ADD ci-cd config file

.github/workflows/r-cmd-check.yml

@@ -0,0 +1,29 @@
+name: R-testthat
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "4.1"  # or any version you need
+
+      - name: Install dependencies
+        run: |
+          Rscript -e 'install.packages("devtools")'
+          Rscript -e 'devtools::install_deps(dependencies = TRUE)'
+
+      - name: Run testthat tests
+        run: |
+          Rscript -e 'library(testthat); test_dir("tests/testthat")'

README.md

@@ -75,4 +75,7 @@ This project is licensed under the MIT License - see the LICENSE file for detail
 - The models presented are based on plant pathology research in the University of Madison Wisconsin, paper: [Nature Scientific Reports, 2023](https://www.nature.com/articles/s41598-023-44338-6)
 - This software was created by the [Data Science Institute](https://datascience.wisc.edu) at the [University of Wisconsin-Madison](https://www.wisc.edu)
 
-Mantainer: Maria Oros, [email protected]
+Mantainer: Maria Oros, [email protected]
+
+
+![R-CMD-check](https://github.com/mariaob1201/corn_disease_forecast_api/actions/workflows/r-cmd-check.yml/badge.svg)

tests/testthat/test-logit_functions.R

@@ -0,0 +1,24 @@
+install.packages("testthat")
+
+library(testthat)
+library(here)       # Use here for flexible paths if needed
+
+source(here("R/logit_functions.R"))  # Ensure this path correctly points to the functions you want to test
+
+test_that("logistic function returns probabilities between 0 and 1", {
+  expect_true(all(logistic(c(-5, 0, 5)) >= 0 & logistic(c(-5, 0, 5)) <= 1))
+})
+
+test_that("calculate_disease_risk handles threshold values correctly", {
+  logit_values <- c(-1, 0, 1)
+  thresholds <- c(0.3, 0.7)
+  result <- calculate_disease_risk(logit_values, thresholds, "Test Disease")
+  expect_equal(result$disease, "Test Disease")
+  expect_true(result$probability >= 0 && result$probability <= 100)
+})
+
+test_that("classify_risk categorizes risk correctly", {
+  expect_equal(classify_risk(0.2, 0.3, 0.7), "Low")
+  expect_equal(classify_risk(0.5, 0.3, 0.7), "Medium")
+  expect_equal(classify_risk(0.8, 0.3, 0.7), "High")
+})