Code supplement for "Simple models of non-random mating and environmental transmission bias standard human genetics statistical methods."

Manifest

• ascertainment_sims.py: family GWAS simulations with ascertainment
• ey_sim.py: education years case study simulation
• general_simulations.py: primary simulations incorporating xAM, VT, and/or GxE
• gwas_pwr_t1e.r: computations of on- / off-target assocation power / type i error rates
• pheno_defn_supplement.r: additional phenotype definitions
• psych_cors.csv: inputs for psychiatric disorder simulations
• nhird_cca.r: canonical correlation analysis of NHIRD phenotypes
• nhird_cors.csv: inputs for NHIRD cca
• psychiatric_sims.py: simulations involving psychiatric disorders
• sibdiff.nb: Mathematica notebook for computation of expected sibling-difference GWAS estimates

Final-submission source data (2026)

• final_submission_2026/: verified numerical source data, final artwork and figure-style sources for the final submission. See final_submission_2026/README.txt; SHA256SUMS.txt and MANIFEST.json there identify the exact files. The three *_source_data.zip archives each carry their own README, reproduction code and verification record.

Release v4.3 corrects source-data documentation, phenotype field mappings and portable paths. Extended Data Figure 10 now uses the original four-scenario processed export matching the submitted figure; see the source correction note.