pg-phenotype 0.1.0__tar.gz

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pg_phenotype-0.1.0/Cargo.toml

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+[workspace]
+resolver = "2"
+members = ["crates/core", "crates/python"]
+
+[workspace.package]
+version = "0.1.0"
+edition = "2021"
+# pedigree-graph-core's floor; the R binding crate states the same.
+rust-version = "1.85"
+license = "MIT"
+repository = "https://github.com/rwaples/pg-phenotype"
+
+[workspace.dependencies]
+# Re-pinned on purpose only (ADR 0001): pg-core is unpublished until 1.0.
+# This rev is pedigree-graph v0.12.2.
+pedigree-graph-core = { git = "https://github.com/rwaples/pedigree-graph", rev = "62c82fa6468aec0f579dc9286c5dbebe7d077500" }
+rayon = "1.10"
+
+[profile.release]
+opt-level = 3
+debug = 1
+codegen-units = 1

pg_phenotype-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Ryan Waples
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pg_phenotype-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pg-phenotype
+Version: 0.1.0
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Dist: numpy>=2.2,<3
+Requires-Dist: scipy>=1.14,<2 ; extra == 'test'
+Requires-Dist: pedigree-graph>=0.12.2,<0.13 ; extra == 'test'
+Requires-Dist: pytest>=9,<10 ; extra == 'test'
+Requires-Dist: pytest-xdist>=3.8,<4 ; extra == 'test'
+Requires-Dist: ruff>=0.16,<0.17 ; extra == 'test'
+Requires-Dist: hypothesis>=6,<7 ; extra == 'test'
+Requires-Dist: pandas>=3.0,<4 ; extra == 'test'
+Requires-Dist: polars>=1.43.2,<2 ; extra == 'test'
+Requires-Dist: ty==0.0.84 ; extra == 'typecheck'
+Provides-Extra: test
+Provides-Extra: typecheck
+License-File: LICENSE
+Summary: Phenotypes in the context of a pedigree, on pedigree-graph's Rust core: PA-FGRS and more
+Author: Ryan Waples
+License-Expression: MIT
+Requires-Python: >=3.13
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Homepage, https://github.com/rwaples/pg-phenotype
+Project-URL: Repository, https://github.com/rwaples/pg-phenotype
+
+# pg-phenotype
+
+Phenotypes in the context of a pedigree, as an extension of
+[pedigree-graph](https://github.com/rwaples/pedigree-graph): a Rust core with
+Python and R bindings.  Relationships and kinship come from pedigree-graph's
+core; each method is a module on top.
+
+| Method | Module | Status |
+|---|---|---|
+| PA-FGRS family genetic risk scores (Dybdahl Krebs et al., Am J Hum Genet 2024, doi:10.1016/j.ajhg.2024.09.009) | `pg_phenotype.pafgrs` | available |
+| Assortative mating: the Mate Correlation of one or two traits, ported from pedsum #13 | `pg_phenotype.assortative` | available |
+
+## Python
+
+```python
+import pg_phenotype as pgp
+from pg_phenotype import pafgrs
+
+trait = pgp.Trait(dx, kind="binary")  # one value per pedigree row
+prep = pafgrs.prepare(pedigree, ndegree=2)  # once per pedigree
+cip = pafgrs.Cip(ages, cip_values)  # K is the last value
+scores = pafgrs.score_univariate(prep, trait, age=dx_age, cip=cip, h2=0.4)
+scores.est, scores.var, scores.n_relatives, scores.metadata
+
+both = pafgrs.score_bivariate(prep, (t1, t2), age=(a1, a2), cip=(c1, c2), h2=(0.4, 0.6), rg=0.5)
+```
+
+- `pedigree`: columns `id`, `mother`, `father` (`-1` or NA when missing) and
+  optional `twin`, `sex` (`0` female, `1` male), as a polars or pandas frame
+  or a mapping of arrays.  It is validated by pedigree-graph's rules.
+- `Trait(values, kind=None)`: one phenotype column on the pedigree's rows,
+  NA where unknown.  The kind is continuous, binary, ordinal or categorical,
+  inferred when unambiguous.
+- PA-FGRS takes a binary trait.  `age` is the onset age for a case and the
+  last observed age for a control; a control without an age is unobserved
+  and counted.
+- `probands=` restricts the scored rows; relatives are drawn from the whole
+  pedigree.  Output is one record per proband in input-row order.
+- `configure_threads(n)` or `PG_PHENOTYPE_THREADS` sets the thread budget
+  (default 1).  Results are identical for every budget.
+
+Errors are `pg_phenotype.ValidationError`, `ParameterError` and
+`ResourceError`, each with a stable `.code` and `.fields`.
+
+### Assortative mating
+
+```python
+from pg_phenotype.assortative import mate_correlation
+
+res = mate_correlation(pedigree, [pgp.Trait(liab), pgp.Trait(dx)], stratum=birth_decade, bootstrap=1000, seed=1)
+cell = res.cell(0, 1)  # mothers' trait 0 x fathers' trait 1
+cell.primary.value, cell.primary.ci, cell.primary.permutation.p
+cell.stratified.result.value  # within birth-decade strata
+res.within_person["mothers"]
+```
+
+The Mate Correlation is the correlation between the mother's and the
+father's value of a trait over a pedigree's Mating Pairs.  Each cell uses
+the estimators its trait kinds call for (Pearson, tetrachoric, polychoric,
+biserial or polyserial, with their closed-form companions), a Mate Network
+sandwich SE, an optional Mate Network bootstrap, and a sequential
+father-permutation p-value.  [docs/assortative-mating.md](docs/assortative-mating.md)
+describes the inputs, rules and every result field, and
+[docs/assortative-mating-design.md](docs/assortative-mating-design.md)
+explains the design.
+
+## R
+
+```r
+library(pgphenotype)
+
+dx <- trait(ped$dx, kind = "binary")
+prep <- pafgrs_prepare(ped, ndegree = 2L)
+cip <- pafgrs_cip(ages, cip_values)
+scores <- pafgrs_score_univariate(prep, dx, age = ped$dx_age, cip = cip, h2 = 0.4)
+both <- pafgrs_score_bivariate(prep, list(t1, t2), ages = list(a1, a2),
+                               cips = list(c1, c2), h2 = c(0.4, 0.6), rg = 0.5)
+am <- assortative_mate_correlation(ped, list(trait(ped$liab), trait(ped$dx)),
+                                   stratum = ped$birth_decade, bootstrap = 1000, seed = 1)
+```
+
+The R package runs the same core as Python and returns the same scores bit
+for bit.  Errors are conditions of class `pgphenotype_error` (with
+`pgphenotype_validation_error` and friends) carrying `$code` and `$fields`,
+positions 1-based.
+
+## Correctness (PA-FGRS)
+
+- Rust against NumPy reference cores (fitACE's, verbatim) given the same
+  covariance and order: within 1e-10.
+- Against BioPsyk/PAFGRS's own `pa_fgrs` on stored fixtures: within 1e-10
+  (1.1e-15 observed).
+- Every kinship value bit-identical to pedigree-graph's `pair_kinship`.
+
+## Correctness (assortative mating)
+
+- Against pedsum #13 at `142adf3` on 74 stored cases (28 fixtures, pedsum's
+  own benchmark pedigrees at 10^4 pairs, and 40 random pedigrees), every
+  count, reason, flag and p-value is identical.  Closed-form estimates agree
+  within 4.5e-15, and latent ones within 3.2e-10, inside Brent's 1e-7
+  tolerance.  One case differs on float noise in pedsum.  The
+  [gate report](docs/gates/assortative-mating/README.md) has the details.
+- On pedsum's benchmark pedigrees at 10^4 to 10^6 pairs and up to 12
+  threads, pg-phenotype's median wall time and peak memory are at most
+  0.994 and 0.981 of pedsum's
+  ([benchmark report](docs/gates/assortative-mating/benchmark.md)).
+- The SciPy and C-library functions pedsum calls are ported bit for bit
+  ([ADR 0005](docs/adr/0005-assortative-mating-reproduces-pedsums-numerics.md)).
+
+Design decisions are in `docs/adr/`; vocabulary in `CONTEXT.md`.
+
+## Development
+
+```bash
+pixi run test        # rebuilds the extension with test hooks, then pytest
+pixi run test-rust
+pixi run -e r r-test
+pixi run test-against-pg ../pedigree-graph   # every suite against a pg checkout
+```
+
+To release a version, follow [How to release pg-phenotype](docs/releasing.md).
+

pg_phenotype-0.1.0/README.md

@@ -0,0 +1,121 @@
+# pg-phenotype
+
+Phenotypes in the context of a pedigree, as an extension of
+[pedigree-graph](https://github.com/rwaples/pedigree-graph): a Rust core with
+Python and R bindings.  Relationships and kinship come from pedigree-graph's
+core; each method is a module on top.
+
+| Method | Module | Status |
+|---|---|---|
+| PA-FGRS family genetic risk scores (Dybdahl Krebs et al., Am J Hum Genet 2024, doi:10.1016/j.ajhg.2024.09.009) | `pg_phenotype.pafgrs` | available |
+| Assortative mating: the Mate Correlation of one or two traits, ported from pedsum #13 | `pg_phenotype.assortative` | available |
+
+## Python
+
+```python
+import pg_phenotype as pgp
+from pg_phenotype import pafgrs
+
+trait = pgp.Trait(dx, kind="binary")  # one value per pedigree row
+prep = pafgrs.prepare(pedigree, ndegree=2)  # once per pedigree
+cip = pafgrs.Cip(ages, cip_values)  # K is the last value
+scores = pafgrs.score_univariate(prep, trait, age=dx_age, cip=cip, h2=0.4)
+scores.est, scores.var, scores.n_relatives, scores.metadata
+
+both = pafgrs.score_bivariate(prep, (t1, t2), age=(a1, a2), cip=(c1, c2), h2=(0.4, 0.6), rg=0.5)
+```
+
+- `pedigree`: columns `id`, `mother`, `father` (`-1` or NA when missing) and
+  optional `twin`, `sex` (`0` female, `1` male), as a polars or pandas frame
+  or a mapping of arrays.  It is validated by pedigree-graph's rules.
+- `Trait(values, kind=None)`: one phenotype column on the pedigree's rows,
+  NA where unknown.  The kind is continuous, binary, ordinal or categorical,
+  inferred when unambiguous.
+- PA-FGRS takes a binary trait.  `age` is the onset age for a case and the
+  last observed age for a control; a control without an age is unobserved
+  and counted.
+- `probands=` restricts the scored rows; relatives are drawn from the whole
+  pedigree.  Output is one record per proband in input-row order.
+- `configure_threads(n)` or `PG_PHENOTYPE_THREADS` sets the thread budget
+  (default 1).  Results are identical for every budget.
+
+Errors are `pg_phenotype.ValidationError`, `ParameterError` and
+`ResourceError`, each with a stable `.code` and `.fields`.
+
+### Assortative mating
+
+```python
+from pg_phenotype.assortative import mate_correlation
+
+res = mate_correlation(pedigree, [pgp.Trait(liab), pgp.Trait(dx)], stratum=birth_decade, bootstrap=1000, seed=1)
+cell = res.cell(0, 1)  # mothers' trait 0 x fathers' trait 1
+cell.primary.value, cell.primary.ci, cell.primary.permutation.p
+cell.stratified.result.value  # within birth-decade strata
+res.within_person["mothers"]
+```
+
+The Mate Correlation is the correlation between the mother's and the
+father's value of a trait over a pedigree's Mating Pairs.  Each cell uses
+the estimators its trait kinds call for (Pearson, tetrachoric, polychoric,
+biserial or polyserial, with their closed-form companions), a Mate Network
+sandwich SE, an optional Mate Network bootstrap, and a sequential
+father-permutation p-value.  [docs/assortative-mating.md](docs/assortative-mating.md)
+describes the inputs, rules and every result field, and
+[docs/assortative-mating-design.md](docs/assortative-mating-design.md)
+explains the design.
+
+## R
+
+```r
+library(pgphenotype)
+
+dx <- trait(ped$dx, kind = "binary")
+prep <- pafgrs_prepare(ped, ndegree = 2L)
+cip <- pafgrs_cip(ages, cip_values)
+scores <- pafgrs_score_univariate(prep, dx, age = ped$dx_age, cip = cip, h2 = 0.4)
+both <- pafgrs_score_bivariate(prep, list(t1, t2), ages = list(a1, a2),
+                               cips = list(c1, c2), h2 = c(0.4, 0.6), rg = 0.5)
+am <- assortative_mate_correlation(ped, list(trait(ped$liab), trait(ped$dx)),
+                                   stratum = ped$birth_decade, bootstrap = 1000, seed = 1)
+```
+
+The R package runs the same core as Python and returns the same scores bit
+for bit.  Errors are conditions of class `pgphenotype_error` (with
+`pgphenotype_validation_error` and friends) carrying `$code` and `$fields`,
+positions 1-based.
+
+## Correctness (PA-FGRS)
+
+- Rust against NumPy reference cores (fitACE's, verbatim) given the same
+  covariance and order: within 1e-10.
+- Against BioPsyk/PAFGRS's own `pa_fgrs` on stored fixtures: within 1e-10
+  (1.1e-15 observed).
+- Every kinship value bit-identical to pedigree-graph's `pair_kinship`.
+
+## Correctness (assortative mating)
+
+- Against pedsum #13 at `142adf3` on 74 stored cases (28 fixtures, pedsum's
+  own benchmark pedigrees at 10^4 pairs, and 40 random pedigrees), every
+  count, reason, flag and p-value is identical.  Closed-form estimates agree
+  within 4.5e-15, and latent ones within 3.2e-10, inside Brent's 1e-7
+  tolerance.  One case differs on float noise in pedsum.  The
+  [gate report](docs/gates/assortative-mating/README.md) has the details.
+- On pedsum's benchmark pedigrees at 10^4 to 10^6 pairs and up to 12
+  threads, pg-phenotype's median wall time and peak memory are at most
+  0.994 and 0.981 of pedsum's
+  ([benchmark report](docs/gates/assortative-mating/benchmark.md)).
+- The SciPy and C-library functions pedsum calls are ported bit for bit
+  ([ADR 0005](docs/adr/0005-assortative-mating-reproduces-pedsums-numerics.md)).
+
+Design decisions are in `docs/adr/`; vocabulary in `CONTEXT.md`.
+
+## Development
+
+```bash
+pixi run test        # rebuilds the extension with test hooks, then pytest
+pixi run test-rust
+pixi run -e r r-test
+pixi run test-against-pg ../pedigree-graph   # every suite against a pg checkout
+```
+
+To release a version, follow [How to release pg-phenotype](docs/releasing.md).

pg_phenotype-0.1.0/crates/core/Cargo.toml

@@ -0,0 +1,17 @@
+[package]
+name = "pg-phenotype-core"
+version.workspace = true
+edition.workspace = true
+rust-version.workspace = true
+license.workspace = true
+repository.workspace = true
+publish = false
+description = "Host-neutral phenotype-in-pedigree methods on pedigree-graph-core"
+
+[lib]
+name = "pg_phenotype_core"
+
+[dependencies]
+pedigree-graph-core.workspace = true
+rayon.workspace = true
+libm = "0.2"