From b1d489675a55bf58ee17c21e05132f719effc177 Mon Sep 17 00:00:00 2001
From: aduvermy <arnaud.duvermy@ens-lyon.fr>
Date: Thu, 4 Apr 2024 14:21:22 +0200
Subject: [PATCH] mu hided for user exp
Former-commit-id: 56250a80365d410770eb3dd038abe0e4b6e0d1d7
Former-commit-id: 79d7ca4c3bb2f1ed291d428b31ff5050cce2235c
Former-commit-id: a5d2468176136bf03843ea163e98657e6450988a
---
R/simulation_initialization.R | 21 +++++++++++----------
R/subsetgenes.R | 2 +-
R/wrapper_dds.R | 4 ++--
tests/testthat/test-simulation_report.R | 11 ++++++-----
4 files changed, 20 insertions(+), 18 deletions(-)
diff --git a/R/simulation_initialization.R b/R/simulation_initialization.R
index 416a0ae..de40d8d 100644
--- a/R/simulation_initialization.R
+++ b/R/simulation_initialization.R
@@ -4,17 +4,17 @@
#'
#' @param list_var Either c() or output of init_variable
#' @param name Variable name
-#' @param mu Either a numeric value or a numeric vector (of length = level)
-#' @param sd Either numeric value or NA
+#' @param sd Either numeric value or NA. Use to specify range of effect sizes.
#' @param level Numeric value to specify the number of levels to simulate
+#' @param mu Either a numeric value or a numeric vector (of length = level). Default : 0. Not recommended to modify.
#'
#' @return
#' A list with initialized variables
#' @export
#'
#' @examples
-#' init_variable(name = "my_varA", mu = 2, sd = 9, level = 200)
-init_variable <- function(list_var = c(), name = "myVariable", mu = c(2,3), sd = NA, level = NA) {
+#' init_variable(name = "my_varA", sd = 9, level = 200)
+init_variable <- function(list_var = c(), name = "myVariable", sd = NA, level = NA, mu = 0) {
name <- clean_variable_name(name)
@@ -200,18 +200,19 @@ build_sub_obj_return_to_user <- function(level, metaData, effectsGivenByUser, co
#'
#' @param list_var A list of variables (already initialized)
#' @param between_var A vector of variable names to include in the interaction
-#' @param mu Either a numeric value or a numeric vector (of length = level)
-#' @param sd Either numeric value or NA
+#' @param sd Either numeric value or NA. Use to specify range of effect sizes.
+#' @param mu Either a numeric value or a numeric vector (of length = level). Default : 0. Not recommended to modify.
+
#'
#' @return
#' A list with initialized interaction
#' @export
#'
#' @examples
-#' init_variable(name = "myvarA", mu = 2, sd = 3, level = 200) %>%
-#' init_variable(name = "myvarB", mu = 1, sd = 0.2, level = 2 ) %>%
-#' add_interaction(between_var = c("myvarA", "myvarB"), mu = 3, sd = 2)
-add_interaction <- function(list_var, between_var, mu, sd = NA) {
+#' init_variable(name = "myvarA", sd = 3, level = 200) %>%
+#' init_variable(name = "myvarB", sd = 0.2, level = 2 ) %>%
+#' add_interaction(between_var = c("myvarA", "myvarB"), sd = 2)
+add_interaction <- function(list_var, between_var, sd = NA, mu = 0) {
name_interaction <- paste(between_var, collapse = ":")
check_input2interaction(name_interaction, list_var, between_var, mu, sd)
diff --git a/R/subsetgenes.R b/R/subsetgenes.R
index 351d045..81cb56b 100644
--- a/R/subsetgenes.R
+++ b/R/subsetgenes.R
@@ -22,7 +22,7 @@
#' N_GENES = 100
#' MAX_REPLICATES = 5
#' MIN_REPLICATES = 5
-#' input_var_list <- init_variable(name = "varA", mu = 10, sd = 0.1, level = 3)
+#' input_var_list <- init_variable(name = "varA", sd = 0.1, level = 3)
#' mock_data <- mock_rnaseq(input_var_list, N_GENES,
#' min_replicates = MIN_REPLICATES,
#' max_replicates = MAX_REPLICATES)
diff --git a/R/wrapper_dds.R b/R/wrapper_dds.R
index b2c050c..7191f50 100644
--- a/R/wrapper_dds.R
+++ b/R/wrapper_dds.R
@@ -22,8 +22,8 @@
#' MAX_REPLICATES = 5
#' MIN_REPLICATES = 5
#' ## --init variable
-#' input_var_list <- init_variable( name = "genotype", mu = 12, sd = 0.1, level = 3) %>%
-#' init_variable(name = "environment", mu = c(0,1), NA , level = 2)
+#' input_var_list <- init_variable( name = "genotype", sd = 0.1, level = 3) %>%
+#' init_variable(name = "environment", NA , level = 2)
#'
#' mock_data <- mock_rnaseq(input_var_list, N_GENES, MIN_REPLICATES, MAX_REPLICATES)
#' dds <- DESeq2::DESeqDataSetFromMatrix(mock_data$counts ,
diff --git a/tests/testthat/test-simulation_report.R b/tests/testthat/test-simulation_report.R
index d69aafd..da6f226 100644
--- a/tests/testthat/test-simulation_report.R
+++ b/tests/testthat/test-simulation_report.R
@@ -63,8 +63,6 @@ test_that("isValidEvalInput with valid input", {
test_that("evaluation_report returns correct output", {
-
-
N_GENES <- 100
MAX_REPLICATES <- 5
MIN_REPLICATES <- 5
@@ -126,8 +124,12 @@ test_that("get_performances_metrics_obj returns correct output", {
recall = c(0.09, 0.88)),
aggregate = data.frame(from = c("Glm", "Hglm"),
accuracy = c(0.7, 0.6), recall = c(0.1, 0.8)))
+ r2_agg <- data.frame(from = c("Glm", "Hglm"),
+ RMSE = c(0.22, 0.55),
+ R2 = c(0.9, 0.7))
+
# Call the function
- result <- get_performances_metrics_obj(r2_params, r2_dispersion,
+ result <- get_performances_metrics_obj(r2_params, r2_agg, r2_dispersion,
pr_obj, roc_obj, ml_metrics_obj)
# Test the output
@@ -137,7 +139,7 @@ test_that("get_performances_metrics_obj returns correct output", {
expect_equal(nrow(result$byparams), 6)
expect_equal(ncol(result$byparams), 7)
expect_equal(nrow(result$aggregate), 2)
- expect_equal(ncol(result$aggregate), 5)
+ expect_equal(ncol(result$aggregate), 7)
})
@@ -195,7 +197,6 @@ test_that("get_ml_metrics_obj returns correct output", {
-
# Test get_eval_data_from_ltmb
test_that("get_eval_data_from_ltmb returns correct output", {
--
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