initial version (#1)

* initial version

.arduino-ci.yml

@@ -0,0 +1,11 @@
+compile:
+  # Choosing to run compilation tests on 2 different Arduino platforms
+  platforms:
+    - uno
+    # - due
+    # - zero
+    # - leonardo
+    - m4
+    - esp32
+    # - esp8266
+    # - mega2560

.github/workflows/arduino-lint.yml

@@ -0,0 +1,13 @@
+
+name: Arduino-lint
+
+on: [push, pull_request]
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: arduino/arduino-lint-action@v1
+        with:
+          library-manager: update
+          compliance: strict

.github/workflows/arduino_test_runner.yml

@@ -0,0 +1,17 @@
+---
+name: Arduino CI
+
+on: [push, pull_request]
+
+jobs:
+  runTest:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: 2.6
+      - run: |
+          gem install arduino_ci
+          arduino_ci.rb

.github/workflows/jsoncheck.yml

@@ -0,0 +1,18 @@
+name: JSON check
+
+on:
+  push:
+    paths:
+      - '**.json'
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: json-syntax-check
+        uses: limitusus/json-syntax-check@v1
+        with:
+          pattern: "\\.json$"
+

GST.h

@@ -0,0 +1,112 @@
+#pragma once
+//
+//    FILE: GST.h
+// VERSION: 0.1.0
+// PURPOSE: Arduino library for Gold Standard Test metrics
+//     URL: https://github.com/RobTillaart/GST
+//          https://en.wikipedia.org/wiki/Sensitivity_and_specificity
+//          https://en.wikipedia.org/wiki/Confusion_matrix
+//
+// formula's based upon wikipedia.
+
+
+#define GST_LIB_VERSION           (F("0.1.0"))
+
+
+class GST
+{
+public:
+  GST() {};
+
+  // These 4 need to be filled in.
+  void setTruePositive(float v)   { TP = v; P = TP + FN; };
+  void setTrueNegative(float v)   { TN = v; N = TN + FP; };
+  void setFalsePositive(float v)  { FP = v; N = TN + FP; };
+  void setFalseNegative(float v)  { FN = v; P = TP + FN; };
+
+  float getTruePositive()   { return TP; };
+  float getTrueNegative()   { return TN; };
+  float getFalsePositive()  { return FP; };
+  float getFalseNegative()  { return FN; };
+
+  float getTotal()          { return  P + N; };
+  float getActualPositive() { return  P; };
+  float getActualNegative() { return  N; };
+  float getTestedPositive() { return TP + FP; };
+  float getTestedNegative() { return TN + FN; };
+
+  float sensitivity()       { return TPR(); };
+  float specificity()       { return TNR(); };
+
+
+
+  //  true positive rate
+  float TPR() { return TP / P; };
+  //  true negative rate
+  float TNR() { return TN / N; };
+
+  //  false negative rate
+  float FNR() { return FN / (FN + TP); };
+  //  false positive rate
+  float FPR() { return FP / (FP + TN); };
+
+
+
+  //  positive predictive value
+  float PPV() { return TP / (TP + FP); };
+  //  negative predictive value
+  float NPV() { return TN / (TN + FN); };
+
+  //  false discovery rate
+  float FDR() { return FP / (FP + TP); };
+  //  false omission rate
+  float FOR() { return FN / (FN + TN); };
+
+
+
+  //  positive likelihood ratio
+  float LRplus()  { return TPR() / FPR(); };
+  //  negative likelihood ratio
+  float LRminus() { return FNR() / TNR(); };
+
+
+
+  float prevalenceThreshold()  { return sqrt(FPR()) / (sqrt(TPR()) + sqrt(FPR())); };
+  float threatScore()  { return TP / (TP + FN + FP); };
+  float criticalSuccessIndex() { return threatScore(); };
+
+
+
+  float prevalence()       { return P / (P + N); };
+  float accuracy()         { return (TP + TN) / (P + N); };
+  float balancedAccuracy() { return (TPR() + TNR()) / 2; };
+  float F1Score()          { return (2 * TP)/(2 * TP + FP + FN); };
+
+
+
+  //  Matthews correlation coefficient
+  float MCC() { return (TP*TN-FP*FN)/sqrt((TP+FP)*(TP+FN)*(TN+FP)*(TN+FN)); };
+  float phi() { return MCC(); };
+  //  Fowlkes–Mallows index
+  float FM() { return sqrt(PPV()*TPR()); };
+  //  Bookmaker informedness
+  float BM() { return TPR() + TNR() - 1; };
+  //  markedness
+  float MK() { return PPV() + NPV() - 1; };
+  float deltaP() { return MK(); };
+  //  diagnostic odds ratio
+  float DOR() { return LRplus() / LRminus(); };
+
+
+private:
+  float P  = 0;
+  float N  = 0;
+  float TP = 0;
+  float TN = 0;
+  float FP = 0;
+  float FN = 0;
+};
+
+
+// -- END OF FILE --
+

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022 Rob Tillaart
+Copyright (c) 2022-2022 Rob Tillaart
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,2 +1,42 @@
+
+[![Arduino CI](https://github.com/RobTillaart/GST/workflows/Arduino%20CI/badge.svg)](https://github.com/marketplace/actions/arduino_ci)
+[![Arduino-lint](https://github.com/RobTillaart/GST/actions/workflows/arduino-lint.yml/badge.svg)](https://github.com/RobTillaart/GST/actions/workflows/arduino-lint.yml)
+[![JSON check](https://github.com/RobTillaart/GST/actions/workflows/jsoncheck.yml/badge.svg)](https://github.com/RobTillaart/GST/actions/workflows/jsoncheck.yml)
+[![License: MIT](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/RobTillaart/GST/blob/master/LICENSE)
+[![GitHub release](https://img.shields.io/github/release/RobTillaart/GST.svg?maxAge=3600)](https://github.com/RobTillaart/GST/releases)
+
+
 # GST
-Arduino library for Gold Standard Test metrics
+
+Arduino library for Gold Standard Test metrics.
+
+
+## Description
+
+The GST library is **experimental**.
+
+
+#### Links
+
+- https://en.wikipedia.org/wiki/Sensitivity_and_specificity
+- https://en.wikipedia.org/wiki/Confusion_matrix
+
+
+## Interface
+
+See .h file
+
+
+## Future
+
+- documentation
+  - improve
+  - more links?
+- test
+  - complete the CI test coverage.
+- examples
+  - add real life examples.
+  - combination with a sensor? batch testing?
+- code
+  - full name functions instead of acronyms. (wrap?)
+  - is GST a good class name?

changelog.md

@@ -0,0 +1,9 @@
+
+# GST Changelog
+
+
+## 0.1.0 2022-02-25
+- initial version
+-
+
+