This file is indexed.

/usr/share/dynare/matlab/gmhmaxlik.m is in dynare-common 4.4.1-1build1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
function [PostMod,PostVar,Scale,PostMean] = ...
    gmhmaxlik(ObjFun,xparam1,mh_bounds,options,iScale,info,MeanPar,VarCov,varargin)  

%function [PostMod,PostVar,Scale,PostMean] = ...
%gmhmaxlik(ObjFun,xparam1,mh_bounds,num,iScale,info,MeanPar,VarCov,varargin)  
% (Dirty) Global minimization routine of (minus) a likelihood (or posterior density) function. 
% 
% INPUTS 
%   o ObjFun     [char]     string specifying the name of the objective function.
%   o xparam1    [double]   (p*1) vector of parameters to be estimated.
%   o mh_bounds  [double]   (p*2) matrix defining lower and upper bounds for the parameters.
%   o options    [structure] options for the optimization algorithm (options_.gmhmaxlik).
%   o iScale     [double]   scalar specifying the initial of the jumping distribution's scale parameter.
%   o info       [char]     string, empty or equal to 'LastCall'.
%   o MeanPar    [double]   (p*1) vector specifying the initial posterior mean.
%   o VarCov     [double]   (p*p) matrix specifying the initial posterior covariance matrix. 
%   o gend       [integer]  scalar specifying the number of observations ==> varargin{1}.
%   o data       [double]   (T*n) matrix of data ==> varargin{2}.
%  
% OUTPUTS 
%   o PostMod    [double]   (p*1) vector, evaluation of the posterior mode.
%   o PostVar    [double]   (p*p) matrix, evaluation of the posterior covariance matrix.
%   o Scale      [double]   scalar specifying the scale parameter that should be used in 
%                           an eventual metropolis-hastings algorithm. 
%   o PostMean   [double]   (p*1) vector, evaluation of the posterior mean.  
%
% ALGORITHM 
%   Metropolis-Hastings with an constantly updated covariance matrix for
%   the jump distribution. The posterior mean, variance and mode are
%   updated (in step 2) with the following rules:
%
%   \[ 
%       \mu_t = \mu_{t-1} + \frac{1}{t}\left(\theta_t-\mu_{t-1}\right) 
%   \]    
%
%   \[ 
%       \Sigma_t = \Sigma_{t-1} + \mu_{t-1}\mu_{t-1}'-\mu_{t}\mu_{t}' + 
%                  \frac{1}{t}\left(\theta_t\theta_t'-\Sigma_{t-1}-\mu_{t-1}\mu_{t-1}'\right) 
%   \]
%
%   and
%
%   \[
%       \mathrm{mode}_t = \left\{
%                       \begin{array}{ll}
%                         \theta_t, & \hbox{if } p(\theta_t|\mathcal Y) > p(\mathrm{mode}_{t-1}|\mathcal Y) \\
%                         \mathrm{mode}_{t-1}, & \hbox{otherwise.}
%                       \end{array}
%                     \right. 
%   \]
%
%   where $t$ is the iteration, $\mu_t$ the estimate of the posterior mean
%   after $t$ iterations, $\Sigma_t$ the estimate of the posterior
%   covariance matrix after $t$ iterations, $\mathrm{mode}_t$ is the
%   evaluation of the posterior mode after $t$ iterations and
%   $p(\theta_t|\mathcal Y)$ is the posterior density of parameters
%   (specified by the user supplied function "fun").       
%
% SPECIAL REQUIREMENTS
%   None.

% Copyright (C) 2006-2012 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 <http://www.gnu.org/licenses/>.

global bayestopt_ estim_params_ options_

options_.lik_algo = 1;
npar = length(xparam1);

NumberOfIterations = options.number;
MaxNumberOfTuningSimulations   = options.nscale;
MaxNumberOfClimbingSimulations = options.nclimb;
AcceptanceTarget               = options.target;

CovJump = VarCov;
ModePar = xparam1;

%% [1] I tune the scale parameter.
hh = dyn_waitbar(0,'Tuning of the scale parameter...');
set(hh,'Name','Tuning of the scale parameter.');
j = 1; jj  = 1;
isux = 0; jsux = 0; test = 0;
ix2 = ModePar;% initial condition!
ilogpo2 = - feval(ObjFun,ix2,varargin{:});% initial posterior density
mlogpo2 = ilogpo2;
try 
    dd = transpose(chol(CovJump));
catch
    dd = eye(length(CovJump));
end
while j<=MaxNumberOfTuningSimulations
    proposal = iScale*dd*randn(npar,1) + ix2;
    if all(proposal > mh_bounds(:,1)) && all(proposal < mh_bounds(:,2))
        logpo2 = - feval(ObjFun,proposal,varargin{:});
    else
        logpo2 = -inf;
    end
    % I move if the proposal is enough likely...
    if logpo2 > -inf && log(rand) < logpo2 - ilogpo2
        ix2 = proposal; 
        if logpo2 > mlogpo2
            ModePar = proposal;
            mlogpo2 = logpo2;
        end
        ilogpo2 = logpo2;
        isux = isux + 1;
        jsux = jsux + 1;
    end% ... otherwise I don't move.
    prtfrc = j/MaxNumberOfTuningSimulations;
    if mod(j, 10)==0
        dyn_waitbar(prtfrc,hh,sprintf('Acceptance ratio [during last 500]: %f [%f]',isux/j,jsux/jj));
    end
    if  j/500 == round(j/500)
        test1 = jsux/jj;
        cfactor = test1/AcceptanceTarget;
        if cfactor>0
            iScale = iScale*cfactor;
        else
            iScale = iScale/10;
        end
        jsux = 0; jj = 0;
        if cfactor>0.90 && cfactor<1.10
            test = test+1;
        end
        if test>4
            break
        end
    end
    j = j+1;
    jj = jj + 1;
end

dyn_waitbar_close(hh);
%% [2] One block metropolis, I update the covariance matrix of the jumping distribution
hh = dyn_waitbar(0,'Metropolis-Hastings...');
set(hh,'Name','Estimation of the posterior covariance...'),
j = 1;
isux = 0;
ilogpo2 = - feval(ObjFun,ix2,varargin{:});
while j<= NumberOfIterations
    proposal = iScale*dd*randn(npar,1) + ix2;
    if all(proposal > mh_bounds(:,1)) && all(proposal < mh_bounds(:,2))
        logpo2 = - feval(ObjFun,proposal,varargin{:});
    else
        logpo2 = -inf;
    end
    % I move if the proposal is enough likely...
    if logpo2 > -inf && log(rand) < logpo2 - ilogpo2
        ix2 = proposal;
        if logpo2 > mlogpo2
            ModePar = proposal;
            mlogpo2 = logpo2;
        end
        ilogpo2 = logpo2;
        isux = isux + 1;
        jsux = jsux + 1;
    end% ... otherwise I don't move.    
    prtfrc = j/NumberOfIterations;
    if mod(j, 10)==0
        dyn_waitbar(prtfrc,hh,sprintf('Acceptance ratio: %f',isux/j));
    end
    % I update the covariance matrix and the mean:
    oldMeanPar = MeanPar;
    MeanPar = oldMeanPar + (1/j)*(ix2-oldMeanPar);
    CovJump = CovJump + oldMeanPar*oldMeanPar' - MeanPar*MeanPar' + ...
              (1/j)*(ix2*ix2' - CovJump - oldMeanPar*oldMeanPar');
    j = j+1;
end
dyn_waitbar_close(hh);
PostVar = CovJump;
PostMean = MeanPar;
%% [3 & 4] I tune the scale parameter (with the new covariance matrix) if
%% this is the last call to the routine, and I climb the hill (without
%% updating the covariance matrix)...
if strcmpi(info,'LastCall')
    
    hh = dyn_waitbar(0,'Tuning of the scale parameter...');
    set(hh,'Name','Tuning of the scale parameter.'),
    j = 1; jj  = 1;
    isux = 0; jsux = 0;
    test = 0;
    ilogpo2 = - feval(ObjFun,ix2,varargin{:});% initial posterior density
    dd = transpose(chol(CovJump));
    while j<=MaxNumberOfTuningSimulations
        proposal = iScale*dd*randn(npar,1) + ix2;
        if all(proposal > mh_bounds(:,1)) && all(proposal < mh_bounds(:,2))
            logpo2 = - feval(ObjFun,proposal,varargin{:});
        else
            logpo2 = -inf;
        end
        % I move if the proposal is enough likely...
        if logpo2 > -inf && log(rand) < logpo2 - ilogpo2
            ix2 = proposal;
            if logpo2 > mlogpo2
                ModePar = proposal;
                mlogpo2 = logpo2;
            end
            ilogpo2 = logpo2;
            isux = isux + 1;
            jsux = jsux + 1;
        end% ... otherwise I don't move.
        prtfrc = j/MaxNumberOfTuningSimulations;
        if mod(j, 10)==0
            dyn_waitbar(prtfrc,hh,sprintf('Acceptance ratio [during last 1000]: %f [%f]',isux/j,jsux/jj));
        end
        if j/1000 == round(j/1000) 
            test1 = jsux/jj;  
            cfactor = test1/AcceptanceTarget;
            iScale = iScale*cfactor;
            jsux = 0; jj = 0;
            if cfactor>0.90 && cfactor<1.10
                test = test+1;
            end
            if test>4
                break
            end
        end
        j = j+1;
        jj = jj + 1;
    end
    dyn_waitbar_close(hh);
    Scale = iScale;
    %%
    %% Now I climb the hill
    %%
    if options.nclimb
        hh = dyn_waitbar(0,' ');
        set(hh,'Name','Now I am climbing the hill...'),
        j = 1; jj  = 1;
        jsux = 0;
        test = 0;
        while j<=MaxNumberOfClimbingSimulations
            proposal = iScale*dd*randn(npar,1) + ModePar;
            if all(proposal > mh_bounds(:,1)) && all(proposal < mh_bounds(:,2))
                logpo2 = - feval(ObjFun,proposal,varargin{:});
            else
                logpo2 = -inf;
            end
            if logpo2 > mlogpo2% I move if the proposal is higher...
                ModePar = proposal;
                mlogpo2 = logpo2;
                jsux = jsux + 1;
            end% otherwise I don't move...
            prtfrc = j/MaxNumberOfClimbingSimulations;
            if mod(j, 10)==0
                dyn_waitbar(prtfrc,hh,sprintf('%f Jumps / MaxStepSize %f',jsux,sqrt(max(diag(iScale*CovJump)))));
            end
            if  j/200 == round(j/200)
                if jsux<=1
                    test = test+1;
                else
                    test = 0;
                end
                jsux = 0;
                jj = 0;
                if test>4% If I do not progress enough I reduce the scale parameter
                         % of the jumping distribution (cooling down the system).
                    iScale = iScale/1.10;
                end
                if sqrt(max(diag(iScale*CovJump)))<10^(-4)
                    break% Steps are too small!
                end
            end
            j = j+1;
            jj = jj + 1;
        end
        dyn_waitbar_close(hh);
    end%climb
else
    Scale = iScale;
end
PostMod = ModePar;