metrics-adjuster 1.0.1

Adjusted group-aware clinical prediction metrics with Python API and CLI.

metrics-adjuster

metrics-adjuster computes conventional and adjusted group-aware metrics for binary prediction models. It provides a typed Python API, a command-line interface, and an end-to-end synthetic demo for users who want to validate the workflow before running it on their own data.

The codebase is organized around a small functional core: IO lives at the boundaries, public options are captured in typed configuration objects, and tests describe the expected contracts for validation and output shape.

What it computes

For each requested adjusted metric, the package now returns the conventional metric and adjusted metric side by side:

Output file/key	Conventional column	Adjusted column
aTPR	TPR	aTPR
aPPV	PPV	aPPV
aNB	NB	aNB
aHR	HR	aHR

Metrics are computed by group across caller-selected risk-score quantiles. The main pipeline is:

1. validate typed configuration and input columns
2. calibrate predicted risk within groups
3. estimate density ratios against a reference group
4. compute conventional and adjusted metrics at risk thresholds
5. optionally bootstrap adjusted-metric uncertainty summaries
6. optionally render a self-contained HTML report with tables and plots
7. return metric tables through the API or write one CSV per metric through the CLI

Installation

Released versions are on PyPI (Python 3.11+).

python -m pip install metrics-adjuster

That installs both the CLI and the Python API. Parquet input works out of the box (pyarrow is included).

Other setups:

• uv project: uv add metrics-adjuster
• CLI only: pipx install metrics-adjuster
• conda or mamba env: run the pip command above inside your activated environment
• pinned release: python -m pip install "metrics-adjuster==1.0.1"

From source

For checkout-based development, see Development.

To install the latest main branch from GitHub:

python -m pip install "metrics-adjuster @ git+https://github.com/SaehwanPark/metrics-adjuster.git"

In a uv project:

uv add "metrics-adjuster @ git+https://github.com/SaehwanPark/metrics-adjuster.git"

Python API

from metrics_adjuster import (
  CalibrationConfig,
  ColumnSpec,
  DensityRatioConfig,
  MetricConfig,
  MetricName,
  adjusted_metrics,
)
from metrics_adjuster.synthetic import generate_synthetic_metrics_data

frame = generate_synthetic_metrics_data(n=600, seed=2026)
config = MetricConfig(
  columns=ColumnSpec(
    group="group",
    response="outcome",
    risk="risk",
    id="patient_id",
  ),
  ref_group="ref",
  quantiles=(0.2, 0.4, 0.6, 0.8),
  metrics=tuple(MetricName),
  calibration=CalibrationConfig(degree=2, cv=False),
  density_ratio=DensityRatioConfig(degree=1, cv=False),
  random_state=2026,
)

result = adjusted_metrics(frame, config)
print(result.metrics["aTPR"])

For an end-user report, call adjusted_metrics_report(...):

from metrics_adjuster import ReportConfig, ReportLabelConfig, adjusted_metrics_report

bundle = adjusted_metrics_report(
  frame,
  config,
  ReportConfig(
    title="Adjusted metrics report",
    x_scale="log_odds",
    labels=ReportLabelConfig(
      columns={"group": "Cohort group"},
      groups={"group": {"ref": "Reference group"}},
      metrics={"aTPR": "True positive rate"},
    ),
  ),
)
html = bundle.html
table = bundle.metric_table

result.metrics["aTPR"] contains columns like:

group,quantile,tau,TPR,aTPR

The return value is a MetricFrames object containing:

• metrics: a dictionary from adjusted metric name to pandas.DataFrame
• bootstrap: optional raw long-form bootstrap records when bootstrapping is enabled
• as_dict(): a compatibility-shaped dictionary for older integrations

Compatibility API

Existing callers can keep using the previous function-style entry point:

from metrics_adjuster import compute_adjusted_metrics
from metrics_adjuster.synthetic import generate_synthetic_metrics_data

frame = generate_synthetic_metrics_data(n=600, seed=2026)
result = compute_adjusted_metrics(
  df=frame,
  idvar="patient_id",
  group_col="group",
  ref_group="ref",
  response_col="outcome",
  orig_risk_col="risk",
  metrics=["aTPR"],
  quantiles=[0.2, 0.4, 0.6, 0.8],
  random_state=2026,
)

Historical import shims from the private development repository are preserved under legacy/ for migration research only and are not part of the supported v1 package.

CLI

Run the built-in synthetic demo:

uv run metrics-adjuster demo --output-dir demo_outputs

By default, the CLI computes aTPR. Pass --metrics aTPR,aPPV,aNB,aHR when you want every supported metric.

Run on your own CSV or Parquet file:

uv run metrics-adjuster run \
  --input path/to/input.csv \
  --output-dir adjusted_metric_outputs \
  --group-col group \
  --ref-group ref \
  --response-col outcome \
  --risk-col risk \
  --id-col patient_id \
  --quantiles 0.2,0.4,0.6,0.8 \
  --metrics aTPR,aPPV,aNB,aHR \
  --seed 2026

The CLI writes one CSV per adjusted metric, such as aTPR.csv and aPPV.csv. Each file includes the conventional companion column as well as the adjusted metric column.

Add --report to write a self-contained report.html with compact metric tables, calibrated probability density plots, and densities normalized to the reference group:

uv run metrics-adjuster run \
  --input path/to/input.csv \
  --output-dir adjusted_metric_outputs \
  --group-col group \
  --ref-group ref \
  --response-col outcome \
  --risk-col risk \
  --report \
  --report-title "Adjusted metrics report" \
  --report-config-yaml path/to/report.yml

The optional report YAML can provide human-friendly display names and choose plot x-axis scaling:

x_scale: log_odds
labels:
  columns:
    Prior1245: Veteran Priority Group
  groups:
    Prior1245:
      "0": Default Priority
      "99": Priority Group 5
  metrics:
    aTPR: True positive rate

Without uv, use the same commands after installing the package, but drop the uv run prefix.

Numeric reference groups are supported through the public CLI. For example, --ref-group 0 will match an integer-valued group column such as Prior1245.

Required input columns

Your input table must include:

• a group column, such as group, sex, or race
• a binary outcome column encoded as 0 and 1
• a predicted risk/probability column
• optionally, a stable identifier column

The reference group named by ref_group must be present in the group column.

End-to-end integration demo

The demo script is intentionally outside src/ so it remains a runnable example rather than package code:

uv run python scripts/run_synthetic_integration.py \
  --output-dir demo_outputs \
  --n 600 \
  --seed 2026

It writes:

• synthetic_metrics_data.csv
• aTPR.csv with TPR and aTPR
• additional metric CSVs only when --metrics requests them

Sampled real-data evaluation

For a bounded real-data report review, first prepare an ignored sampled input:

uv run python scripts/prepare_sampled_report_input.py \
  --input /path/to/input.parquet \
  --output-dir data/generated/va-can-2019-prior1245-hosp1y-sample50k \
  --group-col Prior1245 \
  --ref-group 0 \
  --response-col Hosp_1y \
  --risk-col pHosp_1y \
  --sample-size 50000 \
  --bootstrap-iterations 25 \
  --seed 20260521 \
  --report-config-yaml scripts/va_can_report_config.yml

Then reproduce the report through the public CLI:

uv run metrics-adjuster run \
  --input data/generated/va-can-2019-prior1245-hosp1y-sample50k/sample.parquet \
  --output-dir results/va-can-2019-prior1245-hosp1y-sample50k \
  --group-col Prior1245 \
  --ref-group 0 \
  --response-col Hosp_1y \
  --risk-col pHosp_1y \
  --quantiles 0.1,0.3,0.5,0.7,0.9 \
  --metrics aTPR,aPPV,aNB,aHR \
  --bootstrap \
  --n-boot 25 \
  --seed 20260521 \
  --report \
  --report-config-yaml scripts/va_can_report_config.yml

The preparation script reads only the required columns, samples rows deterministically, writes row-level data under ignored data/generated/, and records copy-pasteable commands in its README. Metric CSVs, bootstrap.csv, and report.html are produced only by metrics-adjuster run. By default, the generated CLI report command mirrors the generated-data path under results/; pass --report-output-dir to the preparation script to record a different report destination.

Full user manuals

• API Manual
• CLI Manual

Development

Preferred setup:

uv sync --extra dev

Common checks:

uv run pytest
uv run ruff check .
uv run mypy src/metrics_adjuster