more tests

.Rbuildignore

@@ -1,2 +1,2 @@
 .github/
-exec/tests/
+exec/

.gitignore

@@ -49,4 +49,5 @@ po/*~
 rsconnect/
 
 # Test files
-exec/tests/outdir/
+exec/tests/outdir/
+exec/tests/logfile

R/main.R

@@ -473,7 +473,7 @@ gp = function(args) {
             GENOMIC_PREDICTIONS = NA
         } else {
             ### Find the best model in the args$population
-            df_agg = aggregate(corr ~ model, data=METRICS_WITHIN_POP, FUN=mean, na.rm=TRUE)
+            df_agg = stats::aggregate(corr ~ model, data=METRICS_WITHIN_POP, FUN=mean, na.rm=TRUE)
             idx = which(df_agg$corr == max(df_agg$corr, na.rm=TRUE))[1]
             model = df_agg$model[idx]
             ### Define additional model input/s

exec/tests/test.sh

@@ -1,4 +1,8 @@
 #!/bin/bash
+
+#############
+### GRAPE ###
+#############
 DIR='gp/exec/tests/'
 cd $DIR
 time \
@@ -17,7 +21,9 @@ Rscript ../gp.R \
 --n-threads 32 \
 --verbose TRUE
 
-
+################
+### RYEGRASS ###
+################
 DIR='/group/pasture/Jeff/gp/exec/tests'
 cd $DIR
 fname_geno='/group/pasture/Jeff/ryegrass/workdir/STR_NUE_WUE_HS-1717536141.3435302.3200855812-IMPUTED.tsv'
@@ -47,6 +53,43 @@ tail logfile
 grep -A1 "ERROR:" logfile
 ls -lhtr outdir/*.Rds
 
+
+###############
+### LUCERNE ###
+###############
+DIR='/group/pasture/Jeff/gp/exec/tests'
+cd $DIR
+fname_geno='/group/pasture/Jeff/lucerne/workdir/FINAL-IMPUTED-noTrailingAllele-filteredSNPlist.Rds'
+fname_pheno='/group/pasture/Jeff/lucerne/workdir/Lucerne_PhenomicsDB_2024-05-27-BiomassPredicted.tsv'
+n_traits=$(head -n1 $fname_pheno | awk '{print NF}')
+touch outdir/lucerne/logfile
+time \
+for idx_pheno in $(seq 3 $n_traits)
+do
+    time \
+    Rscript ../gp.R \
+        --fname-geno $fname_geno \
+        --fname-pheno $fname_pheno \
+        --population "DB-MS-31-22-001" \
+        --dir-output outdir/lucerne \
+        --pheno-idx-col-y $idx_pheno \
+        --bool-within TRUE \
+        --bool-across TRUE \
+        --n-folds 5 \
+        --n-reps 1 \
+        --bool-parallel TRUE \
+        --max-mem-Gb 60 \
+        --n-threads 32 \
+        --verbose TRUE >> outdir/lucerne/logfile
+done
+tail outdir/lucerne/logfile
+grep -A1 "ERROR:" outdir/lucerne/logfile
+ls -lhtr outdir/lucerne/*.Rds
+
+
+########################################
+### COMPLETE SET OF INPUT PARAMETERS ###
+########################################
 # Rscript ../gp.R \
 # --fname-geno= \
 # --fname-pheno= \