diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 79c89e7..7611f68 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -46,7 +46,7 @@ jobs: name: win-luna.zip path: ./win-luna.zip macos-build: - runs-on: macos-12 + runs-on: macos-13 steps: - uses: actions/checkout@v2 - name: Install LightGBM diff --git a/cmddefs.cpp b/cmddefs.cpp index c794315..cfc46eb 100644 --- a/cmddefs.cpp +++ b/cmddefs.cpp @@ -1903,17 +1903,26 @@ void cmddefs_t::init() add_param( "GPA" , "X" , "TST" , "Predictor variable(s)" ); add_param( "GPA" , "Z" , "AGE,SEX" , "Covariates (nuissance variables)" ); add_param( "GPA" , "nreps" , "1000" , "Number of permutations" ); - add_param( "GPA" , "nreps" , "1000" , "Number of permutations" ); + add_param( "GPA" , "adj" , "" , "Run all adjusted p-value corrections" ); + add_param( "GPA" , "bonf" , "" , "Add Bonferroni-adjusted p-values" ); + add_param( "GPA" , "holm" , "" , "Add Holm-adjusted p-values" ); + add_param( "GPA" , "fdr-by" , "" , "Add FDR(B&Y)-adjusted p-values" ); + add_param( "GPA" , "fdr" , "F" , "Turn off default FDR(B&H) adjusted p-values" ); + add_param( "GPA" , "dump" , "" , "Dump data matrix to stdout" ); add_param( "GPA" , "manifest" , "" , "Dump variable maifest to stdout" ); add_table( "GPA" , "X,Y" , "GPA results per pair of predictor (X) and outcome (Y)" ); add_var( "GPA" , "X,Y" , "B" , "Regression coefficient" ); - add_var( "GPA" , "X,Y" , "B" , "Regression coefficient" ); add_var( "GPA" , "X,Y" , "T" , "t-statistic" ); - add_var( "GPA" , "X,Y" , "P" , "Empirical p-value" ); - add_var( "GPA" , "X,Y" , "PADJ" , "Adjusted empirical p-value" ); add_var( "GPA" , "X,Y" , "N" , "Number of observations" ); + add_var( "GPA" , "X,Y" , "P" , "Asymptotic p-value" ); + add_var( "GPA" , "X,Y" , "P_FDR" , "FDR-adjusted p-value" ); + add_var( "GPA" , "X,Y" , "P_FDR_BY" , "FDR(B&Y)-adjusted p-value" ); + add_var( "GPA" , "X,Y" , "P_HOLM" , "Holm-adjusted p-value" ); + add_var( "GPA" , "X,Y" , "P_BONF" , "Bonferroni-adjusted p-value" ); + add_var( "GPA" , "X,Y" , "EMP" , "Empircal p-value" ); + add_var( "GPA" , "X,Y" , "EMPADJ" , "Adjusted empirical p-value" ); add_var( "GPA" , "X,Y" , "STRAT" , "DV stratum" ); add_var( "GPA" , "X,Y" , "XSTRAT" , "IV stratum (if X-factors)" ); diff --git a/defs/defs.cpp b/defs/defs.cpp index daaa59c..830e334 100644 --- a/defs/defs.cpp +++ b/defs/defs.cpp @@ -234,7 +234,7 @@ void globals::init_defs() version = "v1.1.0 "; - date = "05-Dec-2024"; + date = "09-Dec-2024"; // // Return code diff --git a/stats/gpa.cpp b/stats/gpa.cpp index 197086d..ac7aecc 100644 --- a/stats/gpa.cpp +++ b/stats/gpa.cpp @@ -1345,10 +1345,10 @@ void gpa_t::run() writer.value( "B" , results.beta[ xvar ][ var ] ); writer.value( "T" , results.t[xvar][ var ] ); - + writer.value( "N" , (int)X.rows() ); writer.value( "P" , results.p[xvar][ var ] ); writer.value( "P_FDR" , results.fdr_bh( xvar , var ) ); - + if ( nreps != 0 ) { writer.value( "EMP" , results.emp[xvar][ var ] ); @@ -1503,7 +1503,7 @@ void gpa_t::run1X() // correction within X { writer.value( "B" , results.beta[ xvar ][ var ] ); writer.value( "T" , results.t[ xvar ][ var ] ); - + writer.value( "N" , (int)X.rows() ); writer.value( "P" , results.p[xvar][ var ] ); writer.value( "P_FDR" , results.fdr_bh( xvar , var ) );