Merge branch 'master' of https://github.com/remnrem/luna-base

remnrem · Dec 10, 2024 · ea20091 · ea20091
2 parents 660f6e2 + a62a455
commit ea20091
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Showing 4 changed files with 18 additions and 9 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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 ) );