robustmargin 0.1.1__tar.gz

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robustmargin-0.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: robustmargin
+Version: 0.1.1
+Summary: Robustness margins with confidence intervals, via dose-response threshold estimation.
+Author: robustmargin contributors
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/robustmargin/robustmargin
+Project-URL: Source, https://github.com/robustmargin/robustmargin
+Project-URL: Issues, https://github.com/robustmargin/robustmargin/issues
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Typing :: Typed
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.26
+Requires-Dist: scipy>=1.11.1
+Requires-Dist: statsmodels>=0.14
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: pytest-cov>=5.0; extra == "dev"
+Requires-Dist: hypothesis>=6.100; extra == "dev"
+Requires-Dist: ruff>=0.5; extra == "dev"
+Requires-Dist: mypy>=1.10; extra == "dev"
+Requires-Dist: pre-commit>=3.5; extra == "dev"
+Requires-Dist: jsonschema>=4.20; extra == "dev"
+Dynamic: license-file
+
+# robustmargin
+Robustness margins with confidence intervals, via dose-response threshold estimation. Model-agnostic — no GPU, no ML framework required
+
+> **Status: latest release `0.1.1`.** Binomial dose-response fits, thresholds with profile-likelihood or delta
+> confidence intervals, censoring, ratios of two thresholds with Fieller or log-delta intervals,
+> fit diagnostics, and the grid break-point rule. Continuous outcomes, clustered and paired
+> inference, and design helpers are planned for `0.2`. While the version is below 1.0, a minor
+> release may change the public API.
+
+## What it does
+
+You test a system at increasing levels of some stress (the *severity*) and count successes at
+each level. robustmargin fits a dose-response curve to those counts and reports the severity at
+which performance crosses a level you choose, with a confidence interval. When the data cannot
+support a number, it says so: a threshold beyond the tested range is censored and reported as a
+bound, and a failed fit carries a status flag and no estimate.
+
+## Install
+
+Requires Python 3.11 or later.
+
+```bash
+pip install robustmargin
+```
+
+Runtime dependencies are `numpy`, `scipy`, and `statsmodels`, with loose minimum versions.
+
+## Worked example
+
+Finney's (1971) toxicity data: groups of insects exposed to increasing doses, with the number
+affected in each group. The outcome here is survival, which decreases with dose. The dose-0 group
+is an untreated control.
+
+```python
+from robustmargin import (
+    Axis,
+    Censoring,
+    Definition,
+    Observations,
+    Status,
+    fit_dose_response,
+    threshold,
+)
+
+dose = [0.0, 2.6, 3.8, 5.1, 7.7, 10.2]
+affected = [0, 6, 16, 24, 42, 44]
+total = [49, 50, 48, 46, 49, 50]
+
+obs = Observations.from_counts(
+    Axis(name="dose", unit="mg", scale="log"),
+    severity=dose,
+    successes=[n - a for n, a in zip(total, affected, strict=True)],
+    trials=total,
+    outcome="survival",
+    direction="decreasing",
+)
+
+# The link and the asymptotes are chosen before looking at the data; nothing is auto-selected.
+fit = fit_dose_response(obs, model="binomial", link="probit", upper=1.0, lower=0.0)
+assert fit.status is Status.OK
+
+# The dose at which survival falls to 50%, with a 95% profile-likelihood interval.
+t50 = threshold(fit, definition=Definition.absolute(0.5), interval_method="profile", level=0.95)
+assert t50.censoring is Censoring.NONE
+assert abs(t50.value - 4.85) < 0.01
+assert 4.3 < t50.lo < t50.value < t50.hi < 5.4
+
+# A successful fit carries goodness-of-fit diagnostics, and every fit, failed or not, carries a
+# monotonicity check on the raw counts. Both are reported and never acted on: nothing is
+# rescaled, and the link you chose is never swapped for a better-scoring one.
+diag = fit.diagnostics
+assert diag.df == 3  # five dosed groups, two estimated parameters
+assert diag.dispersion < 1.5  # no sign of overdispersion
+assert set(diag.link_aic) == {"probit", "logit", "cloglog"}
+assert not fit.monotonicity.any_flagged  # survival never rises between adjacent doses
+```
+
+### Comparing two curves
+
+Two curves from the `selenium` data: survival against concentration for two forms of a
+compound. `baseline_fraction(0.5)` asks where survival falls to half of what the control group
+achieves, and the upper asymptote is estimated rather than fixed at 1. The second form shows
+what the diagnostics are for.
+
+```python
+from robustmargin import (
+    Axis,
+    Definition,
+    Observations,
+    fit_dose_response,
+    ratio_interval,
+    threshold,
+)
+
+conc = [0.0, 100.0, 200.0, 300.0, 400.0, 500.0]
+curves = {
+    "form_a": ([151, 146, 116, 159, 150, 140], [3, 40, 31, 85, 102, 112]),
+    "form_b": ([141, 153, 142, 139, 154, 155], [2, 30, 59, 82, 62, 85]),
+}
+
+thresholds = {}
+fits = {}
+for name, (total, dead) in curves.items():
+    obs = Observations.from_counts(
+        Axis(name="concentration", unit="ug/L", scale="log"),
+        severity=conc,
+        successes=[n - d for n, d in zip(total, dead, strict=True)],
+        trials=total,
+        outcome="survival",
+        direction="decreasing",
+    )
+    fits[name] = fit_dose_response(
+        obs, model="binomial", link="probit", upper="estimate", lower=0.0
+    )
+    thresholds[name] = threshold(
+        fits[name],
+        definition=Definition.baseline_fraction(0.5),
+        interval_method="profile",
+        level=0.95,
+    )
+
+ratio = ratio_interval(
+    thresholds["form_a"], thresholds["form_b"], method="fieller", dependence="independent"
+)
+assert 0.5 < ratio.lo < ratio.estimate < ratio.hi < 0.9  # form_a fails at a lower concentration
+
+# form_b is where diagnostics earn their place: survival rises from 300 to 400, more than chance
+# allows, and the groups vary far more than a binomial model expects. Both are reported on the
+# fit. The reversal is also repeated as a warning on every threshold and ratio built from it.
+# Neither changes a number.
+form_b = fits["form_b"]
+flagged = [(p.severity_low, p.severity_high) for p in form_b.monotonicity.pairs if p.flagged]
+assert flagged == [(300.0, 400.0)]
+assert form_b.diagnostics.dispersion > 1.5
+assert any(w.startswith("OVERDISPERSED: ") for w in form_b.diagnostics.warnings)
+assert any(w.startswith("NON_MONOTONE_DATA: ") for w in ratio.warnings)
+```
+
+Treat an overdispersed fit's intervals as too narrow. Clustered inference, which addresses this,
+is planned for `0.2`.
+
+## Grid break-point rule
+
+`grid_break_point` finds the smallest tested severity at which observed performance falls
+strictly below a criterion. It reports an **observed grid statistic, not an estimated
+threshold**. The reported value is always one of the severities you tested. It is never
+interpolated, and it has no confidence interval.
+
+
+```python
+from robustmargin import Censoring, grid_break_point
+
+severity = [0.0, 0.5, 1.0, 2.0, 4.0]
+performance = [1.0, 0.98, 0.96, 0.91, 0.40]  # e.g. success rate at each level
+
+result = grid_break_point(severity, performance, criterion=0.95)
+assert result.value == 2.0  # first tested level strictly below 0.95
+assert result.max_tested == 4.0
+assert result.censoring is Censoring.NONE
+```
+
+When no tested level fails, there is no value. The result is right-censored and records how far
+testing went, so it reads as "held up to 2.0", never as "cannot fail":
+
+```python
+from robustmargin import Censoring, grid_break_point
+
+held = grid_break_point([0.0, 1.0, 2.0], [1.0, 0.99, 0.97], criterion=0.95)
+assert held.value is None
+assert held.max_tested == 2.0
+assert held.censoring is Censoring.RIGHT
+```
+
+On a signed axis, pass `signed=True`. The rule then breaks on magnitude, on whichever side fails
+first:
+
+```python
+from robustmargin import grid_break_point
+
+signed = grid_break_point(
+    [-0.2, -0.1, 0.0, 0.1, 0.2],
+    [0.05, 0.77, 0.99, 0.33, 0.0],
+    criterion=0.95,
+    signed=True,
+)
+assert signed.value == 0.1
+assert signed.max_tested == 0.2
+```
+
+Some points about the rule:
+
+- A level sitting exactly on the criterion passes. Only `performance < criterion` fails.
+- Monotonicity is neither assumed nor checked, and nothing is pooled or fitted.
+- Invalid input raises `ValueError` rather than returning a placeholder. That covers empty or
+  mismatched arrays, non-finite values, and negative severities without `signed=True`.
+
+## Results and JSON
+
+Every result is a frozen dataclass carrying a `schema_version` and a `provenance` mapping.
+`provenance` records where the inputs came from; robustmargin stores it and never interprets it.
+
+- `GridBreakPoint` is what `grid_break_point` returns.
+- `Fit`, `Threshold` and `Ratio` are what `fit_dose_response`, `threshold` and `ratio_interval`
+  return. They check their own consistency when constructed. For example, a failed fit cannot
+  carry parameters, and a censored threshold cannot carry a point estimate.
+
+Results are collected in a `Scorecard` and written to JSON with `robustmargin.report`:
+
+```python
+import json
+
+from robustmargin import Scorecard, grid_break_point
+from robustmargin.report import from_dict, load_schema, to_dict
+
+held = grid_break_point([0.0, 1.0, 2.0], [1.0, 0.99, 0.97], criterion=0.95)
+card = Scorecard(results=(held,), provenance={"run": "example"})
+
+text = json.dumps(to_dict(card), allow_nan=False)
+assert from_dict(json.loads(text)) == card
+assert load_schema()["$schema"] == "https://json-schema.org/draft/2020-12/schema"
+```
+
+The JSON follows `schema/scorecard-v1.json`, a JSON Schema shipped inside the package. It
+covers binary outcomes only, and reading is strict: a card with fields this version does not know
+is rejected, not silently trimmed. To read a stored card, use a robustmargin at least as new as the
+one that wrote it. The card's `library_version` field records which version that was.
+
+For your own tests, `robustmargin.testing` provides `fake_fit`, `fake_threshold` and `fake_ratio`.
+They return schema-valid results in every status and censoring state, and each is labelled as a
+fake rather than an estimate.
+
+## Development
+
+```bash
+pip install -e ".[dev]"
+ruff check . && ruff format --check .
+mypy
+pytest            # enforces 90% branch coverage
+```
+
+CI runs the tests on Python 3.11, 3.12, and 3.13 against current dependencies. It also runs them
+on Python 3.11 against the oldest supported versions, pinned in
+[`ci/constraints-min.txt`](https://github.com/robustmargin/robustmargin/blob/main/ci/constraints-min.txt).
+
+## License
+
+Apache-2.0. See [`LICENSE`](https://github.com/robustmargin/robustmargin/blob/main/LICENSE).