dlnm 0.1.0

Distributed Lag Non-Linear Models for Python

PyDLNM — Distributed Lag Non-Linear Models for Python

CI PyPI version Python License: GPL v2+

A Python implementation of Distributed Lag Non-Linear Models (DLNMs), based on the widely-used R package [dlnm](https://github.com/gasparrini/dlnm) by Antonio Gasparrini, Ben Armstrong, and Fabian Scheipl.

DLNMs are a modelling framework for describing simultaneously the non-linear and delayed effects of exposures on health outcomes. They are extensively used in environmental epidemiology, pharmacology, and other fields studying lagged exposure-response relationships.

Attribution

This package is a Python port of the original R package:

Gasparrini A. Distributed lag linear and non-linear models in R: the package dlnm. Journal of Statistical Software. 2011; 43(8):1–20. doi:10.18637/jss.v043.i08

Original R source code: https://github.com/gasparrini/dlnm

All core algorithms and methodology are from the original R implementation. If you use this package in academic work, please cite the original publication. Acknowledging this Python adaptation in your citations is also appreciated.

Installation

pip install dlnm

For development:

git clone https://github.com/Victorivus/PyDLNM.git
cd PyDLNM
pip install -e ".[dev]"

Quick Start

import numpy as np
import statsmodels.api as sm
from dlnm import crossbasis, crosspred, logknots, load_chicagoNMMAPS

# Load example data (Chicago NMMAPS)
df = load_chicagoNMMAPS()

# Define the cross-basis for temperature with 21-day lag
lknots = logknots(21, nk=3)
cb_temp = crossbasis(
    df["temp"].values,
    lag=21,
    argvar={"fun": "ns", "df": 4},
    arglag={"fun": "ns", "knots": lknots},
)

# Fit a model (e.g., quasi-Poisson GLM)
# Build design matrix with cross-basis + covariates
time = df["time"].values
X = np.column_stack([np.ones(len(df)), cb_temp, time])
y = df["death"].values

# Use coefficients and vcov directly
# (or extract from a fitted statsmodels model)

Features

Basis Functions

Function	Description
ns	Natural cubic splines
bs	B-splines
ps	P-splines (penalised B-splines)
cr	Natural cubic regression splines (with penalty)
strata	Indicator (dummy) variables
thr	Threshold / hockey-stick
integer	Categorical coding for integer values
lin	Simple linear term
poly	Scaled polynomial basis

Core Functions

• **onebasis(x, fun, ...)** — Create a single-dimension basis matrix
• **crossbasis(x, lag, argvar, arglag)** — Create a cross-basis matrix (tensor product of variable and lag bases)
• **crosspred(basis, model, ...)** — Compute predictions (lag-specific, overall, cumulative)
• **crossreduce(basis, model, type, ...)** — Reduce to uni-dimensional summaries

Utilities

• **logknots(x, nk)** — Log-spaced knot placement (ideal for lag dimension)
• **equalknots(x, nk)** — Equally-spaced knot placement
• **exphist(exp, times, lag)** — Build exposure history matrices
• **cb_pen(cb)** — Penalty matrices for penalised regression

Plotting

• **plot_crosspred(pred, ptype)** — 3D surfaces, contour plots, slices, overall effects
• **plot_crossreduce(red)** — Plot reduced uni-dimensional associations

Datasets

• **load_chicagoNMMAPS()** — Daily mortality/weather/pollution data, Chicago 1987–2000
• **load_drug()** — Simulated RCT with time-varying drug doses
• **load_nested()** — Simulated nested case-control study

Usage Examples

Exposure-Response at a Specific Lag

from dlnm import crossbasis, crosspred, plot_crosspred

# After fitting a model...
pred = crosspred(cb, coef=coef, vcov=vcov, at=np.arange(-20, 35), cen=21)
fig = plot_crosspred(pred, ptype="slices", lag=0)  # Exposure-response at lag 0

Lag-Response at a Specific Exposure

fig = plot_crosspred(pred, ptype="slices", var=30)  # Lag-response at 30°C

3D Surface Plot

fig = plot_crosspred(pred, ptype="3d")

Overall Cumulative Effect

fig = plot_crosspred(pred, ptype="overall")

Reduced to One Dimension

from dlnm import crossreduce, plot_crossreduce

# Overall cumulative exposure-response
red_overall = crossreduce(cb, coef=coef, vcov=vcov, type="overall", cen=21)
fig = plot_crossreduce(red_overall)

# Lag-response at a specific exposure value
red_var = crossreduce(cb, coef=coef, vcov=vcov, type="var", value=30, cen=21)
fig = plot_crossreduce(red_var)

R Compatibility Notes

PyDLNM is designed to produce results numerically identical to R's dlnm package (within floating-point tolerance). Several non-obvious implementation choices were required to match R's behaviour exactly. These are documented here for maintainers and contributors.

1. Natural spline basis — linear extrapolation outside boundary knots

Location: [src/dlnm/basis.py](src/dlnm/basis.py), _ns_basis()

R's splines::ns() extrapolates linearly beyond the boundary knots (zero second derivative, by the natural spline constraint). scipy's BSpline(extrapolate=True) continues the cubic polynomial instead, producing completely different values outside the boundary. This matters whenever prediction points fall outside the training data range (a common case for crosspred).

Fix: After computing the B-spline basis values, points outside [boundary_knots[0], boundary_knots[1]] are replaced with a linear extrapolation anchored at the boundary value and first derivative:

if left_mask.any():
    val_l  = spl(boundary_knots[0])
    slope_l = spl(boundary_knots[0], 1)
    basis[left_mask, i] = val_l + slope_l * (x[left_mask] - boundary_knots[0])

2. Natural spline basis — intercept=False constraint row

Location: [src/dlnm/basis.py](src/dlnm/basis.py), _ns_basis()

R excludes the "intercept" B-spline (B-spline 0, the leftmost) by adding the unit vector e0 = [1, 0, 0, …] as a third constraint row before the QR null-space projection, not an all-ones row.

Fix:

if not intercept:
    e0 = np.zeros((1, n_basis))
    e0[0, 0] = 1.0
    const = np.vstack([const, e0])

3. crosspred — prediction grid ordering (varvec / lagvec)

Location: [src/dlnm/crosspred.py](src/dlnm/crosspred.py), _mkXpred()

R builds the flat prediction vector as rep(predvar, length(predlag)) (the full predvar sequence repeated once per lag) with lagvec = rep(predlag, each=length(predvar)). This means predvar varies fastest (inner loop), predlag slowest (outer loop). The opposite ordering breaks both the allfit accumulation loop and the matfit reshape.

Fix:

varvec = np.tile(predvar, len(predlag))       # predvar repeats for each lag
lagvec = np.repeat(predlag, len(predvar))     # each lag repeated len(predvar) times

4. crosspred — matfit / matse reshape order

Location: [src/dlnm/crosspred.py](src/dlnm/crosspred.py), crosspred()

With the corrected predvar-fastest ordering (point 3), the flat Xpred @ coef vector is laid out as [predvar@lag0, predvar@lag1, …]. Reshaping it directly as (n_pred, n_lag) gives the wrong column assignments. The correct reshape matches R's column-major (Fortran-order) matrix filling:

matfit = (Xpred @ coef).reshape(len(predlag), len(predvar)).T
matse  = np.sqrt(...).reshape(len(predlag), len(predvar)).T

5. Generating R golden-reference fixtures

The test suite compares Python output against fixtures produced by R. To regenerate them, run the script from the PyDLNM repository root:

Rscript tests/fixtures/generate_fixtures.R

On Windows, Rscript may not be in PATH. Use the full path:

Rscript tests\fixtures\generate_fixtures.R

---

Differences from the R Package

Feature	R dlnm	Python dlnm
Model fitting	Integrated with glm, gam, coxph, etc.	Works with statsmodels or manual coef/vcov
Penalised smoothing	Via mgcv::gam	Penalty matrices provided via cb_pen()
Plotting	Base R graphics	matplotlib
S3 classes	crossbasis, crosspred, etc.	Python dataclasses and numpy.ndarray subclasses
Function naming	crossbasis, crosspred	Same names, snake_case helpers (cb_pen, plot_crosspred)

Dependencies

• NumPy >= 1.22
• SciPy >= 1.9
• pandas >= 1.5
• matplotlib >= 3.5
• patsy >= 0.5
• statsmodels >= 0.13

Development

# Run tests
pytest

# Run tests with coverage
pytest --cov=dlnm --cov-report=html

# Lint
ruff check src/ tests/

# Type check
mypy src/dlnm/

References

1. Gasparrini A. Distributed lag linear and non-linear models in R: the package dlnm. Journal of Statistical Software. 2011; 43(8):1–20. doi:10.18637/jss.v043.i08
2. Gasparrini A, Armstrong B, Kenward MG. Distributed lag non-linear models. Statistics in Medicine. 2010; 29(21):2224–2234. doi:10.1002/sim.3940
3. Gasparrini A. Modeling exposure-lag-response associations with distributed lag non-linear models. Statistics in Medicine. 2014; 33(5):881–899. doi:10.1002/sim.5963

License

GPL-2.0-or-later — same as the original R package.