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Add NHANES covariate sampling method#3

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roninsightrx merged 13 commits intomainfrom
add-nhanes-sampling
Mar 11, 2026
Merged

Add NHANES covariate sampling method#3
roninsightrx merged 13 commits intomainfrom
add-nhanes-sampling

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@roninsightrx roninsightrx commented Mar 5, 2026

Summary

  • Adds sample_covariates_nhanes() to sample clinical trial subjects from the NHANES database using the nhanesA package
  • Supports downloading and merging multiple NHANES tables (joined on SEQN), with conditional filtering and variable selection — the same interface as the existing bootstrap, mice, and mvtnorm methods
  • Optional probability-proportional sampling via NHANES survey weights (WTMEC2YR, use_weights = TRUE) for population-representative samples
  • Survey year "2017-2018" is the default; all cycles from 1999–2020 are supported
  • nhanesA added to Suggests (checked at runtime, not a hard dependency)
  • "nhanes" added to the method argument of the top-level sample_covariates() dispatcher

Test plan

  • test-sample_covariates_nhanes.R covers: correct row count, SEQN dropped from output, variables selection, missing-variable error, single/multi-variable conditional filtering, empty-filter error, use_weights sampling, missing-weight error, unsupported year, single-table case, and dispatcher routing
  • All tests mock nhanesA::nhanes() so no network access is required during R CMD check
  • Run devtools::test() locally to confirm all tests pass

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@roninsightrx @claude
Add NHANES covariate sampling method
5ca77fa 
Adds `sample_covariates_nhanes()` to sample clinical trial subjects from
the NHANES database via the nhanesA package. Supports multi-table merging,
conditional filtering, variable selection, and optional probability-proportional
sampling using NHANES survey weights (WTMEC2YR).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Copilot AI reviewed Mar 6, 2026
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Pull request overview

Adds a new NHANES-backed covariate sampling implementation to the existing sample_covariates() family, enabling sampling from downloaded/merged NHANES tables with optional survey-weighted sampling.

Changes:

  • Adds sample_covariates_nhanes() to download, join (by SEQN), filter, and sample from NHANES tables (optionally using WTMEC2YR weights).
  • Extends the sample_covariates() dispatcher to accept method = "nhanes".
  • Adds nhanesA to Suggests and introduces a dedicated test suite for NHANES sampling (with nhanesA::nhanes() mocked).

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 6 comments.

File Description
R/sample_covariates_nhanes.R Implements NHANES download/join/filter/sample logic and year-to-suffix mapping.
R/sample_covariates.R Adds "nhanes" to the dispatcher’s method argument and updates roxygen docs.
DESCRIPTION Adds nhanesA to Suggests.
tests/testthat/test-sample_covariates_nhanes.R Adds tests covering NHANES sampling behavior and dispatcher routing.

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@roninsightrx @claude
Add offline NHANES cache: download_nhanes_cache() and cache_dir param
c14d866 
Adds download_nhanes_cache() to pre-download NHANES tables as local RDS
files. sample_covariates_nhanes() gains a cache_dir parameter that loads
from those files instead of downloading, removing the need for nhanesA or
internet access at sampling time.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@roninsightrx roninsightrx marked this pull request as draft March 6, 2026 07:43
roninsightrx and others added 8 commits March 9, 2026 15:17
@roninsightrx @claude
Auto-download NHANES cache on package load
95403f9 
On first load, .onLoad() downloads DEMO and BMX (2017-2018) into a cache
inside the package installation directory. sample_covariates_nhanes() now
defaults cache_dir to that location, so no internet access is needed for
subsequent calls. Cache misses fall back to nhanesA rather than erroring.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@roninsightrx @claude
Redesign NHANES interface: merged cache and covariates argument
68761c0 
download_nhanes_cache() now takes `groups` (DEMO/LAB/EXAM) instead of
individual table names, downloads all tables in each group via
nhanesTables(), and saves a single merged nhanes_<year>.rds per year.

sample_covariates_nhanes() replaces the `tables` argument with `covariates`
(column selection from the merged data) and loads the pre-merged RDS.
.onLoad() downloads DEMO+LAB+EXAM for 2017-2018 on first package load.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@roninsightrx @claude
Add NHANES covariate reference table to sample_covariates_nhanes() docs
9902d2c 
Lists key measurement variables from DEMO_J, BMX_J, BPX_J, GHB_J,
BIOPRO_J, CBC_J, TCHOL_J, HDL_J, TRIGLY_J, and ALB_CR_J with
descriptions sourced from the CDC NHANES 2017-2018 data documentation.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@roninsightrx @claude
Add dictionary argument to sample_covariates_nhanes()
1e7483a 
Allows users to map their own covariate names to NHANES variable names,
e.g. dictionary = list("WT" = "BMXWT", "AGE" = "RIDAGEYR"). Translation
applies to both covariates selection and conditional filtering keys;
output columns are returned under the user-defined names.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@roninsightrx
update docs
cfd92f7
@roninsightrx @claude
Fix failing tests: tempdir scoping, duplicate-SEQN warning, onLoad mo…
45aa906 
…cking

- nhanes_temp_cache(): pass parent.frame() to local_tempdir() so the
  temp dir lives for the duration of the calling test, not just the helper
- Duplicate-SEQN test: expect the "No tables downloaded" warning that the
  function correctly emits when every table is skipped
- .onLoad tests: split local_mocked_bindings into two calls so that
  nhanes_default_cache_dir is mocked in irxforge (not nhanesA)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@roninsightrx @claude
Fix dictionary test: add BMXHT to mock_nhanes
8bf53da 
The test mapped "HT" -> "BMXHT" via dictionary but mock_nhanes did not
contain a BMXHT column, causing a "Covariates not found" error in CI.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@roninsightrx @claude
Add seed argument to all sample_covariates_* functions
0e34db6 
Each function now accepts seed = NULL; when non-NULL, set.seed() is called
at the top of the function body so results are fully reproducible.
sample_covariates() also gains seed and passes it explicitly to the
dispatched child function.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@roninsightrx roninsightrx marked this pull request as ready for review March 10, 2026 04:04
roninsightrx and others added 3 commits March 9, 2026 21:15
@roninsightrx @claude
Add rm.na argument to drop NA rows before sampling
455efd6 
Both sample_covariates_nhanes() and sample_covariates_bootstrap() now
accept rm.na = TRUE (default), which filters out rows containing NA in
any of the requested covariates before sampling.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@roninsightrx
rm NAs + add docs
da690d2
@roninsightrx
update default
a8a66b6
@roninsightrx roninsightrx merged commit b2857e3 into main Mar 11, 2026
3 checks passed
@roninsightrx roninsightrx deleted the add-nhanes-sampling branch March 11, 2026 04:23
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