{
  "script": "09_rda.Rmd",
  "date": "2026-10-03T12:53:48Z",
  "runtime_seconds": 502.5,
  "parameters": {
    "predictors": ["temp_summer_mean", "sal_range", "chl_summer_mean"],
    "geography": "dbMEM 1-2 (step 08)",
    "structure": "population means of PCAngsd PC1 and PC2 (step 06)",
    "permutations": 999,
    "seed": 42,
    "min_maf": 0.05,
    "allele_frequencies": "EM on genotype likelihoods per population (ANGSD Beagle, step 06)",
    "individual_dosages": "posterior mean under HWE at the all-sample frequency",
    "outlier_test": "robust (MCD) Mahalanobis on constrained-axis loadings, median-rescaled chi-square, BH q-values",
    "slurm": {
      "account": "coenv",
      "python_jobs": "cpu-g2",
      "r_jobs": "compute"
    },
    "container": "/mmfs1/gscratch/srlab/containers/srlab-R4.4-bioinformatics-container-46b5d9e.sif"
  },
  "inputs": ["output/06_angsd_structure/gl/NNN_*.beagle.gz", "output/06_angsd_structure/samples/samples.tsv", "output/06_angsd_structure/tables/pca_scores.tsv", "output/08_environmental_predictors/tables/site-env-matrix.tsv"],
  "sets": {
    "env": {
      "n_units": 14,
      "n_snp": 7263864,
      "rank": 13
    },
    "all": {
      "n_units": 15,
      "n_snp": 7373591,
      "rank": 14
    },
    "env_merge_fidalgo": {
      "n_units": 13,
      "n_snp": 7269414,
      "rank": 12
    },
    "individual": {
      "set": "env",
      "n_individuals": 102,
      "n_snp": 7418858,
      "rank": 101
    }
  },
  "outlier_scan": {
    "set": "env",
    "n_axes": 3,
    "n_snp": 7263864,
    "n_q_lt_0.05": 0,
    "n_q_lt_0.10": 0,
    "n_q_lt_0.20": 0,
    "min_q": 0.9797,
    "median_p": 0.5,
    "inflation": 2.3541,
    "mcd_subsample": 50000
  },
  "software": {
    "R": "R version 4.4.3 (2025-02-28)",
    "vegan": "2.7.5",
    "python": {
      "python": "3.13.15",
      "numpy": "2.5.3",
      "pandas": "3.0.6"
    }
  },
  "outputs": {
    "inputs": ["output/09_rda/inputs/all-pcoa.tsv", "output/09_rda/inputs/env-pcoa.tsv", "output/09_rda/inputs/env_merge_fidalgo-pcoa.tsv", "output/09_rda/inputs/individual-pcoa.tsv", "output/09_rda/inputs/population-sets.tsv", "output/09_rda/inputs/reduce-metadata.json"],
    "tables": ["output/09_rda/tables/axis-unit-scores.tsv", "output/09_rda/tables/forward-selection.tsv", "output/09_rda/tables/individual-level-tests.tsv", "output/09_rda/tables/individual-permutation-null.tsv", "output/09_rda/tables/manhattan-thinned.tsv.gz", "output/09_rda/tables/outlier-summary.tsv", "output/09_rda/tables/outlier-top-loci.tsv", "output/09_rda/tables/rda-biplot-scores.tsv", "output/09_rda/tables/rda-eigenvalues.tsv", "output/09_rda/tables/rda-unit-scores.tsv", "output/09_rda/tables/sensitivity-refits.tsv", "output/09_rda/tables/significance-tests.tsv", "output/09_rda/tables/snps-per-window.tsv", "output/09_rda/tables/temperature-only-models.tsv", "output/09_rda/tables/variance-partition.tsv", "output/09_rda/tables/vif.tsv"],
    "figures": ["output/09_rda/figures/outlier-manhattan.png", "output/09_rda/figures/rda-summary.png"]
  }
}