FixedBugs.md

@@ -210,35 +210,35 @@ Bugs in version 4.4.3 that have been fixed in version 4.5.0
  - Forecasts
 
    + In contrast to what is stated in the manual, the confidence interval size
-     `conf_sig` was 0.6 by default instead of 0.9.
+     `conf_sig` was 0.6 by default instead of 0.9 [(#338)](https://github.com/DynareTeam/dynare/pull/338),
 
    + Forecasting with exogenous deterministic variables provided wrong decision
-     rules, yielding wrong forecasts.
+     rules, yielding wrong forecasts [(#711)](https://github.com/DynareTeam/dynare/pull/711),
 
    + Forecasting with exogenous deterministic variables crashed when the
-     `periods` option was not explicitly specified,
+     `periods` option was not explicitly specified [(#1325)](https://github.com/DynareTeam/dynare/pull/1325),
 
    + Option `forecast` when used with `initval` was using the initial values in
      the `initval` block and not the steady state computed from these initial
-     values as the starting point of forecasts.
+     values as the starting point of forecasts [(#692)](https://github.com/DynareTeam/dynare/pull/692).
 
 
  - Global Sensitivity Analysis
 
    + Sensitivity with ML estimation could result in crashes,
 
-   + Option `mc` must be forced if `neighborhood_width` is used,
+   + Option `mc` must be forced if `neighborhood_width` is used [(link)](https://github.com/DynareTeam/dynare/commit/e32cbf626f9f0b9e322b2ac44d93461afcb320a0),
 
-   + Fixed dimension of `stock_logpo` and `stock_ys`,
+   + Fixed dimension of `stock_logpo` and `stock_ys` [(link)](https://github.com/DynareTeam/dynare/commit/a44b3fbfe7c0214c19f6eecabe368c2e72c9346f),
 
    + Incomplete variable initialization could lead to crashes with `prior_range=1`.
 
 
- - Indentification
+ - Identification
 
    + Identification did not correctly pass the `lik_init` option,
      requiring the manual setting of `options_.diffuse_filter=1` in
-     case of unit roots,
+     case of unit roots ,
 
    + Testing identification of standard deviations as the only
      parameters to be estimated with ML leaded to crashes,
@@ -247,49 +247,49 @@ Bugs in version 4.4.3 that have been fixed in version 4.5.0
      number of parameters is bigger than the number of non-zero moments
      was broken,
 
-   + When using ML, the asymptotic Hessian was not computed,
+   + When using ML, the asymptotic Hessian was not computed [(#1238)](https://github.com/DynareTeam/dynare/pull/1238),
 
    + Checking for singular values when the eigenvectors contained only
-     one column did not work correctly,
+     one column did not work correctly [(#1238)](https://github.com/DynareTeam/dynare/pull/1238),
 
 
  - Model comparison
 
-   + Selection of the `modifiedharmonicmean` estimator was broken,
+   + Selection of the `modifiedharmonicmean` estimator was broken [(#1015)](https://github.com/DynareTeam/dynare/pull/1015).
 
 
  - Optimal Simple Rules
 
    + When covariances were specified, variables that only entered with
      their variance and no covariance term obtained a wrong weight,
-     resulting in wrong results,
+     resulting in wrong results [(#767)](https://github.com/DynareTeam/dynare/pull/767),
 
    + Results reported for stochastic simulations after `osr` were based
      on the last parameter vector encountered during optimization,
      which does not necessarily coincide with the optimal parameter
-     vector,
+     vector [(#767)](https://github.com/DynareTeam/dynare/pull/767),
 
-   + Using only one (co)variance in the objective function resulted in crashes,
+   + Using only one (co)variance in the objective function resulted in crashes [(#767)](https://github.com/DynareTeam/dynare/pull/767),
 
-   + For models with non-stationary variables the objective function was computed wrongly.
+   + For models with non-stationary variables the objective function was computed wrongly [(#767)](https://github.com/DynareTeam/dynare/pull/767).
 
 
  - Ramsey policy
 
    + If a Lagrange multiplier appeared in the model with a lead or a lag
-     of more than one period, the steady state could be wrong.
+     of more than one period, the steady state could be wrong [(#633)](https://github.com/DynareTeam/dynare/pull/633).
 
    + When using an external steady state file, incorrect steady states
      could be accepted,
 
    + When using an external steady state file with more than one
-     instrument, Dynare crashed,
+     instrument, Dynare crashed [(#696)](https://github.com/DynareTeam/dynare/pull/696),
 
    + When using an external steady state file and running `stoch_simul`
      after `ramsey_planner`, an incorrect steady state was used,
 
    + When the number of instruments was not equal to the number of
-     omitted equations, Dynare crashed with a cryptic message,
+     omitted equations, Dynare crashed with a cryptic message [(#1241)](https://github.com/DynareTeam/dynare/pull/1241),
 
    + The `planner_objective` accepted `varexo`, but ignored them for computations,
 
@@ -297,46 +297,46 @@ Bugs in version 4.4.3 that have been fixed in version 4.5.0
  - Shock decomposition
 
    + Did not work with the `parameter_set=calibration` option if an
-     `estimated_params` block is present,
+     `estimated_params` block is present [(link)](http://www.dynare.org/phpBB3/viewtopic.php?f=1&t=6913),
 
-   + Crashed after MLE.
+   + Crashed after MLE [(#1220)](https://github.com/DynareTeam/dynare/pull/1220).
 
 
  - Perfect foresight models
 
    + The perfect foresight solver could accept a complex solution
-     instead of continuing to look for a real-valued one,
+     instead of continuing to look for a real-valued one [(#896)](https://github.com/DynareTeam/dynare/pull/896),
 
-   + The `initval_file` command only accepted column and not row vectors,
+   + The `initval_file` command only accepted column and not row vectors [(link)](http://www.dynare.org/phpBB3/viewtopic.php?f=1&t=6261&p=17592#p17592),
 
-   + The `initval_file` command did not work with Excel files,
+   + The `initval_file` command did not work with Excel files [(link)](http://www.dynare.org/phpBB3/viewtopic.php?f=1&t=6261&p=17592#p17592),
 
    + Deterministic simulations with one boundary condition crashed in
      `solve_one_boundary` due to a missing underscore when passing
      `options_.simul.maxit`,
 
    + Deterministic simulation with exogenous variables lagged by more
-     than one period crashed,
+     than one period crashed [(#617)](https://github.com/DynareTeam/dynare/pull/617),
 
    + Termination criterion `maxit` was hard-coded for `solve_algo=0`
      and could no be changed,
 
-   + When using `block`/`bytecode`, relational operators could not be enforced,
+   + When using `block`/`bytecode`, relational operators could not be enforced [(#439)](https://github.com/DynareTeam/dynare/pull/439),
 
    + When using `block` some exceptions were not properly handled,
-     leading to code crashes,
+     leading to code crashes [(#1245)](https://github.com/DynareTeam/dynare/pull/1245),
 
-   + Using `periods=1` crashed the solver (bug only partially fixed).
+   + Using `periods=1` crashed the solver (bug only partially fixed) [(#1205)](https://github.com/DynareTeam/dynare/pull/1205).
 
 
  - Smoothing
 
    + The univariate Kalman smoother returned wrong results when used
-     with correlated measurement error,
+     with correlated measurement error [(#1235)](https://github.com/DynareTeam/dynare/pull/1235),
 
    + The diffuse smoother sometimes returned linear combinations of the
      smoothed stochastic trend estimates instead of the original trend
-     estimates.
+     estimates [(#1312)](https://github.com/DynareTeam/dynare/pull/1312).
 
  - Perturbation reduced form
 
@@ -348,28 +348,28 @@ Bugs in version 4.4.3 that have been fixed in version 4.5.0
      when using the `loglinear` option,
 
    + Using `bytcode` when declared exogenous variables were not
-     used in the model leaded to crashes in stochastic simulations,
+     used in the model leaded to crashes in stochastic simulations [(#841)](https://github.com/DynareTeam/dynare/pull/841),
 
    + Displaying decision rules involving lags of auxiliary variables of
-     type 0 (leads>1) crashed.
+     type 0 (leads>1) crashed [(#1367)](https://github.com/DynareTeam/dynare/pull/1367).
 
    + The `relative_irf` option resulted in wrong output at `order>1` as
-     it implicitly relies on linearity.
+     it implicitly relies on linearity [(#740)](https://github.com/DynareTeam/dynare/pull/740).
 
 
  - Displaying of the MH-history with the `internals` command crashed
-   if parameter names did not have same length.
+   if parameter names did not have same length [(link)](https://github.com/DynareTeam/dynare/commit/caa6d5d93e7382165167fbaefbaf9d38e26ca909).
 
  - Dynare crashed when the user-defined steady state file returned an
-   error code, but not an conformable-sized steady state vector.
+   error code, but not an conformable-sized steady state vector [(#1001)](https://github.com/DynareTeam/dynare/pull/1001).
 
  - Due to a bug in `mjdgges.mex` unstable parameter draws with
    eigenvalues up to 1+1e-6 could be accepted as stable for the
-   purpose of the Blanchard-Kahn conditions, even if `qz_criterium<1`.
+   purpose of the Blanchard-Kahn conditions, even if `qz_criterium<1`[(link)](https://github.com/DynareTeam/dynare/commit/e3fbefc616941d0df3624bfc49a1a743171f8814).
 
  - The `use_dll` option on Octave for Windows required to pass a
    compiler flag at the command line, despite the manual stating this
-   was not necessary.
+   was not necessary [(#1314)](https://github.com/DynareTeam/dynare/pull/1314).
 
  - Dynare crashed for models with `block` option if the Blanchard-Kahn
    conditions were not satisfied instead of generating an error
@@ -378,7 +378,7 @@ Bugs in version 4.4.3 that have been fixed in version 4.5.0
  - The `verbose` option did not work with `model(block)`.
 
  - When falsely specifying the `model(linear)` for nonlinear models,
-   incorrect steady states were accepted instead of aborting.
+   incorrect steady states were accepted instead of aborting [(#726)](https://github.com/DynareTeam/dynare/pull/726).
 
  - The `STEADY_STATE` operator called on model local variables
    (so-called pound variables) did not work as expected.
@@ -391,15 +391,11 @@ Bugs in version 4.4.3 that have been fixed in version 4.5.0
 
  - A bug when external functions were used in model local variables
    that were contained in equations that required auxiliary
-   variable/equations led to crashes of Matlab.
+   variable/equations led to crashes of Matlab [(link)](https://github.com/DynareTeam/dynare/commit/2ab8e2a122afd253e7ea315ef49adccca5ced53f).
 
  - Sampling from the prior distribution for an inverse gamma II
    distribution when `prior_trunc>0` could result in incorrect
-   sampling.
+   sampling [(#997)](https://github.com/DynareTeam/dynare/pull/997).
 
  - Sampling from the prior distribution for a uniform distribution
-   when `prior_trunc>0` was ignoring the prior truncation.
-
+   when `prior_trunc>0` was ignoring the prior truncation [(#997)](https://github.com/DynareTeam/dynare/pull/997).
\ No newline at end of file
- - Conditional forecasts were wrong when the declaration of endogenous
-   variables was not preceeding the declaration of the exogenous
-   variables and parameters.