drafted metrics.R + working on models.R now

jeffersonfparil · May 31, 2024 · 09b7491 · 09b7491
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diff --git a/man/fn_estimate_memory_footprint.Rd b/man/fn_estimate_memory_footprint.Rd
diff --git a/man/fn_filter_genotype.Rd b/man/fn_filter_genotype.Rd
diff --git a/man/fn_filter_phenotype.Rd b/man/fn_filter_phenotype.Rd
diff --git a/man/fn_load_phenotype.Rd b/man/fn_load_phenotype.Rd
diff --git a/man/fn_merge_genotype_and_phenotype.Rd b/man/fn_merge_genotype_and_phenotype.Rd
diff --git a/man/fn_prediction_performance_metrics.Rd b/man/fn_prediction_performance_metrics.Rd
diff --git a/tests/testthat/test-metrics.R b/tests/testthat/test-metrics.R
@@ -0,0 +1,24 @@
+# library(testthat)
+# source("/group/pasture/Jeff/gp/R/load.R")
+# source("/group/pasture/Jeff/gp/R/metrics.R")
+
+test_that("fn_prediction_performance_metrics", {
+    n = 100
+    y_true = 1:n
+    y_pred = y_true + pi
+    list_metrics_1 = fn_prediction_performance_metrics(y_true, y_true)
+    list_metrics_2 = fn_prediction_performance_metrics(y_true, y_pred)
+    list_metrics_3 = fn_prediction_performance_metrics(y_true, NA)
+    list_metrics_4 = fn_prediction_performance_metrics(y_true, rep(NA, length(y_true)))
+    expect_equal(list_metrics_1, list(mbe=0, mae=0, rmse=0, r2=1, corr=1, power_t10=1, power_b10=1, h2=1))
+    expect_equal(list_metrics_2, list(mbe=-pi, mae=pi, rmse=pi, r2=(1-(n*(pi^2)/sum((y_true-mean(y_true))^2))), corr=1, power_t10=1, power_b10=1, h2=1))
+    expect_equal(methods::is(list_metrics_3, "gpError"), TRUE)
+    expect_equal(is.na(list_metrics_4$mbe), TRUE)
+    expect_equal(is.na(list_metrics_4$mae), TRUE)
+    expect_equal(is.na(list_metrics_4$rmse), TRUE)
+    expect_equal(is.na(list_metrics_4$r2), TRUE)
+    expect_equal(is.na(list_metrics_4$corr), TRUE)
+    expect_equal(is.na(list_metrics_4$power_t10), TRUE)
+    expect_equal(is.na(list_metrics_4$power_b10), TRUE)
+    expect_equal(is.na(list_metrics_4$h2), TRUE)
+})
diff --git a/tests/testthat/test-models.R b/tests/testthat/test-models.R
@@ -0,0 +1,8 @@
+# library(testthat)
+# source("/group/pasture/Jeff/gp/R/load.R")
+# source("/group/pasture/Jeff/gp/R/metrics.R")
+# source("/group/pasture/Jeff/gp/R/models.R")
+
+test_that("fn_least_squares_moore_penrose", {
+
+})