Stéphane Adjemian (Charybdis)
cad7adc01f
Added routine for testing if we are currently estimating a model.
2017-03-16 15:03:46 +01:00
Stéphane Adjemian (Charybdis)
5f5c093b2e
Renamed isestimation function + Cosmetic changes.
2017-03-16 15:00:02 +01:00
Stéphane Adjemian (Charybdis)
feee6f8b7a
Fixed typo.
2017-03-15 17:24:45 +01:00
Stéphane Adjemian (Charybdis)
284df20445
Closes #1403 .
2017-03-15 16:51:59 +01:00
Stéphane Adjemian
d0ab90275b
Merge pull request #1402 from JohannesPfeifer/prior_asymptote
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Add warning if prior has an asymptote
2017-03-15 16:33:10 +01:00
Stéphane Adjemian (Charybdis)
1ff816d7bf
Updates particles submodule.
2017-03-15 16:30:29 +01:00
Houtan Bastani
e2b30857a0
preprocessor: split equation output into lhs and rhs. #1387
2017-03-15 12:52:55 +01:00
Stéphane Adjemian (Charybdis)
4f3b35acba
Account for Matlab 2017a.
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(cherry picked from commit f3a1619040fbb831830791424015d3d3bf8bdbae)
2017-03-13 23:42:48 +01:00
Houtan Bastani
425bab1461
preprocessor: write JSON output for cross refs #1387
2017-03-10 17:28:25 +01:00
Houtan Bastani
9f7b084970
Merge branch 'master' into json
2017-03-10 17:20:15 +01:00
Houtan Bastani
99d948463e
Revert "preprocessor: write equation cross references in JSON. #1387"
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This reverts commit 0ccc82300c
.
2017-03-10 17:18:41 +01:00
Houtan Bastani
ea13b12cf2
preprocessor: add lag info to equation cross references. closes #1398
2017-03-10 16:59:52 +01:00
Johannes Pfeifer
87fc09863d
Add warning if prior has an asymptote
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Can happen with beta and gamma distribution. Closes #1401
2017-03-10 15:16:33 +01:00
Houtan Bastani
38f36091a9
test suite: increase timeout option for downloading files to 30 seconds
2017-03-08 12:30:58 +01:00
Houtan Bastani
7341ca4e6d
Merge pull request #1399 from JohannesPfeifer/dname
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Fix check for existence of dname variable
2017-03-07 13:58:29 +01:00
Johannes Pfeifer
56edaf5cb0
Fix check for existence of dname variable
2017-03-07 13:55:29 +01:00
Houtan Bastani
0ccc82300c
preprocessor: write equation cross references in JSON. #1387
2017-03-06 16:34:08 +01:00
Houtan Bastani
defe06d513
preprocessor: create two different static and dynamic files with the option jsonprintderivdetail. #1387
2017-03-03 14:42:37 +01:00
Houtan Bastani
5063020c5d
Merge branch 'master' into json
2017-03-03 14:42:25 +01:00
Houtan Bastani
f500b8385d
preprocessor: make JSON output start counting at 1 instead of 0. #1387
2017-03-02 17:34:34 +01:00
Houtan Bastani
33b38ab643
preprocessor: write error messages to cerr instead of cout, replace \n with endl
2017-03-01 12:44:31 +01:00
Houtan Bastani
2d25858886
preprocessor: fix bug that caused temporary terms not to be printed for the parameter derivatives of the static model. closes #1397
2017-03-01 12:20:55 +01:00
Houtan Bastani
ed3e74994f
preprocessor: add onlyjson option to allow exit upon writing of JSON output. #1387
2017-02-28 14:34:22 +01:00
Houtan Bastani
5e5a9e3b9a
preprocessor: JSON output aesthetic fixes, support planner objective. #1387
2017-02-27 15:40:34 +01:00
Houtan Bastani
e07e393642
preprocessor: fix JSON bugs. #1387
2017-02-27 14:23:55 +01:00
Houtan Bastani
a4171ad4ab
preprocessor: output JSON after different steps, write static, dynamic, params derivs files in JSON. #1387
2017-02-24 17:43:22 +01:00
Houtan Bastani
0b52b778ed
preprocessor: for consistency, use equations.size() instead of equation_number() in classes that have equations as a field
2017-02-24 11:20:54 +01:00
Houtan Bastani
1007ea1301
preprocessor: JSON output for statements, #1387
2017-02-20 11:23:10 +01:00
Stéphane Adjemian (Charybdis)
927b813ed8
Removed printing of debugging info.
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Introduced in ffebf6b262
.
2017-02-15 13:35:33 +01:00
Stéphane Adjemian (Charybdis)
ffebf6b262
Check positive steady state for loglinear option...
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1e-9 is too far from zero. Set 1e-16 as a threshold value for the positivity test.
2017-02-15 12:41:56 +01:00
Stéphane Adjemian (Charybdis)
8925e7ca1f
Cosmetic patch (remove some warnings about potentially uninitialized variables in bytecode).
2017-02-13 19:22:26 +01:00
Houtan Bastani
181ffd65c5
preprocessor: bug fix for writing of parameter values. Closes #1394
2017-02-13 14:03:44 +01:00
Houtan Bastani
a45333a520
Merge pull request #1393 from albop/fix_json
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FIX: JSON remove space before symbols + quote values
2017-02-12 17:35:24 +01:00
Winant Pablo
8ee9d081e8
FIX: JSON remove space before symbols + quote values
2017-02-12 16:45:05 +01:00
Houtan Bastani
39855c95d2
preprocessor: aesthetic fix
2017-02-10 12:47:43 +01:00
Houtan Bastani
fabca90345
preprocessor: aesthetic fix
2017-02-09 16:23:42 +01:00
Houtan Bastani
7ced4b5580
preprocessor: change error to warning because we don’t end processing in this situation; fix error message
2017-02-09 16:21:18 +01:00
Houtan Bastani
edd2e98086
preprocessor: replace exit(1) with exit(EXIT_FAILURE)
2017-02-09 12:46:37 +01:00
Stéphane Adjemian (Charybdis)
593d62a7c1
Removed optimizers/fs2000_12.mod from testsuite...
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Because the Global Optimization Toolbox is not installed on dynbot@sedna.
2017-02-08 14:29:34 +01:00
Stéphane Adjemian (Charybdis)
9fbef0c107
Removed penalty_hessian routine.
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+ 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 2446ab02ba
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An option is available for computing the hessian with the penalized
objective function.
2017-02-08 13:07:25 +00:00
Stéphane Adjemian (Charybdis)
b14cf33c8f
Changed priors in tests/optimizers/fs2000_* integration tests.
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To avoid asymptote at zero on the autoregressive parameter rho.
2017-02-08 13:07:25 +00:00
Stéphane Adjemian (Charybdis)
5b73d7d59c
Added new optimization routine (particleswarm).
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Only available under Matlab if the Global Optimization Toolbox is installed.
2017-02-08 13:07:25 +00:00
Stéphane Adjemian (Charybdis)
35078e13ee
Completed header + cosmetic changes.
2017-02-08 13:07:25 +00:00
Stéphane Adjemian (Charybdis)
8d4abe4a9f
Cosmetic changes.
2017-02-08 13:07:24 +00:00
Stéphane Adjemian (Charybdis)
e71e89bb38
Added check on Octave version.
2017-02-08 13:07:24 +00:00
Houtan Bastani
d05dd34d30
preprocessor: write JSON output. #1387
2017-02-06 17:41:18 +01:00
Houtan Bastani
e88739a5ea
doc: add preprocessor copyright info
2017-02-01 18:16:51 +01:00
Houtan Bastani
25e9a81b71
doc: update for preprocessor
2017-02-01 18:06:44 +01:00
Houtan Bastani
3776b910a1
preprocessor: remove introduction to C++ programming
2017-01-31 17:11:28 +01:00
Houtan Bastani
5b6a888d7f
preprocessor: fix typo
2017-01-31 17:11:03 +01:00