statsformula 0.1.0__tar.gz

statsformula-0.1.0/.gitignore

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+.venv/
+__pycache__/
+*.pyc
+dist/
+build/
+*.egg-info/
+.pytest_cache/

statsformula-0.1.0/CHANGELOG.md

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+# Changelog
+
+## 0.1.0 (2026-11-09)
+
+First release.
+
+* Parser and deparser for R formulas (R operator precedence, `**` → `^`, backticks).
+* Port of R 4.5 `termsform`: all formula operators, `.` expansion, offsets, specials, keep.order, simplify.
+* `model.frame` (subset, weights, offset, na.action, drop.unused.levels, xlev) and `model.matrix`
+  (port of `modelmatrix`: contrasts, column names, assign attribute).
+* `sparse.model.matrix` (Matrix package conventions), `model.response/offset/weights/extract`.
+* `update`, `reformulate`, `drop.terms`, `delete.response`, `all.vars`, `all.names`, `get_all_vars`.
+* Formula package: multi-part formulas, `model.part`, `as.Formula`, `update.Formula`.
+* R functions inside formulas, including `poly`, `bs`, `ns`, `scale`, `C`, `cut`, `interaction`, `relevel`.
+* mgcv `s()`, `te()`, `ti()` with `tp`, `ts`, `cr`, `cs`, `cc`, `ps`, `cp`, `bs`, `re` bases and `by` variables.
+* Stateful transforms re-applied to new data (`ModelSpec`, `GamSpec`).
+* Validated against R 4.5.1: 367 reference cases, 500 random `terms()` and 400 random `model.matrix()` formulas.

statsformula-0.1.0/LICENSE

@@ -0,0 +1,338 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
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statsformula-0.1.0/PKG-INFO

@@ -0,0 +1,208 @@
+Metadata-Version: 2.5
+Name: statsformula
+Version: 0.1.0
+Summary: R model formulas for Python: terms, model.frame, model.matrix, sparse.model.matrix, Formula (multi-part) and mgcv smooths, validated against R.
+Project-URL: Homepage, https://github.com/PedroBSB/statsformula
+Project-URL: Source, https://github.com/PedroBSB/statsformula
+Project-URL: Issues, https://github.com/PedroBSB/statsformula/issues
+Project-URL: Changelog, https://github.com/PedroBSB/statsformula/blob/main/CHANGELOG.md
+Author-email: Pedro Albuquerque <pedro.melo.albuquerque@gmail.com>
+License-Expression: GPL-2.0-or-later
+License-File: LICENSE
+Keywords: R,design matrix,formula,formulaic,gam,mgcv,model matrix,patsy,regression,splines,statistics,statsmodels
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.22
+Requires-Dist: pandas>=1.4
+Requires-Dist: scipy>=1.8
+Provides-Extra: statsmodels
+Requires-Dist: statsmodels>=0.13; extra == 'statsmodels'
+Provides-Extra: test
+Requires-Dist: pytest>=7; extra == 'test'
+Description-Content-Type: text/markdown
+
+# statsformula
+
+**R model formulas for Python — the same terms, columns, names and numbers as R.**
+
+`statsformula` re-implements R's formula machinery (`terms`, `model.frame`,
+`model.matrix`, `update`, ...), the [Formula](https://cran.r-project.org/package=Formula)
+package (multi-part formulas), `Matrix::sparse.model.matrix`, and the model-matrix side of
+[mgcv](https://cran.r-project.org/package=mgcv) (`s()`, `te()`, `ti()` smooths). It is a port of
+R's own algorithms (`termsform` and `modelmatrix` from `stats/src/model.c`, mgcv's `smoothCon`,
+`PredictMat` and thin plate spline code, LINPACK/LAPACK numerics), and it is tested against R.
+
+```python
+import pandas as pd
+import statsformula as sf
+
+df = pd.read_csv("data.csv")
+
+X = sf.model_matrix("Y ~ C(X1):C(X2) + log(X3)/sqrt(X4) + X5**4", df)
+X.columns          # identical to colnames(model.matrix(...)) in R
+X.assign           # attr(, "assign")
+X.contrasts        # attr(, "contrasts")
+
+sf.formula("Y~C(X1):C(X2)+log(X3)/sqrt(X4)+X5**4")
+# <formula: Y ~ C(X1):C(X2) + log(X3)/sqrt(X4) + X5^4>     (R prints exactly this)
+```
+
+## Why
+
+`patsy` and `formulaic` are *inspired by* R formulas but differ in many details (operator
+semantics, contrast coding of interactions without main effects, column names, `C()`, `poly()`
+and spline bases, `.` expansion, `-` / `0` / `1` handling, ...). `statsformula` aims for
+**bit-for-bit agreement with R** so that models, coefficients and code can move between R and
+Python unchanged. Its API borrows from statsmodels (`dmatrices`) and formulaic (`ModelMatrix`,
+`ModelSpec` for applying a fitted design to new data).
+
+## Validation against R
+
+The test-suite compares against results produced by R 4.5.1 (mgcv 1.9-3, Formula 1.2-5,
+Matrix 1.7-3); the fixtures are in `tests/fixtures` and can be regenerated with
+`python tools/make_fixtures.py`, `tools/make_fuzz.py` and `tools/make_fuzz_mm.py` (needs R).
+
+* 367 hand-written cases: `terms` attributes, `model.matrix` values, column names, `assign` and
+  `contrasts`, `sparse.model.matrix`, `model.frame` (NA handling, subset, weights, offset,
+  `drop.unused.levels`), `update`, `reformulate`, `drop.terms`, `delete.response`, the Formula
+  package, prediction on new data, error messages and 41 mgcv smooth models;
+* 500 randomly generated formulas compared with R's `terms()` (2,000 more checked during
+  development);
+* 400 randomly generated formulas compared with R's `model.matrix()`.
+
+Numbers agree to ~1e-12 relative error; names, orderings and attributes are identical.
+
+## Installation
+
+```
+pip install statsformula
+```
+
+Requires Python ≥ 3.10, numpy, pandas and scipy. R is **not** needed.
+
+## What is supported
+
+### Formula operators (exact R semantics)
+
+| syntax | meaning |
+|---|---|
+| `a + b` | both terms |
+| `a:b` | interaction |
+| `a*b` | `a + b + a:b` |
+| `a/b` | nesting, `a + a:b` |
+| `b %in% a` | `b` nested in `a` |
+| `(a + b + c)^2` | all interactions up to order 2 (`**` is accepted and printed as `^`) |
+| `- b`, `- 1`, `+ 0`, `0 +` | remove terms / intercept |
+| `.` | all other columns of `data` |
+| `offset(x)` | offset terms |
+| `I(expr)` | arithmetic inside formulas |
+| `cbind(y1, y2) ~ x` | matrix responses |
+| `y1 | y2 ~ x | z` | multi-part formulas (Formula package) |
+| `` `my var` `` | non-syntactic names |
+
+R's corner cases are reproduced too (`y ~ x^1` is an error, `(-a * b)` drops everything,
+`y ~ 0/x` drops `x`, the response on the right-hand side, terms deduplication and ordering,
+the factor coding heuristic of *Statistical Models in S* for interactions without main effects, ...).
+
+### Functions available inside formulas
+
+* **math:** `log(x, base)`, `log2`, `log10`, `log1p`, `exp`, `expm1`, `sqrt`, `abs`, `sign`,
+  `floor`, `ceiling`, `round`, `signif`, `trunc`, trigonometric and hyperbolic functions,
+  `gamma`, `lgamma`, `beta`, `choose`, `factorial`, `pmin`, `pmax`, `cumsum`, ...
+* **operators:** `+ - * / ^ %% %/%`, comparisons, `& | ! xor`, `%in%`, `ifelse`, `is.na`
+* **summaries:** `mean`, `median`, `sd`, `var`, `sum`, `min`, `max`, `quantile`, `length`
+* **factors:** `factor`, `as.factor`, `ordered`, `relevel`, `droplevels`, `interaction`, `cut`,
+  `C(f, contr, how.many)`
+* **contrasts:** `contr.treatment`, `contr.sum`, `contr.helmert`, `contr.poly`, `contr.SAS`
+  (via `C()`, the `contrasts=` argument or `sf.options(contrasts=...)`)
+* **bases:** `poly(x, degree, raw=)`, multivariate `poly(x, z, degree=)`, `splines::bs`,
+  `splines::ns` (exactly as R, including extrapolation), `scale`, `cbind`
+* **mgcv smooths:** `s()`, `te()`, `ti()` with bases `tp`, `ts`, `cr`, `cs`, `cc`, `ps`, `cp`,
+  `bs`, `re`; numeric, factor and ordered `by=`; `k`, `m`, `bs`, `d`, `knots`
+* **conversions:** `as.numeric`, `as.integer`, `as.character`, `as.logical`, `c`, `rep`, `seq`
+* **your own Python functions:** any function or object visible where you call statsformula
+  (e.g. `center(x)`, `np.log1p(x)`), or registered with `sf.register_function()`.
+
+Data-dependent transformations (`poly`, `bs`, `ns`, `scale`, factor levels, contrasts, mgcv
+smooths) are remembered and re-applied to new data, like R's `predict()`.
+
+### R functions
+
+| R | statsformula |
+|---|---|
+| `formula()`, `as.formula()` | `sf.formula()` → `RFormula` |
+| `terms(f, data, keep.order, specials, simplify)` | `sf.terms()` → `Terms` (`.term_labels`, `.factors`, `.order`, `.intercept`, `.response`, `.offset`, `.variables`, `.specials`) |
+| `model.frame(f, data, subset, na.action, weights, offset, drop.unused.levels, xlev)` | `sf.model_frame()` |
+| `model.matrix(f, data, contrasts.arg, xlev)` | `sf.model_matrix()` |
+| `Matrix::sparse.model.matrix()` | `sf.sparse_model_matrix()` (scipy.sparse CSC) |
+| `model.response`, `model.offset`, `model.weights`, `model.extract` | same names with `_` |
+| `update()` | `sf.update()` (formulas and Formulas) |
+| `reformulate`, `drop.terms`, `delete.response`, `all.vars`, `all.names`, `get_all_vars`, `deparse` | same names with `_` |
+| `Formula::Formula`, `as.Formula`, `model.part`, `formula(F, lhs, rhs, collapse)` | `sf.Formula`, `sf.as_Formula`, `sf.model_part`, `F.formula(lhs=, rhs=, collapse=)` |
+| `mgcv::interpret.gam`, `smoothCon`, `PredictMat`, `model.matrix(gam(...))`, `predict(gam, type = "lpmatrix")` | `sf.interpret_gam`, `sf.smooth_con`, `sf.predict_mat`, `sf.gam_model_matrix`, `X.model_spec.get_model_matrix(new)` |
+| `options(contrasts = ...)`, `options(na.action = ...)` | `sf.options(contrasts=..., na_action=...)` |
+
+### Python conveniences (statsmodels / formulaic style)
+
+```python
+y, X = sf.dmatrices("y ~ x + C(g, sum)", df)        # pandas frames, NA rows removed jointly
+import statsmodels.api as sm
+fit = sm.OLS(y, X).fit()
+
+X = sf.model_matrix("y ~ poly(x, 3) + ns(z, df = 4) + g", train)
+X_test = X.model_spec.get_model_matrix(test)        # same transformation, levels and contrasts
+
+S = sf.sparse_model_matrix("~ user * item", big_df)  # scipy.sparse
+```
+
+## Data types
+
+| pandas / numpy | R equivalent |
+|---|---|
+| `Categorical` (ordered or not) | factor / ordered factor (categories are the levels) |
+| `bool` / nullable `boolean` | logical |
+| integer | integer |
+| float | double (`NaN` is `NA`) |
+| strings / `object` | character (converted to factors by `model.matrix`, as in R) |
+
+String levels are sorted the way R sorts them under ICU collation (macOS/Windows R, and Linux
+R built with ICU). Use `sf.set_collation("C")` to mimic `LC_COLLATE=C`. Unlike R, `C()` and
+`relevel()` also accept character vectors (R would require a factor).
+
+## Differences from R and limitations
+
+* **Thin plate splines (`tp`, `ts`).** mgcv's basis depends on the eigenvector signs from
+  its Lanczos solver, which come from reference LAPACK. statsformula reimplements mgcv's Lanczos
+  iteration, LAPACK `DSTEQR`/`DSTEDC` (including divide and conquer) and R's random number
+  generator (used for knot sampling above 2,000 unique points), so the basis matches R's
+  reference LAPACK build exactly. R linked against a vendor LAPACK (OpenBLAS, MKL, Accelerate)
+  can itself produce a different, equally valid sign convention.
+* **`gam.side()`** (side constraints mgcv adds when smooths share covariates, e.g.
+  `s(x) + te(x, z)`) is not implemented: a warning is issued and the columns can differ from R.
+  Use `ti()` for interaction terms (the mgcv recommendation), which needs no side constraints.
+* mgcv bases not yet available: `t2`, `fs`, `gp`, `ds`, `so`, `mrf`, `ad`, `sos`, `sz`, `re`
+  inside tensor products, smooths with matrix (summation convention) arguments; `id=`, `sp=` and
+  `fx=` only affect penalties, which statsformula does not compute (it builds model matrices).
+* R syntax that is not formula-related (`function`, `if`, assignment) is not supported inside
+  formulas.
+* By default, R's functions take precedence over Python objects of the same name (for example a
+  Python `log` in your namespace does not replace R's `log`); use `sf.register_function(...,
+  override=True)` to change that.
+
+## License
+
+GPL-2.0-or-later. statsformula contains translations of code from R (GPL-2 | GPL-3), mgcv
+(GPL ≥ 2), Formula (GPL-2 | GPL-3) and Matrix (GPL ≥ 2), so it is distributed under the same
+terms. The ported LAPACK routines are BSD-licensed.