_the_name(j+nshock,options_.TeX,M_,estim_params_,options_);
[param_name_temp2, param_name_tex_temp2]= get_the_name(i2(jx)+nshock,options_.TeX,M_,estim_params_,options_);
[param_name_temp1, param_name_tex_temp1]= get_the_name(j+nshock,options_.TeX,M_,estim_params_,options_.varobs);
[param_name_temp2, param_name_tex_temp2]= get_the_name(i2(jx)+nshock,options_.TeX,M_,estim_params_,options_.varobs);
tmp_name=(['[',param_name_temp1,',',param_name_temp2,']']);
tmp_name_tex=(['[',param_name_tex_temp1,',',param_name_tex_temp2,']']);
name{entry_iter,1}=tmp_name;
name_tex{entry_iter,1}=tmp_name_tex;
else
[param_name_temp1]= get_the_name(j+nshock,options_.TeX,M_,estim_params_,options_);
[param_name_temp2]= get_the_name(i2(jx)+nshock,options_.TeX,M_,estim_params_,options_);
[param_name_temp1]= get_the_name(j+nshock,options_.TeX,M_,estim_params_,options_.varobs);
[param_name_temp2]= get_the_name(i2(jx)+nshock,options_.TeX,M_,estim_params_,options_.varobs);
tmp_name=(['[',param_name_temp1,',',param_name_temp2,']']);
name{entry_iter,1}=tmp_name;
end

2
matlab/mh_autocorrelation_function.m
View File

@ -105,5 +105,5 @@ if ~exist([M_.dname filesep 'graphs'])
mkdir(M_.dname,'graphs');
end
plot_name=get_the_name(column,0,M_,estim_params_,options_);
plot_name=get_the_name(column,0,M_,estim_params_,options_.varobs);
dyn_saveas(hh_fig,[M_.dname, filesep, 'graphs', filesep, 'MH_Autocorrelation_' plot_name],options_.nodisplay,options_.graph_format)

2
matlab/mode_check.m
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@ -95,7 +95,7 @@ for plt = 1:nbplt
for k = 1:min(nstar,length(xparam)-(plt-1)*nstar)
subplot(nr,nc,k)
kk = (plt-1)*nstar+k;
[name,texname] = get_the_name(kk,options_.TeX,M_,estim_params_,options_);
[name,texname] = get_the_name(kk,options_.TeX,M_,estim_params_,options_.varobs);
xx = xparam;
if xparam(kk)~=0 && ~isinf(bounds.lb(kk)) && ~isinf(bounds.ub(kk))
l1 = max(bounds.lb(kk),(1-sign(xparam(kk))*ll)*xparam(kk)); m1 = 0; % lower bound

4
matlab/nonlinear-filters/online_auxiliary_filter.m
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@ -389,7 +389,7 @@ for plt = 1:nbplt
hh_fig = dyn_figure(options_.nodisplay,'Name','Parameters Trajectories');
for k=1:length(pmean)
subplot(nr,nc,k)
[name,texname] = get_the_name(k,TeX,M_,estim_params_,options_);
[name,texname] = get_the_name(k,TeX,M_,estim_params_,options_.varobs);
% Draw the surface for an interval containing 95% of the particles.
area(1:sample_size, ub95_xparam(k,:), 'FaceColor', [.9 .9 .9], 'BaseValue', min(lb95_xparam(k,:)));
hold on
@ -426,7 +426,7 @@ for plt = 1:nbplt
hh_fig = dyn_figure(options_.nodisplay,'Name','Parameters Densities');
for k=1:length(pmean)
subplot(nr,nc,k)
[name,texname] = get_the_name(k,TeX,M_,estim_params_,options_);
[name,texname] = get_the_name(k,TeX,M_,estim_params_,options_.varobs);
optimal_bandwidth = mh_optimal_bandwidth(xparam(k,:)',number_of_particles,bandwidth,kernel_function);
[density(:,1),density(:,2)] = kernel_density_estimate(xparam(k,:)', number_of_grid_points, ...
number_of_particles, optimal_bandwidth, kernel_function);

2
matlab/optimize_prior.m
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@ -65,7 +65,7 @@ disp('PRIOR OPTIMIZATION')
disp('------------------')
skipline()
for i = 1:length(xparams)
disp(['deep parameter ' int2str(i) ': ' get_the_name(i,0,M_,estim_params_,options_) '.'])
disp(['deep parameter ' int2str(i) ': ' get_the_name(i,0,M_,estim_params_,options_.varobs) '.'])
disp([' Initial condition ....... ' num2str(xinit(i)) '.'])
disp([' Prior mode .............. ' num2str(bayestopt_.p5(i)) '.'])
disp([' Optimized prior mode .... ' num2str(xparams(i)) '.'])

2
matlab/plot_priors.m
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@ -60,7 +60,7 @@ for plt = 1:nbplt
names = [];
i = (plt-1)*nstar + index;
[x,f,abscissa,dens,binf,bsup] = draw_prior_density(i,bayestopt_);
[nam,texnam] = get_the_name(i,TeX,M_,estim_params_,options_);
[nam,texnam] = get_the_name(i,TeX,M_,estim_params_,options_.varobs);
subplot(nr,nc,index)
hh_plt = plot(x,f,'-k','linewidth',2);
set(hh_plt,'color',[0.7 0.7 0.7]);

2
matlab/print_table_prior.m
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@ -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_);
[Name,tmp] = get_the_name(i,1,M_,estim_params_,options_.varobs);
if length(Name)>size(T1,2)
resize = true;
else

2
matlab/trace_plot.m
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@ -153,7 +153,7 @@ end
if strcmpi(type,'PosteriorDensity')
plot_name='Posterior';
else
plot_name=get_the_name(column,0,M_,estim_params_,options_);
plot_name=get_the_name(column,0,M_,estim_params_,options_.varobs);
end
if n_nblocks_to_plot==1
plot_name=[plot_name,'_blck_',num2str(blck)];

2
matlab/utilities/estimation/check_hessian_at_the_mode.m
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@ -48,7 +48,7 @@ catch
params_at_bound = find(abs(xparam1-bounds.ub)<tol_bounds | abs(xparam1-bounds.lb)<tol_bounds);
if ~isempty(params_at_bound)
for ii=1:length(params_at_bound)
params_at_bound_name{ii,1}=get_the_name(params_at_bound(ii),0,M_,estim_params_,options_);
params_at_bound_name{ii,1}=get_the_name(params_at_bound(ii),0,M_,estim_params_,options_.varobs);
end
disp_string=[params_at_bound_name{1,:}];
for ii=2:size(params_at_bound_name,1)

2
matlab/utilities/estimation/set_mcmc_prior_bounds.m
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@ -37,7 +37,7 @@ bounds = prior_bounds(bayestopt_, options_.prior_trunc);
outside_bound_pars = find(xparam < bounds.lb | xparam > bounds.ub);
if ~isempty(outside_bound_pars)
for ii = 1:length(outside_bound_pars)
outside_bound_par_names{ii,1} = get_the_name(ii,0,M_,estim_params_,options_);
outside_bound_par_names{ii,1} = get_the_name(ii,0,M_,estim_params_,options_.varobs);
end
disp_string = [outside_bound_par_names{1,:}];
for ii = 2:size(outside_bound_par_names,1)

2
matlab/write_latex_prior_table.m
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@ -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_);
[tmp,TexName] = get_the_name(i, 1, M_, estim_params_, options_.varobs);
PriorShape = PriorNames{ BayesOptions.pshape(i) };
PriorMean = BayesOptions.p1(i);
PriorMode = BayesOptions.p5(i);