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Fixing negative binomial phi cutoff#1497

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bob-carpenter merged 103 commits intostan-dev:developstan-dev/math:developfrom martinmodrak:bugfix/1496-poisson-phi-cutoffmartinmodrak/math:bugfix/1496-poisson-phi-cutoffCopy head branch name to clipboardMar 29, 2020

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Commits on Dec 9, 2019

• Failing test for cutoff when delegate neg_binomial_2 to poisson

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• Failing test for vectors needing cutoff

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• Phi cutoff no longer overrides logp accumulator

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• Failing test for propto conservation around the cutoff

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• Merge commit 'fd244866e1ff9fd3988516b39f54c8870d46fba1' into HEAD

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Commits on Dec 10, 2019

• Using binomial_coefficient_log, better Poisson defer, further tests

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• Fixed formatting issues

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Commits on Dec 11, 2019

• Improved tests and their reporting

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• Merge commit '45231d114908d5a7d236fed9dffa2501ee8e368b' into HEAD

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• Updated precomputed test values

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• Changing order of operations, passing precomputed test

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• Removed unnecessary debug info

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• Use precomputed values

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• Test for continuity of gradients at cutoff

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• Updated Mathematica code+reference

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• Removing old code

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Commits on Dec 18, 2019

• Test with complex_step WIP

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Commits on Dec 19, 2019

• Merge branch 'develop' into bugfix/1496-poisson-phi-cutoff

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• Changing finite diffs to complex step

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• Merge remote-tracking branch 'origin/bugfix/1496-poisson-phi-cutoff' into bugfix/1496-poisson-phi-cutoff

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• Moved test values to separate namespace

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• Updated comments

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Commits on Jan 2, 2020

• Fixed stan-dev#1531 for neg_binomial_2_lpmf

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• Merge remote-tracking branch 'stan-dev/develop' into bugfix/1496-poisson-phi-cutoff

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• Moved tests touched by the flattening

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• Fixed missing length reference

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• Merge remote-tracking branch 'origin/bugfix/1496-poisson-phi-cutoff' into bugfix/1496-poisson-phi-cutoff

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• Using for range-based for loops

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Commits on Jan 3, 2020

• Addressing review

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• Merge remote-tracking branch 'stan-dev/develop' into bugfix/1496-poisson-phi-cutoff

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• Merge remote-tracking branch 'stan-dev/develop' into bugfix/1496-poisson-phi-cutoff

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• Test large n in derivativesComplexStep, correctly name tests

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Commits on Jan 6, 2020

• Merge remote-tracking branch 'stan-dev/develop' into bugfix/1496-poisson-phi-cutoff

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• Addressing review, boost upgrade

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• Fixed include typo

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• Merge remote-tracking branch 'origin/bugfix/1496-poisson-phi-cutoff' into bugfix/1496-poisson-phi-cutoff

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• Removed use of unsigned int

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• Tightened test acuraccy

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Commits on Jan 7, 2020

• Precomputed (failing) test for binomial_coefficient_log

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• More tests, avoiding Poisson

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• Merge commit 'e33558fefaa40ebf5f5153d585b968491b494f98' into HEAD

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Commits on Jan 8, 2020

• Dummy and failing test for lgamma_stirling_diff

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• Merge commit '821d3b15263f6e4a6d27c7fe77f0f80d3eafb8ed' into HEAD

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Commits on Jan 9, 2020

• Some progress towards better binomial_coefficient_log (messy)

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• Merge commit '77fe4a0e493ed3b26bb08a33d0c18b7cf40602cb' into HEAD

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Commits on Jan 10, 2020

• Merge remote-tracking branch 'stan-dev/develop' into bugfix/1496-poisson-phi-cutoff

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• Some more tweaks to stirling_diff

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• More (still failing) work on lgamma_stirling_diff

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Commits on Jan 13, 2020

• Failing test for lbeta (stan-dev#1611)

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• More strict criteria in expect_near_rel

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• Fixing lbeta and binomial_coefficient_log (stan-dev#1611, stan-dev#1592)

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• Fixing derivative w.r.t. phi for large difference between mu and phi

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• Merge remote-tracking branch 'stan-dev/develop' into bugfix/1496-poisson-phi-cutoff

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• Fixes after merge

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• More fixes after merge

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• Merge remote-tracking branch 'origin/bugfix/1496-poisson-phi-cutoff' into bugfix/1496-poisson-phi-cutoff

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• LOG_TWO_PI

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• Minor optimization in lgamma_stirling_dff

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Commits on Jan 14, 2020

• Fixing lint, cleanup

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• Merge branch 'bugfix/1592-binomial_coefficient_log' into bugfix/1496-poisson-phi-cutoff

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• Fixing incomplete merge

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• Merge branch 'bugfix/1592-binomial_coefficient_log' into bugfix/1496-poisson-phi-cutoff

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• Improved code style

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Commits on Mar 13, 2020

• Merge remote-tracking branch 'stan-dev/develop' into bugfix/1496-poisson-phi-cutoff

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• Fixed merge

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• Fixes stan-dev#1496

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• Reducing the scope of neg_binomial_2_log_lpmf tests

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Commits on Mar 15, 2020

• Fixed duplicated from merge

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• Merge remote-tracking branch 'stan-dev/develop' into bugfix/1496-poisson-phi-cutoff

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• A bit more cleanup

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• Removed unused headers

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Commits on Mar 29, 2020

• Merge remote-tracking branch 'stan-dev/develop' into bugfix/1496-poisson-phi-cutoff

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• Test against dphi for n = 1, lifted lbeta test restrictions

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