From 7efe11c1bd4c7c37f39c6b3403c82326cbdff71f Mon Sep 17 00:00:00 2001 From: jeffersonfparil Date: Thu, 6 Jun 2024 14:49:57 +1000 Subject: [PATCH] testing --- exec/tests/logfile | 432 ++++ ...3-0.506533726816997ETA_MRK_ScaleBayesA.dat | 2179 ---------------- ...06-14.46.42.658033-0.506533726816997mu.dat | 2179 ---------------- ...-14.46.42.658033-0.506533726816997varE.dat | 2179 ---------------- ...4-0.678508335724473ETA_MRK_ScaleBayesA.dat | 2169 ---------------- ...06-14.46.42.743424-0.678508335724473mu.dat | 2169 ---------------- ...-14.46.42.743424-0.678508335724473varE.dat | 2169 ---------------- ...2-0.617225074209273ETA_MRK_ScaleBayesA.dat | 2167 ---------------- ...06-14.46.42.849002-0.617225074209273mu.dat | 2168 ---------------- ...-14.46.42.849002-0.617225074209273varE.dat | 2168 ---------------- ...1-0.760495992843062ETA_MRK_ScaleBayesA.dat | 2171 ---------------- ...06-14.46.43.038931-0.760495992843062mu.dat | 2171 ---------------- ...-14.46.43.038931-0.760495992843062varE.dat | 2171 ---------------- ...4-0.348103576805443ETA_MRK_ScaleBayesA.dat | 2185 ---------------- ...06-14.46.43.350634-0.348103576805443mu.dat | 2185 ---------------- ...-14.46.43.350634-0.348103576805443varE.dat | 2186 ----------------- ...733-0.698543984442949ETA_MRK_parBayesB.dat | 520 ++++ ...06-14.46.42.668733-0.698543984442949mu.dat | 521 ++++ ...-14.46.42.668733-0.698543984442949varE.dat | 521 ++++ ...764-0.976780039956793ETA_MRK_parBayesB.dat | 510 ++++ ...06-14.46.42.757764-0.976780039956793mu.dat | 509 ++++ ...-14.46.42.757764-0.976780039956793varE.dat | 510 ++++ ...15-0.0576269561424851ETA_MRK_parBayesB.dat | 527 ++++ ...6-14.46.42.881315-0.0576269561424851mu.dat | 528 ++++ ...14.46.42.881315-0.0576269561424851varE.dat | 528 ++++ ...763-0.959135704440996ETA_MRK_parBayesB.dat | 535 ++++ ...06-14.46.43.089763-0.959135704440996mu.dat | 536 ++++ ...-14.46.43.089763-0.959135704440996varE.dat | 536 ++++ ...3465-0.38209713739343ETA_MRK_parBayesB.dat | 1921 --------------- ...-06-14.46.43.843465-0.38209713739343mu.dat | 1920 --------------- ...6-14.46.43.843465-0.38209713739343varE.dat | 1920 --------------- 31 files changed, 6713 insertions(+), 38377 deletions(-) delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.42.658033-0.506533726816997ETA_MRK_ScaleBayesA.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.42.658033-0.506533726816997mu.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.42.658033-0.506533726816997varE.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.42.743424-0.678508335724473ETA_MRK_ScaleBayesA.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.42.743424-0.678508335724473mu.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.42.743424-0.678508335724473varE.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.42.849002-0.617225074209273ETA_MRK_ScaleBayesA.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.42.849002-0.617225074209273mu.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.42.849002-0.617225074209273varE.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.43.038931-0.760495992843062ETA_MRK_ScaleBayesA.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.43.038931-0.760495992843062mu.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.43.038931-0.760495992843062varE.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.43.350634-0.348103576805443ETA_MRK_ScaleBayesA.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.43.350634-0.348103576805443mu.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.43.350634-0.348103576805443varE.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_B-within-pop_1--2024-06-06-14.46.43.843465-0.38209713739343ETA_MRK_parBayesB.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_B-within-pop_1--2024-06-06-14.46.43.843465-0.38209713739343mu.dat delete mode 100644 exec/tests/outdir/bglr_Bayes_B-within-pop_1--2024-06-06-14.46.43.843465-0.38209713739343varE.dat diff --git a/exec/tests/logfile b/exec/tests/logfile index 3372b73..5dcffeb 100644 --- a/exec/tests/logfile +++ b/exec/tests/logfile @@ -1980,3 +1980,435 @@ [1] "Output file names:" [1] " - outdir/within-pop_1-metrics-rep_1-fold_3-model_Bayes_C-1717649328120553.tsv" [1] " - outdir/within-pop_1-y_pred-rep_1-fold_3-model_Bayes_C-1717649328120553.tsv" +[1] "Allele effects distribution:" + +---+-------------+------------+-------------+------------+-+ + | ***** | + | ** ** | +15 + * * + + | ** ** | + | ** ** | + | ** ** | +10 + * * + + | * ** | + | ** ** | + 5 + ** ** + + | *** ** | + | *** *** | + 0 + **************** ************ + + +---+-------------+------------+-------------+------------+-+ + -0.1 -0.05 0 0.05 0.1 +[1] "Relative posisitions of allele effects across the genome:" + 0.1 +-+-------------+-------------+-------------+------------+ + | * * ** * * * * | + | * *** ***** ******* *** **** ******* ** ** ** ** | + 0.05 + ************************************************** + + | ************************************************** | + | ************************************************** | + | *************************************************** | + 0 + *************************************************** + + | *************************************************** | + | ************************************************** | +-0.05 + ************************************************** + + | *********** ********* ********* *************** | + | * * * * ** * | + -0.1 + * * + + +-+-------------+-------------+-------------+------------+ + 0 10000 20000 30000 +[1] "Number of non-zero effects: 36437 (100%)" +[1] "Scatter plot of the observed and predicted phenotypes" + +---------+----------+----------+----------+-----------+----+ + | * | +45 + + + | * | +40 + * * + + | | + | | +35 + * * + + | ** | + | * * * | +30 + * * + + | * ** * | + | * * * | +25 + * * + + +---------+----------+----------+----------+-----------+----+ + 0 20 40 60 80 +[1] "Mean bias error (mbe) = 3.27539294001665" +[1] "Mean absolute error (mae) = 17.326828610925" +[1] "Root mean square error (rmse) = 22.8126052783534" +[1] "Coefficient of determination (r2) = 0.105651798157211" +[1] "Power to identify top 10 (power_t10) = 3.27539294001665" +[1] "Power to identify bottom 10 (power_b10) = 0" +[1] "Pearson's correlation (corr) = 0.367715196494903" +[1] "Variance of predicted phenotypes (var_pred) = 39.6892087477835 (estimator of additive genetic variance)" +[1] "Variance of observed phenotypes (var_true) = 609.602192082208 (estimator of total phenotypic variance)" +[1] "Narrow-sense heritability estimate (h2) = 0.177057506" +[1] "Performance:" + rep fold model pop_training pop_validation n_training n_validation +1 1 5 Bayes_A pop_1 pop_1 86 22 + duration_mins n_non_zero_effects mbe mae rmse r2 +1 2.770621 36437 3.275393 17.32683 22.81261 0.1056518 + corr power_t10 power_b10 var_pred var_true h2 +1 0.3677152 0.5 0 39.68921 609.6022 0.1770575 +[1] "Output file names:" +[1] " - outdir/within-pop_1-metrics-rep_1-fold_5-model_Bayes_A-1717649370711746.tsv" +[1] " - outdir/within-pop_1-y_pred-rep_1-fold_5-model_Bayes_A-1717649370711746.tsv" +[1] "Allele effects distribution:" + +----+------------+------------+------------+------------+--+ + | ***** | + | ** ** | +15 + ** * + + | ** * | + | ** ** | + | * ** | +10 + ** * + + | ** ** | + | ** ** | + 5 + ** ** + + | *** *** | + | *** *** | + 0 + **************** ************ + + +----+------------+------------+------------+------------+--+ + -0.1 -0.05 0 0.05 0.1 +[1] "Relative posisitions of allele effects across the genome:" + 0.1 +-+-------------+-------------+-------------+------------+ + | * * ** * * ** ** * | + | ******* *** ********* * ** * * ** ** **** ** | + | ************************************************** | + 0.05 + ************************************************** + + | ************************************************** | + | ************************************************** | + 0 + *************************************************** + + | *************************************************** | + | ************************************************** | +-0.05 + ************************************************** + + | *** ** ****** ** *** * **** * *** *** **** *** | + | * ** * * * ** ** * | + -0.1 + * * * + + +-+-------------+-------------+-------------+------------+ + 0 10000 20000 30000 +[1] "Number of non-zero effects: 36437 (100%)" +[1] "Scatter plot of the observed and predicted phenotypes" + +-----+--------------+---------------+---------------+------+ + | * | + | | +35 + * + + | * | + | * * | +30 + * * * + + | * * * | + | * * * * | + | * * * | +25 + + + | | + | * | +20 + * + + +-----+--------------+---------------+---------------+------+ + 0 20 40 60 +[1] "Mean bias error (mbe) = 3.97900779059893" +[1] "Mean absolute error (mae) = 14.0979397573186" +[1] "Root mean square error (rmse) = 17.6975124448008" +[1] "Coefficient of determination (r2) = -0.0446444683727172" +[1] "Power to identify top 10 (power_t10) = 3.97900779059893" +[1] "Power to identify bottom 10 (power_b10) = 0" +[1] "Pearson's correlation (corr) = 0.143446544208883" +[1] "Variance of predicted phenotypes (var_pred) = 20.4023618817538 (estimator of additive genetic variance)" +[1] "Variance of observed phenotypes (var_true) = 314.093775522401 (estimator of total phenotypic variance)" +[1] "Narrow-sense heritability estimate (h2) = 0.4528256576" +[1] "Performance:" + rep fold model pop_training pop_validation n_training n_validation +1 1 1 Bayes_A pop_1 pop_1 86 22 + duration_mins n_non_zero_effects mbe mae rmse r2 +1 2.790124 36437 3.979008 14.09794 17.69751 -0.04464447 + corr power_t10 power_b10 var_pred var_true h2 +1 0.1434465 0 0 20.40236 314.0938 0.4528257 +[1] "Output file names:" +[1] " - outdir/within-pop_1-metrics-rep_1-fold_1-model_Bayes_A-1717649370396872.tsv" +[1] " - outdir/within-pop_1-y_pred-rep_1-fold_1-model_Bayes_A-1717649370396872.tsv" +[1] "Allele effects distribution:" +[1] "Allele effects distribution:" + +------+----------+----------+-----------+----------+-------+ + | **** | +15 + ** ** + + | ** ** | + | ** * | + | ** * | +10 + * * + + | * ** | + | ** ** | + | ** ** | + 5 + ** ** + + | ** ** | + | *** *** | + 0 + ************** *************** + + +------+----------+----------+-----------+----------+-------+ + -0.1 -0.05 0 0.05 0.1 +[1] "Relative posisitions of allele effects across the genome:" + +-------+-----------+-----------+-----------+-----------+---+ + | **** | +15 + ** *** + + | ** * | + | ** * | + | * ** | +10 + ** ** + + | ** * | + | ** ** | + | + - + - - - - -*-*- - - - - - - + - - - - - - -*-*- - - - - + - - - - - - - - - - - - - +|- +- -5- -+- - - - - - - + + | * * *** * + + | * | + 0 . 1 + * * * * * * * * * * * * **** * * * * * * * * *| + * * |* + + | ******** * * * * * * * * * * * * * * * * * * * * ******* * * * * * * * * * * * * *|* +* *0* *+* * ** * * * *|* +* *0*.*0*5* *+* * ** * * * * * * * * * * * * * * * * * * * * * * * * * ************************* * * *+* +* * * *+*-*-*- - - - -++ +- - - - - - -|- - -*-*+*-*-*-*-*-*-*-*-*-*-*-*+*-*-*-*-*-*-*-*-*-*-*-*+*-*-*-*-*-*-*-*-*-*-*-*+*-*-*-*+* +* * * * * * * - 0|. +1 | *-*0*.*0*5* * * * * * * * * *0* * * * * * * * * *0*.*0*5* * * * * * * * * *0*.*1* * * * +******* [1] "Relative posisitions of allele effects across the genome:"| + + 0 + *************************************************** + + | *************************************************** | + | *************************************************** | +-0.05 + ************************************************** + + | ************************* ************************ | + -0.1 + ** *** *** ** * * * ** ** **** * * + + | **** * * | + +-+-------------+-------------+-------------+------------+ + 0 10000 20000 30000 +[1] "Number of non-zero effects: 36437 (100%)" +[1] "Scatter plot of the observed and predicted phenotypes" + +----+----------+----------+---------+----------+----------++ +45 + * + + | | +40 + + + | * * * | + | * | +35 + * * + + | *** * * * | + | * | +30 + * * + + | * * | +25 + * + + | * | + | * * | +20 +----+----------+----------+---------+----------+----------++ + 0 20 40 60 80 100 +[1] "Mean bias error (mbe) = 4.48768093265117" +[1] "Mean absolute error (mae) = 18.2815206920932" +[1] "Root mean square error (rmse) = 23.9630307672863" +[1] "Coefficient of determination (r2) = 0.0471611921841942" +[1] "Power to identify top 10 (power_t10) = 4.48768093265117" +[1] "Power to identify bottom 10 (power_b10) = 0" +[1] "Pearson's correlation (corr) = 0.288944770468832" +[1] "Variance of predicted phenotypes (var_pred) = 34.8663765214366 (estimator of additive genetic variance)" +[1] "Variance of observed phenotypes (var_true) = 631.346009447519 (estimator of total phenotypic variance)" +[1] "Narrow-sense heritability estimate (h2) = 0.1911280977" + +-+-------------+-------------+-------------+------------+ + 0.1 + * * * * * * ** * * * + + | *** * ********* ** *********** ************* *** | + | ************************************************** | + 0.05 + ************************************************** + + | ************************************************** | + 0 + ************************************************** + + | *************************************************** | + | ************************************************** | +-0.05 + *************************************************** + + | ************************************************** | + | ************* * **** ***** **** *********** ** | + -0.1 + * ** * ** * * * * * * * ** * + + | * * * * * | + +-+-------------+-------------+-------------+------------+ + 0 10000 20000 30000 +[1] "Number of non-zero effects: 36437 (100%)" +[1] "Scatter plot of the observed and predicted phenotypes" + +------+-------------+------------+------------+------------+ +45 + * + + | * | +40 + * + + | * * * * | + | * * * | +35 + * * + + | * * | +30 + ** * + + | * * | + | * | +25 + + + | | +20 + * + + +------+-------------+------------+------------+------------+ + 0 20 40 60 +[1] "Mean bias error (mbe) = -3.88165160739946" +[1] "Mean absolute error (mae) = 22.0750416172447" +[1] "Root mean square error (rmse) = 25.1007514148354" +[1] "Coefficient of determination (r2) = 0.0631489407178455" +[1] "Power to identify top 10 (power_t10) = -3.88165160739946" +[1] "Power to identify bottom 10 (power_b10) = 0" +[1] "Pearson's correlation (corr) = 0.305256475797912" +[1] "Variance of predicted phenotypes (var_pred) = 32.9313587405896 (estimator of additive genetic variance)" +[1] "Variance of observed phenotypes (var_true) = 706.142242263919 (estimator of total phenotypic variance)" +[1] "Narrow-sense heritability estimate (h2) = 0.1527750983" +[1] "Allele effects distribution:" + +----+---------------+---------------+---------------+------+ + | *** | +15 + ** * + + | * ** | + | * * | + | ** * | +10 + * ** + + | ** * | + | * ** | + 5 + ** * + + | ** ** [1] "Performance:" + | + | ** ** | + | ** *** | + 0 + ************************* ********** + + +----+---------------+---------------+---------------+------+ + -0.2 -0.1 rep fold model pop_training pop_validation n_training0 n_validation +1 1 2 Bayes_A pop_1 pop_1 86 22 + duration_mins n_non_zero_effects mbe mae0 rmse. r21 +1 2.794573 36437 4.487681 18.28152 23.96303 0.04716119 + + corr power_t10 power_b10 var_pred[1] var_true h2 "Relative posisitions of allele effects across the genome:" +1 + 0.2889448 0 0 34.86638 631.346 0.1911281 +[1] "Output file names:" +[1] " - outdir/within-pop_1-metrics-rep_1-fold_2-model_Bayes_A-1717649370307014.tsv" +[1] " - outdir/within-pop_1-y_pred-rep_1-fold_2-model_Bayes_A-1717649370307014.tsv" + +--+------------+-------------+-------------+-------------+ + 0.1 + * * ** ** * * * * * + + | **************** *** ** ************************** | + | *************************************************** | + | *************************************************** | + 0 + *************************************************** + + | *************************************************** | + | *************************************************** | + | *************************************************** | +-0.1 + ** * ***** * * * * * * * * * * *** * + + | * | + | * | + | | +-0.2 + * + + +--+------------+-------------+-------------+-------------+ + 0 10000 20000 30000 +[1] "Number of non-zero effects: 36437 (100%)" +[1] "Scatter plot of the observed and predicted phenotypes" + +------+----------------+----------------+----------------+-+ +55 + * + + | | +50 + + + | | +45 + * + + | | + | * | +40 + + + | * * | +35 + * * * * + + | * * ** * | +30 + * * * * * + + | * * | + +------+----------------+----------------+----------------+-+ + 0 20 40 60 +[1] "Mean bias error (mbe) = -11.1957737687799" +[1] "Mean absolute error (mae) = 17.373357039671" +[1] "Root mean square error (rmse) = 20.6718630059936" +[1] "Coefficient of determination (r2) = -0.789380148377194" +[1] "Power to identify top 10 (power_t10) = -11.1957737687799" +[1] "Power to identify bottom 10 (power_b10) = 0" +[1] "Pearson's correlation (corr) = -0.133027217987788" +[1] "Variance of predicted phenotypes (var_pred) = 38.0746334080612 (estimator of additive genetic variance)" +[1] "Variance of observed phenotypes (var_true) = 250.752874704918 (estimator of total phenotypic variance)" +[1] "Narrow-sense heritability estimate (h2) = NA" +[1] "Performance:" + rep fold model pop_training pop_validation n_training n_validation +1 1 4 Bayes_A pop_1 pop_1 87 21 + duration_mins n_non_zero_effects mbe mae rmse r2 +1 2.790276 36437 -3.881652 22.07504 25.10075 0.06314894 + corr power_t10 power_b10 var_pred var_true h2 +1 0.3052565 0.5 0 32.93136 706.1422 0.1527751 +[1] "Output file names:" +[1] " - outdir/within-pop_1-metrics-rep_1-fold_4-model_Bayes_A-1717649370821133.tsv" +[1] " - outdir/within-pop_1-y_pred-rep_1-fold_4-model_Bayes_A-1717649370821133.tsv" +[1] "Performance:" + rep fold model pop_training pop_validation n_training n_validation +1 1 3 Bayes_A pop_1 pop_1 87 21 + duration_mins n_non_zero_effects mbe mae rmse r2 +1 2.796735 36437 -11.19577 17.37336 20.67186 -0.7893801 + corr power_t10 power_b10 var_pred var_true h2 +1 -0.1330272 0 0 38.07463 250.7529 NA +[1] "Output file names:" +[1] " - outdir/within-pop_1-metrics-rep_1-fold_3-model_Bayes_A-1717649371780757.tsv" +[1] " - outdir/within-pop_1-y_pred-rep_1-fold_3-model_Bayes_A-1717649371780757.tsv" +[1] "Allele effects distribution:" + +--+-------------+------------+-------------+------------+--+ + | **** | + | ** ** | +15 + ** ** + + | * * | + | * * | +10 + ** ** + + | ** ** | + | ** ** | + | ** ** | + 5 + ** ** + + | ** ** | + | *** **** | + 0 + ************** ************ + + +--+-------------+------------+-------------+------------+--+ + -0.1 -0.05 0 0.05 0.1 +[1] "Relative posisitions of allele effects across the genome:" + 0.1 +-+-------------+-------------+-------------+------------+ + | * * * * * | + | *** ***** ******** *** **** ******* ****** *** ** | + | ************************************************** | + 0.05 + ************************************************** + + | ************************************************** | + | *************************************************** | + 0 + *************************************************** + + | ************************************************** | + | *************************************************** | +-0.05 + ************************************************** + + | **************************************** ******** | + | ** * * *** ** ** * * *** ** * | + -0.1 + ** * * * * + + +-+-------------+-------------+-------------+------------+ + 0 10000 20000 30000 +[1] "Number of non-zero effects: 36437 (100%)" +[1] "Scatter plot of the observed and predicted phenotypes" +45 +---------+----------+----------+----------+-----------+----+ + | * | + | | +40 + * * + + | * | + | | + | * | +35 + * + + | ** | + | * * | +30 + * * + + | * * ** | + | * * * | +25 + * * + + +---------+----------+----------+----------+-----------+----+ + 0 20 40 60 80 +[1] "Mean bias error (mbe) = 3.49483911417046" +[1] "Mean absolute error (mae) = 17.5688534039972" +[1] "Root mean square error (rmse) = 22.9681897423372" +[1] "Coefficient of determination (r2) = 0.0934110933622012" +[1] "Power to identify top 10 (power_t10) = 3.49483911417046" +[1] "Power to identify bottom 10 (power_b10) = 0" +[1] "Pearson's correlation (corr) = 0.372783050424897" +[1] "Variance of predicted phenotypes (var_pred) = 26.8673188436884 (estimator of additive genetic variance)" +[1] "Variance of observed phenotypes (var_true) = 609.602192082208 (estimator of total phenotypic variance)" +[1] "Narrow-sense heritability estimate (h2) = 0.1182283562" +[1] "Performance:" + rep fold model pop_training pop_validation n_training n_validation +1 1 5 Bayes_B pop_1 pop_1 86 22 + duration_mins n_non_zero_effects mbe mae rmse r2 +1 3.168884 36437 3.494839 17.56885 22.96819 0.09341109 + corr power_t10 power_b10 var_pred var_true h2 +1 0.3727831 0.5 0 26.86732 609.6022 0.1182284 +[1] "Output file names:" +[1] " - outdir/within-pop_1-metrics-rep_1-fold_5-model_Bayes_B-1717649394708819.tsv" +[1] " - outdir/within-pop_1-y_pred-rep_1-fold_5-model_Bayes_B-1717649394708819.tsv" diff --git a/exec/tests/outdir/bglr_Bayes_A-within-pop_1--2024-06-06-14.46.42.658033-0.506533726816997ETA_MRK_ScaleBayesA.dat 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