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add yule_simon_lpmf by lingium · Pull Request #3220 · stan-dev/math · GitHub

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add yule_simon_lpmf - #3220

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lingium merged 2 commits into
stan-dev:developfrom
lingium:feature/issue-3219-yule-simon-lpmf
Sep 9, 2025
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add yule_simon_lpmf#3220
lingium merged 2 commits into
stan-dev:developfrom
lingium:feature/issue-3219-yule-simon-lpmf

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lingium commented Jul 8, 2025 •
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Summary

With this PR the lpmf of Yule Simon distribution are added.
See issue #3219
Other functions of this distribution will be added in following PRs.

Expressions involved:

PMF

$$ \log f(n) = \log \alpha + \log\text{Beta}(n,\alpha+1), \quad n=1,2,... \quad \alpha>0 $$

Derivatives w.r.t the parameter

$$ \begin{align} \frac{\partial \log f(\alpha)}{\partial \alpha} &= \frac{1}{\alpha} + \text{digamma}(\alpha+1) - \text{digamma}(n + \alpha +1) \end{align} $$

Tests

Test is written follow the guide.

Side Effects

No

Release notes

yule_simon_lpmf is available if merged. Allows modeling power-law count data.

Checklist

  • Copyright holder: Zhi Ling

    The copyright holder is typically you or your assignee, such as a university or company. By submitting this pull request, the copyright holder is agreeing to the license the submitted work under the following licenses:
    - Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
    - Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

  • the basic tests are passing

    • unit tests pass (to run, use: ./runTests.py test/unit)
    • header checks pass, (make test-headers)
    • dependencies checks pass, (make test-math-dependencies)
    • docs build, (make doxygen)
    • code passes the built in C++ standards checks (make cpplint)

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

  • the new changes are tested

stan-buildbot commented Jul 8, 2025

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Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.41 0.34 1.21 17.02% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 1.49 32.77% faster
gp_regr/gen_gp_data.stan 0.03 0.03 1.15 13.18% faster
gp_regr/gp_regr.stan 0.11 0.1 1.1 9.43% faster
sir/sir.stan 98.42 73.15 1.35 25.68% faster
irt_2pl/irt_2pl.stan 4.86 4.42 1.1 9.18% faster
eight_schools/eight_schools.stan 0.06 0.06 1.05 4.64% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.28 0.25 1.09 7.84% faster
pkpd/one_comp_mm_elim_abs.stan 20.61 19.8 1.04 3.94% faster
garch/garch.stan 0.47 0.43 1.08 7.72% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.87 3.45 0.83 -20.23% slower
arK/arK.stan 1.89 1.88 1.01 0.55% faster
gp_pois_regr/gp_pois_regr.stan 2.98 2.87 1.04 3.67% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 11.4 9.11 1.25 20.1% faster
performance.compilation 214.2 197.3 1.09 7.89% faster
Mean result: 1.1244038433145673

Jenkins Console Log
Blue Ocean
Commit hash: 33a134f687329ce0b6e04d20dd485ece49a6f1c4

Machine information No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 20.04.3 LTS Release: 20.04 Codename: focal

CPU:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
Address sizes: 46 bits physical, 48 bits virtual
CPU(s): 80
On-line CPU(s) list: 0-79
Thread(s) per core: 2
Core(s) per socket: 20
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 85
Model name: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Stepping: 4
CPU MHz: 2400.000
CPU max MHz: 3700.0000
CPU min MHz: 1000.0000
BogoMIPS: 4800.00
Virtualization: VT-x
L1d cache: 1.3 MiB
L1i cache: 1.3 MiB
L2 cache: 40 MiB
L3 cache: 55 MiB
NUMA node0 CPU(s): 0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78
NUMA node1 CPU(s): 1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79
Vulnerability Gather data sampling: Mitigation; Microcode
Vulnerability Itlb multihit: KVM: Mitigation: VMX disabled
Vulnerability L1tf: Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable
Vulnerability Mds: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Meltdown: Mitigation; PTI
Vulnerability Mmio stale data: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Reg file data sampling: Not affected
Vulnerability Retbleed: Mitigation; IBRS
Vulnerability Spec rstack overflow: Not affected
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl
Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2: Mitigation; IBRS; IBPB conditional; STIBP conditional; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds: Not affected
Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT vulnerable
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin ssbd mba ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke md_clear flush_l1d arch_capabilities

G++:
g++ (Ubuntu 9.4.0-1ubuntu1~20.04) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Clang:
clang version 10.0.0-4ubuntu1
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin

SteveBronder requested changes Jul 8, 2025
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Choose a reason Spam Abuse Off Topic Outdated Duplicate Resolved Low Quality

Few small changes but looks good!

Comment thread stan/math/prim/prob/yule_simon_lpmf.hpp Outdated
Comment thread stan/math/prim/prob/yule_simon_lpmf.hpp Outdated
Comment thread stan/math/prim/prob/yule_simon_lpmf.hpp

stan-buildbot commented Jul 9, 2025

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Contributor
Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.35 0.32 1.08 7.38% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 1.03 2.72% faster
gp_regr/gen_gp_data.stan 0.03 0.02 1.06 5.43% faster
gp_regr/gp_regr.stan 0.1 0.09 1.02 2.02% faster
sir/sir.stan 72.89 68.08 1.07 6.6% faster
irt_2pl/irt_2pl.stan 4.52 4.05 1.12 10.5% faster
eight_schools/eight_schools.stan 0.06 0.05 1.07 6.53% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.26 0.25 1.06 5.99% faster
pkpd/one_comp_mm_elim_abs.stan 20.19 18.99 1.06 5.93% faster
garch/garch.stan 0.47 0.41 1.14 12.62% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.83 2.65 1.07 6.6% faster
arK/arK.stan 1.85 1.75 1.06 5.48% faster
gp_pois_regr/gp_pois_regr.stan 2.89 2.72 1.06 5.96% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 9.25 8.57 1.08 7.25% faster
performance.compilation 189.06 186.41 1.01 1.4% faster
Mean result: 1.0666130863090002

Jenkins Console Log
Blue Ocean
Commit hash: 33a134f687329ce0b6e04d20dd485ece49a6f1c4

Machine information No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 20.04.3 LTS Release: 20.04 Codename: focal

CPU:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
Address sizes: 46 bits physical, 48 bits virtual
CPU(s): 80
On-line CPU(s) list: 0-79
Thread(s) per core: 2
Core(s) per socket: 20
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 85
Model name: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Stepping: 4
CPU MHz: 2400.000
CPU max MHz: 3700.0000
CPU min MHz: 1000.0000
BogoMIPS: 4800.00
Virtualization: VT-x
L1d cache: 1.3 MiB
L1i cache: 1.3 MiB
L2 cache: 40 MiB
L3 cache: 55 MiB
NUMA node0 CPU(s): 0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78
NUMA node1 CPU(s): 1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79
Vulnerability Gather data sampling: Mitigation; Microcode
Vulnerability Itlb multihit: KVM: Mitigation: VMX disabled
Vulnerability L1tf: Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable
Vulnerability Mds: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Meltdown: Mitigation; PTI
Vulnerability Mmio stale data: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Reg file data sampling: Not affected
Vulnerability Retbleed: Mitigation; IBRS
Vulnerability Spec rstack overflow: Not affected
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl
Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2: Mitigation; IBRS; IBPB conditional; STIBP conditional; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds: Not affected
Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT vulnerable
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin ssbd mba ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke md_clear flush_l1d arch_capabilities

G++:
g++ (Ubuntu 9.4.0-1ubuntu1~20.04) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Clang:
clang version 10.0.0-4ubuntu1
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin

lingium requested a review from SteveBronder July 17, 2025 14:58

SteveBronder commented Jul 31, 2025

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Everything here looks good! We are in a release review period but I'll approve and merge this once that is over.

WardBrian commented Sep 8, 2025

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@SteveBronder want to approve this now?

SteveBronder commented Sep 8, 2025

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Yes!

SteveBronder approved these changes Sep 8, 2025
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Choose a reason Spam Abuse Off Topic Outdated Duplicate Resolved Low Quality

Looks good to me! @lingium are you able to press the merge button? If not I'll add you to the Stan math repo so you can

lingium commented Sep 9, 2025

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Thanks!

lingium merged commit b93e44d into stan-dev:develop Sep 9, 2025
lingium deleted the feature/issue-3219-yule-simon-lpmf branch September 12, 2025 14:23

WardBrian commented Jan 5, 2026

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Hi @lingium -- this never got exposed in the language. Did you want to address #3237 #3238 and #3239 before that happens?

lingium commented Jan 10, 2026

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Hi @WardBrian! yes, let me first address the rest recently before we expose them

WardBrian commented Jan 12, 2026

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Sounds good!

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