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bugfix/issue-17 fvar specialization fix for trace_quad_form#19

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syclik merged 5 commits intodevelopfrom
bugfix/issue-fvar-spec-trace_quad_form
Jul 27, 2015
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bugfix/issue-17 fvar specialization fix for trace_quad_form#19
syclik merged 5 commits intodevelopfrom
bugfix/issue-fvar-spec-trace_quad_form

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@rtrangucci rtrangucci commented Jul 6, 2015

Summary:

Introduces Matrix<double, -1, -1>, Matrix<fvar, -1, -1> specialization of trace_quad_form

Intended Effect:

Admits higher-order autodiff of trace_quad_form for mixed type arguments (e.g. Matrix<double, -1, -1>, Matrix<fvar, -1, -1>). Allows for fvar instantiation of multi_normal_prec_log.

How to Verify:

./runTests.py test/unit/math/mix/mat/fun/trace_quad_form_test.cpp
./runTests.py test/unit/math/fwd/mat/fun/trace_quad_form_test.cpp

These should fail in the current math branch.

Side Effects:

None.

Documentation:

None.

Reviewer Suggestions:

Anyone

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stan-buildbot commented Jul 6, 2015

Refer to this link for build results (access rights to CI server needed):
http://d1m1s1b1.stat.columbia.edu:8080/job/Math%20Pull%20Request/19/

syclik
syclik reviewed Jul 15, 2015
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stan/math/fwd/mat/fun/trace_quad_form.hpp Outdated
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remove namespace qualification.

@syclik syclik added this to the v2.7.0++ milestone Jul 25, 2015
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syclik commented Jul 25, 2015

@rtrangucci, I'm going to reindent the code, which will kick off tests once more. If it passes, we'll get it in.

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rtrangucci commented Jul 25, 2015

Sounds good!

Rob

On Jul 25, 2015, at 11:27 AM, Daniel Lee notifications@github.com wrote:

@rtrangucci, I'm going to reindent the code, which will kick off tests once more. If it passes, we'll get it in.

—
Reply to this email directly or view it on GitHub.

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syclik commented Jul 25, 2015

Jenkins, retest this please.

syclik added a commit that referenced this pull request Jul 27, 2015
@syclik
Merge pull request #19 from stan-dev/bugfix/issue-fvar-spec-trace_qua…
055da57 
…d_form

Fixes #17. bugfix/issue-17 fvar specialization fix for trace_quad_form
@syclik syclik merged commit 055da57 into develop Jul 27, 2015
@syclik syclik deleted the bugfix/issue-fvar-spec-trace_quad_form branch July 27, 2015 01:41
@bob-carpenter bob-carpenter mentioned this pull request Aug 22, 2015
Merged
yizhang-yiz referenced this pull request in yizhang-yiz/math Feb 27, 2018
@billgillespie
Merge pull request #19 from yizhang-cae/bugfix/issue-18-duplicate-symbol
6959534 
comment out Marker() function in Torsten to avoid global variable.
bbbales2 added a commit that referenced this pull request May 6, 2020
@bbbales2
Switched ODE states to be expressed as Eigen Vectors (variadic odes, …
03756de 
…design-doc #19)
bbbales2 added a commit that referenced this pull request May 9, 2020
@bbbales2
Fixed bug with how ode sensitivities with respect to t0 work (design-…
257afa0 
…doc #19)
bbbales2 added a commit that referenced this pull request May 11, 2020
@bbbales2
Updated ode_store_sensitivities references (design-doc #19)
cb602ad
bbbales2 added a commit that referenced this pull request May 16, 2020
@bbbales2
Adjoint ode_bdf passing ode_bdf tests. integrate_ode_bdf not working …
44529fd 
…yet. (design-doc #19)
bbbales2 added a commit that referenced this pull request May 25, 2020
@bbbales2
Made some minor changes with coupled_ode_system to make new code matc…
7f5e7db 
…h speed of old code (design-doc #19)
bbbales2 added a commit that referenced this pull request May 25, 2020
@bbbales2
Allow integer initial times and output times (design-doc #19)
ad58f9d
bbbales2 added a commit that referenced this pull request May 25, 2020
@bbbales2
Add new adams interface (design-doc #19)
8f28f3e
bbbales2 added a commit that referenced this pull request May 25, 2020
@bbbales2
Added tests for new adams ode interface (design-doc #19)
b4e89d3
bbbales2 added a commit that referenced this pull request May 25, 2020
@bbbales2
Times to ODE solvers only need to be sorted, not strictly increasing …
a1f928b 
…(design-doc #19)
bbbales2 added a commit that referenced this pull request May 28, 2020
@bbbales2
Added new prim tests for bdf solver. Added new interfaces that include
ea303ff 
sensitivity in error analysis and include optional relative and absolute
error tolerances of sensitivities (design-doc #19)
bbbales2 added a commit that referenced this pull request Jun 1, 2020
@bbbales2
Hopefully completed adding tests to new ode functions.
6ae558c 
Changed ode_rk45 error behavior to match cvodes_integrator-based ODEs (design-doc #19)
bbbales2 added a commit that referenced this pull request Jun 16, 2020
@bbbales2
Performance optimizations for coupled_ode_system (design-doc #19)
961780f
bbbales2 added a commit that referenced this pull request Jun 23, 2020
@bbbales2
Added tests for cvodes error prints, grad with no argument, and clean…
bae0be9 
…ed up comments (design doc #19)
bbbales2 added a commit that referenced this pull request Jun 24, 2020
@bbbales2
More optimizations to make the new ode interfaces fast (design-doc #19)
9a10def
bbbales2 added a commit that referenced this pull request Jun 30, 2020
@bbbales2
Updated function name in error messages to better reflect which funct…
1ef29d9 
…ion was called

Removed sensitivity tolerance flag (and set to true by default. It was false by default in 2.23 release)

(design-doc #19)
bbbales2 added a commit that referenced this pull request Jul 1, 2020
@bbbales2
Added more time points to ode prim tests (design-doc #19)
9592cba
bbbales2 added a commit that referenced this pull request Jul 1, 2020
@bbbales2
Updated docs, cleaned up template naming, avoided unncessary nested a…
d4f8fe1 
…djoint

stack zeroing, updated default rk45 tolerances, got rid of unnecessary argument tuple,
changed how some casts were done, and removed some experimental error tolerance stuff.

(design-doc #19)
bbbales2 added a commit that referenced this pull request Jul 2, 2020
@bbbales2
Added support for general arguments to variadic ODEs (design-doc #19)
9f923e8
bbbales2 added a commit that referenced this pull request Jul 2, 2020
@bbbales2
Updated value_of implementation to work with holder again. Added test…
7e411bc 
…s for containers of containers (design-doc #19)
bbbales2 added a commit that referenced this pull request Jul 2, 2020
@bbbales2
Added eigen version of harm_osc_ode_fun and reverse mode tests for co…
52c85a4 
…upled_ode_system (design-doc #19)
bbbales2 added a commit that referenced this pull request Jul 3, 2020
@bbbales2
Made zero_adjoints its own standalone function (design-doc #19)
b76e7a5
bbbales2 added a commit that referenced this pull request Jul 3, 2020
@bbbales2
Added tests for old ode interface adapter code (design-docs #19)
64805e3
bbbales2 added a commit that referenced this pull request Jul 4, 2020
@bbbales2
Clean up doxygen and test names (design-doc #19)
66bf060
bbbales2 added a commit that referenced this pull request Jul 4, 2020
@bbbales2
Updated headers in zero_adjoints.hpp (design-doc #19)
f745294
bbbales2 added a commit that referenced this pull request Jul 4, 2020
@bbbales2
Updated types in coupled_ode_system tests (design-doc #19)
444ae2a
bbbales2 added a commit that referenced this pull request Jul 6, 2020
@bbbales2
Added missing error print (design-doc #19)
b8bc8e4
bbbales2 added a commit that referenced this pull request Jul 6, 2020
@bbbales2
Fixed check_finite to work with expressions (design-doc #19)
15eb4ec
bbbales2 added a commit that referenced this pull request Jul 6, 2020
@bbbales2
Updated check_finite to work with eigen arrays (design-doc #19)
5773195
bbbales2 added a commit that referenced this pull request Jul 6, 2020
@bbbales2
Cleanup responding to review comments (design-doc #19)
6d365ce
bbbales2 added a commit that referenced this pull request Jul 6, 2020
@bbbales2
Updated some includes (design-doc #19)
7538e97
bbbales2 added a commit that referenced this pull request Jul 7, 2020
@bbbales2
Responding to comments. Added too much work tests to _tol versions of…
c2499be 
… ode functions (design-doc #19)
bbbales2 added a commit that referenced this pull request Jul 7, 2020
@bbbales2
Added ode_store_sensitivities tests (design-doc #19)
35267b1
bbbales2 added a commit that referenced this pull request Jul 8, 2020
@bbbales2
Responding to reviews (design-doc #19)
19e029c
bbbales2 added a commit that referenced this pull request Jul 9, 2020
@bbbales2
Updated variable naming/docs (design-doc #19)
3e7abbf
bbbales2 added a commit that referenced this pull request Jul 9, 2020
@bbbales2
Added some comments around strange code.
54de59b 
Made deep_copy_vars do perfect forwarding again. (design-doc #19)
bbbales2 added a commit that referenced this pull request Jul 9, 2020
@bbbales2
Fixed wrong pointer name (design-doc #19)
10acf66
bbbales2 added a commit that referenced this pull request Jul 9, 2020
@bbbales2
Added eval function to call .eval() on expressions buried in parame…
a5ee85d 
…ter packs (design-doc #19)
bbbales2 added a commit that referenced this pull request Jul 9, 2020
@bbbales2
Fixed doxygen problem though I'm not sure how (design-doc #19)
2e83467
bbbales2 added a commit that referenced this pull request Jul 10, 2020
@bbbales2
Updated eval implementation and tests (design-docs #19)
3b4c217
bbbales2 added a commit that referenced this pull request Jul 10, 2020
@bbbales2
Removed unnecessary headers (design-doc #19)
a589de9
bbbales2 added a commit that referenced this pull request Jul 13, 2020
@bbbales2
Fixed error message printing with too much work and extended tests to…
1908f1c 
… catch it (design-doc #19)
bbbales2 added a commit that referenced this pull request Jul 24, 2020
@bbbales2
Reverting check_finite to work with vectors of vectors (stuff from de…
27a8c32 
…sign-doc #19)
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