The first part of the following passage of dynare_estimation_init.m seems to be partly redundant due to the subsequent if-clause. Or at least some results seem to be subsequently overwritten. Is this on purpose?

% Define union of observed and state variables

k2 = union(var_obs_index,[dr.nstatic+1:dr.nstatic+dr.npred]', 'rows');

% Set restrict_state to postion of observed + state variables in expanded state vector.

oo_.dr.restrict_var_list = k2;

bayestopt_.restrict_var_list = k2;

% set mf0 to positions of state variables in restricted state vector for likelihood computation.

[junk,bayestopt_.mf0] = ismember([dr.nstatic+1:dr.nstatic+dr.npred]',k2);

% Set mf1 to positions of observed variables in restricted state vector for likelihood computation.

[junk,bayestopt_.mf1] = ismember(var_obs_index,k2);

% Set mf2 to positions of observed variables in expanded state vector for filtering and smoothing.

bayestopt_.mf2  = var_obs_index;

bayestopt_.mfys = k1;

[junk,ic] = intersect(k2,nstatic+(1:npred)');

oo_.dr.restrict_columns = [ic; length(k2)+(1:nspred-npred)'];

k3 = [];

k3p = [];

if options_.selected_variables_only

for i=1:size(var_list_,1)

        k3 = [k3; strmatch(var_list_(i,:),M_.endo_names(dr.order_var,:), ...

'exact')];

        k3p = [k3; strmatch(var_list_(i,:),M_.endo_names, ...

'exact')];

end

else

    k3 = (1:M_.endo_nbr)';

    k3p = (1:M_.endo_nbr)';

end

% Define union of observed and state variables

if options_.block == 1

    k1 = k1';

    [k2, i_posA, i_posB] = union(k1', M_.state_var', 'rows');

% Set restrict_state to postion of observed + state variables in expanded state vector.

    oo_.dr.restrict_var_list  = [k1(i_posA) M_.state_var(sort(i_posB))];

% set mf0 to positions of state variables in restricted state vector for likelihood computation.

    [junk,bayestopt_.mf0] = ismember(M_.state_var',oo_.dr.restrict_var_list);

% Set mf1 to positions of observed variables in restricted state vector for likelihood computation.

    [junk,bayestopt_.mf1] = ismember(k1,oo_.dr.restrict_var_list);

% Set mf2 to positions of observed variables in expanded state vector for filtering and smoothing.

    bayestopt_.mf2  = var_obs_index;

    bayestopt_.mfys = k1;

    oo_.dr.restrict_columns = [size(i_posA,1)+(1:size(M_.state_var,2))];

    [k2, i_posA, i_posB] = union(k3p, M_.state_var', 'rows');

    bayestopt_.smoother_var_list = [k3p(i_posA); M_.state_var(sort(i_posB))'];

    [junk,junk,bayestopt_.smoother_saved_var_list] = intersect(k3p,bayestopt_.smoother_var_list(:));

    [junk,ic] = intersect(bayestopt_.smoother_var_list,M_.state_var);

    bayestopt_.smoother_restrict_columns = ic;

    [junk,bayestopt_.smoother_mf] = ismember(k1, ...

                                             bayestopt_.smoother_var_list);

else

    k2 = union(var_obs_index,[dr.nstatic+1:dr.nstatic+dr.npred]', 'rows');

% Set restrict_state to postion of observed + state variables in expanded state vector.

    oo_.dr.restrict_var_list = k2;

% set mf0 to positions of state variables in restricted state vector for likelihood computation.

    [junk,bayestopt_.mf0] = ismember([dr.nstatic+1:dr.nstatic+dr.npred]',k2);

% Set mf1 to positions of observed variables in restricted state vector for likelihood computation.

    [junk,bayestopt_.mf1] = ismember(var_obs_index,k2);

% Set mf2 to positions of observed variables in expanded state vector for filtering and smoothing.

    bayestopt_.mf2  = var_obs_index;

    bayestopt_.mfys = k1;

    [junk,ic] = intersect(k2,nstatic+(1:npred)');

    oo_.dr.restrict_columns = [ic; length(k2)+(1:nspred-npred)'];

    bayestopt_.smoother_var_list = union(k2,k3);

    [junk,junk,bayestopt_.smoother_saved_var_list] = intersect(k3,bayestopt_.smoother_var_list(:));

    [junk,ic] = intersect(bayestopt_.smoother_var_list,nstatic+(1:npred)');

    bayestopt_.smoother_restrict_columns = ic;

    [junk,bayestopt_.smoother_mf] = ismember(var_obs_index, ...

                                             bayestopt_.smoother_var_list);

end;