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Bugfix/poisson glm - #1510

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rok-cesnovar merged 11 commits into
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bugfix/poisson_glm
Jan 6, 2020
Merged

Bugfix/poisson glm#1510
rok-cesnovar merged 11 commits into
developfrom
bugfix/poisson_glm

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@rok-cesnovar

@rok-cesnovar rok-cesnovar commented Dec 13, 2019

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Summary

Fixes the include_summand bug in poisson_log_glm.

Tests

Added a test that fails on develop but passes on this PR.

Side Effects

/

Checklist

  • Math issue: Fixes poisson_log_glm sampling statement fails to fit #1498

  • Copyright holder: Rok Češnovar, the fix was suggested by Ben Bales

  • the basic tests are passing

  • the code is written in idiomatic C++ and changes are documented in the doxygen

  • the new changes are tested

@stan-buildbot

stan-buildbot commented Dec 14, 2019

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(stat_comp_benchmarks/benchmarks/gp_pois_regr/gp_pois_regr.stan, 0.99)
(stat_comp_benchmarks/benchmarks/low_dim_corr_gauss/low_dim_corr_gauss.stan, 0.96)
(stat_comp_benchmarks/benchmarks/irt_2pl/irt_2pl.stan, 1.0)
(stat_comp_benchmarks/benchmarks/pkpd/one_comp_mm_elim_abs.stan, 0.99)
(stat_comp_benchmarks/benchmarks/eight_schools/eight_schools.stan, 0.99)
(stat_comp_benchmarks/benchmarks/gp_regr/gp_regr.stan, 1.0)
(stat_comp_benchmarks/benchmarks/arK/arK.stan, 1.0)
(performance.compilation, 1.01)
(stat_comp_benchmarks/benchmarks/low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan, 0.99)
(stat_comp_benchmarks/benchmarks/low_dim_gauss_mix/low_dim_gauss_mix.stan, 1.0)
(stat_comp_benchmarks/benchmarks/sir/sir.stan, 1.01)
(stat_comp_benchmarks/benchmarks/pkpd/sim_one_comp_mm_elim_abs.stan, 1.0)
(stat_comp_benchmarks/benchmarks/garch/garch.stan, 1.0)
(stat_comp_benchmarks/benchmarks/gp_regr/gen_gp_data.stan, 1.01)
(stat_comp_benchmarks/benchmarks/arma/arma.stan, 1.0)
Result: 0.99721695221
Commit hash: a42451d

@mcol

mcol commented Dec 30, 2019

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In opencl/prim/poisson_log_glm_lpmf.hpp there's a call to the old signature within a try block that's making the opencl tests fail. Besides that, this looks fine to me, but let's ping @bbbales2 in case he wants to have a look directly. :)

@stan-buildbot

stan-buildbot commented Dec 31, 2019

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(stat_comp_benchmarks/benchmarks/gp_pois_regr/gp_pois_regr.stan, 0.99)
(stat_comp_benchmarks/benchmarks/low_dim_corr_gauss/low_dim_corr_gauss.stan, 0.97)
(stat_comp_benchmarks/benchmarks/irt_2pl/irt_2pl.stan, 0.99)
(stat_comp_benchmarks/benchmarks/pkpd/one_comp_mm_elim_abs.stan, 1.0)
(stat_comp_benchmarks/benchmarks/eight_schools/eight_schools.stan, 0.99)
(stat_comp_benchmarks/benchmarks/gp_regr/gp_regr.stan, 1.01)
(stat_comp_benchmarks/benchmarks/arK/arK.stan, 0.9)
(performance.compilation, 1.01)
(stat_comp_benchmarks/benchmarks/low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan, 1.0)
(stat_comp_benchmarks/benchmarks/low_dim_gauss_mix/low_dim_gauss_mix.stan, 1.0)
(stat_comp_benchmarks/benchmarks/sir/sir.stan, 0.98)
(stat_comp_benchmarks/benchmarks/pkpd/sim_one_comp_mm_elim_abs.stan, 0.96)
(stat_comp_benchmarks/benchmarks/garch/garch.stan, 1.12)
(stat_comp_benchmarks/benchmarks/gp_regr/gen_gp_data.stan, 1.01)
(stat_comp_benchmarks/benchmarks/arma/arma.stan, 1.1)
Result: 1.00286615084
Commit hash: 82ba1ec

@stan-buildbot

stan-buildbot commented Jan 2, 2020

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(stat_comp_benchmarks/benchmarks/gp_pois_regr/gp_pois_regr.stan, 1.0)
(stat_comp_benchmarks/benchmarks/low_dim_corr_gauss/low_dim_corr_gauss.stan, 0.98)
(stat_comp_benchmarks/benchmarks/irt_2pl/irt_2pl.stan, 0.99)
(stat_comp_benchmarks/benchmarks/pkpd/one_comp_mm_elim_abs.stan, 1.02)
(stat_comp_benchmarks/benchmarks/eight_schools/eight_schools.stan, 0.95)
(stat_comp_benchmarks/benchmarks/gp_regr/gp_regr.stan, 1.02)
(stat_comp_benchmarks/benchmarks/arK/arK.stan, 1.0)
(performance.compilation, 1.01)
(stat_comp_benchmarks/benchmarks/low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan, 1.0)
(stat_comp_benchmarks/benchmarks/low_dim_gauss_mix/low_dim_gauss_mix.stan, 1.0)
(stat_comp_benchmarks/benchmarks/sir/sir.stan, 1.02)
(stat_comp_benchmarks/benchmarks/pkpd/sim_one_comp_mm_elim_abs.stan, 0.97)
(stat_comp_benchmarks/benchmarks/garch/garch.stan, 1.0)
(stat_comp_benchmarks/benchmarks/gp_regr/gen_gp_data.stan, 0.97)
(stat_comp_benchmarks/benchmarks/arma/arma.stan, 0.99)
Result: 0.99553095515
Commit hash: 9c1cd3b

@stan-buildbot

stan-buildbot commented Jan 3, 2020

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(stat_comp_benchmarks/benchmarks/gp_pois_regr/gp_pois_regr.stan, 0.98)
(stat_comp_benchmarks/benchmarks/low_dim_corr_gauss/low_dim_corr_gauss.stan, 0.99)
(stat_comp_benchmarks/benchmarks/irt_2pl/irt_2pl.stan, 0.99)
(stat_comp_benchmarks/benchmarks/pkpd/one_comp_mm_elim_abs.stan, 1.01)
(stat_comp_benchmarks/benchmarks/eight_schools/eight_schools.stan, 1.04)
(stat_comp_benchmarks/benchmarks/gp_regr/gp_regr.stan, 1.01)
(stat_comp_benchmarks/benchmarks/arK/arK.stan, 1.0)
(performance.compilation, 1.03)
(stat_comp_benchmarks/benchmarks/low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan, 1.0)
(stat_comp_benchmarks/benchmarks/low_dim_gauss_mix/low_dim_gauss_mix.stan, 1.0)
(stat_comp_benchmarks/benchmarks/sir/sir.stan, 1.0)
(stat_comp_benchmarks/benchmarks/pkpd/sim_one_comp_mm_elim_abs.stan, 1.02)
(stat_comp_benchmarks/benchmarks/garch/garch.stan, 0.99)
(stat_comp_benchmarks/benchmarks/gp_regr/gen_gp_data.stan, 0.99)
(stat_comp_benchmarks/benchmarks/arma/arma.stan, 1.0)
Result: 1.00281000983
Commit hash: 5aed389

bbbales2
bbbales2 approved these changes Jan 6, 2020
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@bbbales2 bbbales2 left a comment

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Code looks good, tests looks good, merge whenever.

@rok-cesnovar
rok-cesnovar merged commit 4dd8da1 into develop Jan 6, 2020
@rok-cesnovar
rok-cesnovar deleted the bugfix/poisson_glm branch January 6, 2020 19:10
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poisson_log_glm sampling statement fails to fit

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@rok-cesnovar @stan-buildbot @mcol @bbbales2