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preprocessor: fix bug that caused temporary terms not to be printed for the parameter derivatives of the static model. closes #1397

preprocessor: for consistency, use equations.size() instead of equation_number() in classes that have equations as a field

preprocessor: change error to warning because we don’t end processing in this situation; fix error message

 + Code factorization.
 + Added an option for using the penalized objective when computing numerically
 the hessian at the mode.

Previous behaviour (introduced with penalty_hessian routine) was to compute the
hessian matrix at the mode with the penalized objective function (instead of
the original objective function). This behaviour hides problematic situations,
where the computed hessian (using the original objective) would not be full
rank. For instance, if the estimation ends up with a parameter on (or very
close to) the bounds of its possible values (which is often not a desirable
outcome), the estimated posterior variance would be zero for this
parameter (with the original objective) because the hessian is not finite in
this direction, while the posterior variance would be positive if the penalized
objective is used instead. But this estimate would not be reliable by
construction of the penalty which is quite ad-hoc (more fundamentally I do not
think that there exists any rational for approximating the covariance matrix
with the inverse of the hessian matrix if the mode is on the border of the set
of possible values).

This commit restore the behaviour previous to 2446ab02ba4b3ed88c9c5021aced076078d96007.

An option is available for computing the hessian with the penalized
objective function.

Houtan Bastani authored Sep 23, 2016 and Stéphane Adjemian committed Jan 27, 2017

preprocessor: issue warnings for undeclared model variables when the end of the model block is encountered. #1286

NO_POSTERIOR_KERNEL_DENSITY option was not modifying the expected field in
options_, consequently this option was no honored.

when >32 nested parens encountered in matlab, print error message once per file in which such a situation occurred. #1201

Implement posterior_nograph option

fix warnings introduced in 3b20d41a92db4267c0ba13278f3885aba67e6c47 related to size_t/int comparison #1201

3b20d41a92db4267c0ba13278f3885aba67e6c47 used to_string from C++11 standard which breaks the snapshot build. #1201

bug fix: end preprocessing with error when more than 32 nested parenthesis are encountered. closes #1201

Prevents general overwriting of results in oo_ and having stale results

robust_lin_solve: Fix mistakes introduced in 4b83c1bf763fe5029c94b7e5…

Interface was still missing and documentation of option was in wrong place in manual and wrong

Three bugfixes for missing_DiffuseKalmanSmootherH1_Z.m that led to wrong results