set n_fold=1, lambda=1 for betteer test performance

lgessl · Dec 14, 2023 · 955b91c · 955b91c
1 parent 2c755bd
commit 955b91c
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Showing 6 changed files with 22 additions and 17 deletions.
diff --git a/man/PerfPlotSpec.Rd b/man/PerfPlotSpec.Rd
diff --git a/tests/testthat/test-assess_model.R b/tests/testthat/test-assess_model.R
@@ -4,7 +4,8 @@ test_that("assess_model() works", {
   n <- 10
 
   dir <- withr::local_tempdir()
-  n_fold <- 3
+  n_fold <- 1
+  lambda <- 1
   data <- generate_mock_data(
     n_samples = n,
     n_genes = 5,
@@ -19,14 +20,14 @@ test_that("assess_model() works", {
   model_spec_1 <- ModelSpec(
     name = "cox-zerosum",
     fitter = zeroSum::zeroSum,
-    optional_fitter_args = list(family = "cox", alpha = 1, nFold = n_fold, zeroSum = FALSE),
+    optional_fitter_args = list(family = "cox", alpha = 1, nFold = n_fold, lambda = lambda),
     response_type = "survival_censored",
     base_dir = dir
   )
   model_spec_2 <- ModelSpec(
     name = "cox-lasso",
     fitter = zeroSum::zeroSum,
-    optional_fitter_args = list(family = "binomial", alpha = 1, nFold = n_fold, zeroSum = FALSE),
+    optional_fitter_args = list(family = "binomial", alpha = 1, nFold = n_fold, lambda = lambda),
     response_type = "binary",
     base_dir = dir
   )

diff --git a/tests/testthat/test-assess_multiple_models.R b/tests/testthat/test-assess_multiple_models.R
@@ -5,7 +5,8 @@ test_that("assess_multiple_models() works", {
   n_samples <- 25
   n_genes <- 5
   n_na_in_pheno <- 5
-  n_fold <- 2
+  n_fold <- 1
+  lambda <- 1
 
   base_dir <- withr::local_tempdir("data")
   data_dir <- file.path(base_dir, "data/mock")
@@ -23,7 +24,7 @@ test_that("assess_multiple_models() works", {
   model_spec_1 <- ModelSpec(
     name = "cox-zerosum",
     fitter = zeroSum::zeroSum,
-    optional_fitter_args = list(family = "cox", alpha = 1, nFold = n_fold, zeroSum = FALSE),
+    optional_fitter_args = list(family = "cox", alpha = 1, nFold = n_fold, lambda = lambda),
     response_type = "survival_censored",
     include_from_continuous_pheno = NULL,
     include_from_discrete_pheno = NULL,
@@ -34,7 +35,7 @@ test_that("assess_multiple_models() works", {
   model_spec_2 <- ModelSpec(
     name = "binomial-zerosum",
     fitter = zeroSum::zeroSum,
-    optional_fitter_args = list(family = "binomial", alpha = 1, nFold = n_fold, zeroSum = FALSE),
+    optional_fitter_args = list(family = "binomial", alpha = 1, nFold = n_fold, lambda = lambda),
     response_type = "binary",
     include_from_continuous_pheno = "continuous_var",
     include_from_discrete_pheno = "discrete_var",

diff --git a/tests/testthat/test-fit.R b/tests/testthat/test-fit.R
@@ -5,7 +5,8 @@ test_that("fit function works correctly", {
   set.seed(4325)
   n_samples = 5
   n_features = 5
-  n_fold = 3
+  n_fold = 1
+  lambda <- 1
 
   x <- matrix(rnorm(n_samples*n_features), nrow = n_samples)
   y <- rnorm(n_samples) |> as.matrix()
@@ -19,7 +20,7 @@ test_that("fit function works correctly", {
     name = "zerosum",
     fitter = zeroSum::zeroSum,
     response_type = "survival_censored",
-    optional_fitter_args = list("alpha" = 0.5, nFold = n_fold, zeroSum = FALSE),
+    optional_fitter_args = list("alpha" = 0.5, nFold = n_fold, lambda = lambda),
     pfs_leq = 2.0,
     plot_fname = "foo.pdf",
     fit_fname = "bar.rds"

diff --git a/tests/testthat/test-prepare_and_fit.R b/tests/testthat/test-prepare_and_fit.R
@@ -6,6 +6,7 @@ test_that("prepare_and_fit() works", {
   n_genes <- 5
   n_na_in_pheno <- 5
   n_fold <- 2
+  lambda <- 1
 
   data <- generate_mock_data(
     n_samples = n_samples,
@@ -21,7 +22,7 @@ test_that("prepare_and_fit() works", {
   model_spec_1 <- ModelSpec(
     name = "cox-zerosum",
     fitter = zeroSum::zeroSum,
-    optional_fitter_args = list(family = "cox", alpha = 1, nFold = n_fold, zeroSum = FALSE),
+    optional_fitter_args = list(family = "cox", alpha = 1, nFold = n_fold, lambda = lambda),
     response_type = "survival_censored",
     include_from_continuous_pheno = NULL,
     include_from_discrete_pheno = NULL,
@@ -30,7 +31,7 @@ test_that("prepare_and_fit() works", {
   model_spec_2 <- ModelSpec(
     name = "binomial-zerosum",
     fitter = zeroSum::zeroSum,
-    optional_fitter_args = list(family = "binomial", alpha = 1, nFold = n_fold, zeroSum = FALSE),
+    optional_fitter_args = list(family = "binomial", alpha = 1, nFold = n_fold, lambda = lambda),
     response_type = "binary",
     include_from_continuous_pheno = "continuous_var",
     include_from_discrete_pheno = "discrete_var",

diff --git a/tests/testthat/test-prepare_and_predict.R b/tests/testthat/test-prepare_and_predict.R
@@ -5,7 +5,8 @@ test_that("prepare_and_fit", {
   n_samples <- 30
   n_genes <- 5
   n_na_in_pheno <- 5
-  n_fold <- 2
+  n_fold <- 1
+  lambda <- 1
 
   data <- generate_mock_data(
     n_samples = n_samples,
@@ -20,7 +21,7 @@ test_that("prepare_and_fit", {
   model_spec_1 <- ModelSpec(
     name = "cox-zerosum",
     fitter = zeroSum::zeroSum,
-    optional_fitter_args = list(family = "cox", alpha = 1, nFold = n_fold, zeroSum = FALSE),
+    optional_fitter_args = list(family = "cox", alpha = 1, nFold = n_fold, lambda = lambda),
     response_type = "survival_censored",
     include_from_continuous_pheno = NULL,
     include_from_discrete_pheno = NULL,
@@ -30,7 +31,7 @@ test_that("prepare_and_fit", {
   model_spec_2 <- ModelSpec(
     name = "binomial-zerosum",
     fitter = zeroSum::zeroSum,
-    optional_fitter_args = list(family = "binomial", alpha = 1, nFold = n_fold, zeroSum = FALSE),
+    optional_fitter_args = list(family = "binomial", alpha = 1, nFold = n_fold, lambda = lambda),
     response_type = "binary",
     include_from_continuous_pheno = "continuous_var",
     include_from_discrete_pheno = "discrete_var",