even more tests with glmnet

lgessl · Jan 9, 2024 · 50f4e35 · 50f4e35
1 parent 62dfd77
commit 50f4e35
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Showing 4 changed files with 17 additions and 13 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -17,7 +17,8 @@ Suggests:
     testthat (>= 3.0.0),
     withr (>= 2.5.2),
     tibble (>= 3.0.0),
-    zeroSum (>= 2.0.6)
+    zeroSum (>= 2.0.6),
+    glmnet(>= 4.1.8)
 Imports:
     dplyr (>= 1.1.3),
     readr (>= 2.1.4),

diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
@@ -48,7 +48,7 @@ generate_mock_data <- function(
 ){
     # expression matrix
     expr_mat <- matrix(
-        sample(1:100, n_samples*n_genes, replace = TRUE),
+        sample(1:10, n_samples*n_genes, replace = TRUE),
         nrow = n_samples
     ) |> log()
     rownames(expr_mat) <- stringr::str_c("sample_", 1:n_samples)
@@ -60,9 +60,10 @@ generate_mock_data <- function(
     pheno_tbl <- tibble::tibble(.rows = n_samples)
     pheno_tbl[["patient_id"]] <- rownames(expr_mat)
     pheno_tbl[["progression"]] <- sample(
-        c(0, 1),
+        0:1,
         size = n_samples,
-        replace = TRUE
+        replace = TRUE,
+        prob = c(.3, .7)
     )
     pheno_tbl[["pfs_years"]] <- runif(n_samples, 0, 4)
     pheno_tbl[["discrete_var"]] <- sample(1:3, size = n_samples, replace = TRUE)

diff --git a/tests/testthat/test-assess_model.R b/tests/testthat/test-assess_model.R
@@ -1,15 +1,15 @@
 test_that("assess_model() works", {
 
-  set.seed(134)
-  n <- 10
+  set.seed(132)
+  n <- 50
 
   dir <- withr::local_tempdir()
-  n_fold <- 1
+  n_fold <- 3
   lambda <- 1
   data <- generate_mock_data(
     n_samples = n,
     n_genes = 5,
-    n_na_in_pheno = 3
+    n_na_in_pheno = 1
   )
   expr_mat <- data[["expr_mat"]]
   pheno_tbl <- data[["pheno_tbl"]]
@@ -20,14 +20,16 @@ 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, lambda = lambda),
+    optional_fitter_args = list(family = "cox", alpha = 1, nFold = n_fold, 
+      lambda = lambda, zeroSum = FALSE),
     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, lambda = lambda),
+    name = "logistic-lasso",
+    fitter = glmnet::cv.glmnet,
+    optional_fitter_args = list(family = "binomial", alpha = 1, 
+      nfolds = n_fold, lambda = c(lambda, 2)),
     response_type = "binary",
     base_dir = dir
   )

diff --git a/tests/testthat/test-assess_multiple_models.R b/tests/testthat/test-assess_multiple_models.R
@@ -58,7 +58,7 @@ test_that("assess_multiple_models() works", {
     fname = file.path(res_dir, "perf_plot.pdf"),
     x_metric = "rpp",
     y_metric = "prec",
-    show_plots = TRUE
+    show_plots = FALSE
   )
 
   expect_no_error(