From e43ac2dce88de43f5d8e26187bcb2e134af35742 Mon Sep 17 00:00:00 2001
From: rosieluain <rosieluain@gmail.com>
Date: Mon, 22 Jan 2024 19:44:42 -0700
Subject: [PATCH] code coverage

---
 .Rbuildignore                        |  1 +
 .github/workflows/test-coverage.yaml | 55 ++++++++++++++++++++++++++++
 DESCRIPTION                          |  1 +
 R/mort.R                             | 28 +++++++++++++-
 README.Rmd                           |  1 +
 README.md                            |  3 ++
 codecov.yml                          | 14 +++++++
 7 files changed, 102 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/test-coverage.yaml
 create mode 100644 codecov.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index 9078b1a..a6f7c68 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -10,3 +10,4 @@
 ^cran-comments\.md$
 ^doc$
 ^Meta$
+^codecov\.yml$
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..729d01a
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,55 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/DESCRIPTION b/DESCRIPTION
index b69fd89..7ad1cae 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -21,6 +21,7 @@ Imports:
     methods,
     rlang
 Suggests: 
+    covr,
     ggplot2,
     knitr,
     plotly,
diff --git a/R/mort.R b/R/mort.R
index 78fc616..e345094 100644
--- a/R/mort.R
+++ b/R/mort.R
@@ -148,6 +148,11 @@ morts<-function(data,type="mort",ID,station,res.start="auto",res.end="auto",
     }
   }
 
+  # Check that all records have a station assigned
+  if (nrow(data[is.na(data[[station]]),])>0){
+    stop("Station must be specified for all records.")
+  }
+
   data.full<-data
   if (!is.null(season.start)|
       !is.null(season.end)){
@@ -680,6 +685,11 @@ infrequent<-function(data,type="mort",ID,station,res.start="auto",
     }
   }
 
+  # Check that all records have a station assigned
+  if (nrow(data[is.na(data[[station]]),])>0){
+    stop("Station must be specified for all records.")
+  }
+
   if (any(data[[station]]=="Break")){
     warning("Either a station name was 'Break' or data included seasonal
             breaks. Breaks were removed.")
@@ -764,7 +774,23 @@ infrequent<-function(data,type="mort",ID,station,res.start="auto",
                           res.temp[[res.end]],
                           units=recent.units)<=recent.period))
         res.temp<-res.temp[j:nrow(res.temp),]
-        if (is.null(ddd)){
+        if (nrow(res.temp)>0&length(unique(res.temp$Station.Name))==1){
+          if (sum(res.temp[[residences]])<threshold){
+            if (tag[i] %in% inf.morts[[ID]]){
+              k<-which(inf.morts[[ID]]==tag[i])
+              if (res.temp[[res.start]][1]<inf.morts[[res.start]][k]){
+                inf.morts[k,]<-res.temp[1,]
+                if (!is.null(morts.prev)&backwards==TRUE){
+                  new.morts<-c(new.morts,k)
+                }
+              }
+            }
+            else {
+              inf.morts[nrow(inf.morts)+1,]<-res.temp[1,]
+            }
+          }
+        }
+        else if (is.null(ddd)){
           if (nrow(res.temp)>=1&
               length(unique(res.temp[[station]]))==1&
               sum(res.temp[[residences]])<threshold){
diff --git a/README.Rmd b/README.Rmd
index ae0083a..cb82965 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -16,6 +16,7 @@ knitr::opts_chunk$set(
 # mort <img src="man/figures/logo.png" align="right" height="139" />
 
 <!-- badges: start -->
+[![Codecov test coverage](https://codecov.io/gh/rosieluain/mort/branch/main/graph/badge.svg)](https://app.codecov.io/gh/rosieluain/mort?branch=main)
 <!-- badges: end -->
 
 The goal of mort is to provide a framework to identify potential mortalities or expelled tags in passive acoustic telemetry arrays with non-overlapping receivers. The potential mortalities that are flagged by mort should be reviewed by the user, and considered for removal from the dataset. 
diff --git a/README.md b/README.md
index 7567244..ddeaf2c 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,9 @@
 # mort <img src="man/figures/logo.png" align="right" height="139" />
 
 <!-- badges: start -->
+
+[![Codecov test
+coverage](https://codecov.io/gh/rosieluain/mort/branch/main/graph/badge.svg)](https://app.codecov.io/gh/rosieluain/mort?branch=main)
 <!-- badges: end -->
 
 The goal of mort is to provide a framework to identify potential
diff --git a/codecov.yml b/codecov.yml
new file mode 100644
index 0000000..04c5585
--- /dev/null
+++ b/codecov.yml
@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true