Merge pull request #70 from olivroy/master

.Rbuildignore

@@ -11,3 +11,4 @@
 ^Meta$
 ^CRAN-RELEASE$
 ^CRAN-SUBMISSION$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,49 @@
+# 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: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# 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

DESCRIPTION

@@ -43,9 +43,6 @@ Suggests:
     tidyquant,
     stringr,
     testthat (>= 2.1.0),
-    covr,
     knitr,
-    rmarkdown,
-    devtools,
-    roxygen2
+    rmarkdown
 VignetteBuilder: knitr

README.Rmd

@@ -2,6 +2,19 @@
 output: github_document
 ---
 
+# Anomalize is being Superceded by Timetk:
+
+# anomalize <img src="man/figures/anomalize-logo.png" width="147" height="170" align="right" />
+
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/business-science/anomalize/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/business-science/anomalize/actions/workflows/R-CMD-check.yaml)
+[![Lifecycle Status](https://img.shields.io/badge/lifecycle-superceded-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)
+[![Coverage status](https://codecov.io/gh/business-science/anomalize/branch/master/graph/badge.svg)](https://app.codecov.io/github/business-science/anomalize?branch=master)
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/anomalize)](https://cran.r-project.org/package=anomalize)
+![](http://cranlogs.r-pkg.org/badges/anomalize?color=brightgreen)
+![](http://cranlogs.r-pkg.org/badges/grand-total/anomalize?color=brightgreen)
+<!-- badges: end -->
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 ```{r setup, include = FALSE}
@@ -14,12 +27,9 @@ knitr::opts_chunk$set(
   message = F,
   warning = F
 )
-
-devtools::load_all()
-library(tidyverse)
+library(anomalize)
 ```
 
-# Anomalize is being Superceded by Timetk:
 
 The `anomalize` package functionality has been superceded by `timetk`. We suggest you begin to use the `timetk::anomalize()` to benefit from enhanced functionality to get improvements going forward. [Learn more about Anomaly Detection with `timetk` here.](https://business-science.github.io/timetk/articles/TK08_Automatic_Anomaly_Detection.html) 
 
@@ -36,13 +46,7 @@ plot_anomalies <- anomalize::plot_anomalies
 
 
 <!-- # anomalize -->
-# anomalize <img src="man/figures/anomalize-logo.png" width="147" height="170" align="right" />
 
-[![Lifecycle Status](https://img.shields.io/badge/lifecycle-superceded-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)
-[![Coverage status](https://codecov.io/gh/business-science/anomalize/branch/master/graph/badge.svg)](https://app.codecov.io/github/business-science/anomalize?branch=master)
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/anomalize)](https://cran.r-project.org/package=anomalize)
-![](http://cranlogs.r-pkg.org/badges/anomalize?color=brightgreen)
-![](http://cranlogs.r-pkg.org/badges/grand-total/anomalize?color=brightgreen)
 
 
 > Tidy anomaly detection
@@ -95,14 +99,15 @@ Next, let's get some data.  `anomalize` ships with a data set called `tidyverse_
 Suppose we want to determine which daily download "counts" are anomalous. It's as easy as using the three main functions (`time_decompose()`, `anomalize()`, and `time_recompose()`) along with a visualization function, `plot_anomalies()`.
 
 ```{r tidyverse_anoms_1, fig.height=8}
+library(magrittr)
 tidyverse_cran_downloads %>%
     # Data Manipulation / Anomaly Detection
     time_decompose(count, method = "stl") %>%
     anomalize(remainder, method = "iqr") %>%
     time_recompose() %>%
     # Anomaly Visualization
     plot_anomalies(time_recomposed = TRUE, ncol = 3, alpha_dots = 0.25) +
-    labs(title = "Tidyverse Anomalies", subtitle = "STL + IQR Methods") 
+    ggplot2::labs(title = "Tidyverse Anomalies", subtitle = "STL + IQR Methods") 
 ```
 
 Check out the [`anomalize` Quick Start Guide](https://business-science.github.io/anomalize/articles/anomalize_quick_start_guide.html). 
@@ -112,16 +117,16 @@ Check out the [`anomalize` Quick Start Guide](https://business-science.github.io
 Yes! Anomalize has a new function, `clean_anomalies()`, that can be used to repair time series prior to forecasting. We have a [brand new vignette - Reduce Forecast Error (by 32%) with Cleaned Anomalies](https://business-science.github.io/anomalize/articles/forecasting_with_cleaned_anomalies.html).
 ```{r}
 tidyverse_cran_downloads %>%
-    filter(package == "lubridate") %>%
-    ungroup() %>%
+    dplyr::filter(package == "lubridate") %>%
+    dplyr::ungroup() %>%
     time_decompose(count) %>%
     anomalize(remainder) %>%
   
     # New function that cleans & repairs anomalies!
     clean_anomalies() %>%
   
-    select(date, anomaly, observed, observed_cleaned) %>%
-    filter(anomaly == "Yes")
+    dplyr::select(date, anomaly, observed, observed_cleaned) %>%
+    dplyr::filter(anomaly == "Yes")
 ```
 
 
@@ -133,12 +138,12 @@ There are a several extra capabilities:
 
 ```{r, fig.height=7}
 tidyverse_cran_downloads %>%
-    filter(package == "lubridate") %>%
-    ungroup() %>%
+    dplyr::filter(package == "lubridate") %>%
+    dplyr::ungroup() %>%
     time_decompose(count) %>%
     anomalize(remainder) %>%
     plot_anomaly_decomposition() +
-    labs(title = "Decomposition of Anomalized Lubridate Downloads")
+    ggplot2::labs(title = "Decomposition of Anomalized Lubridate Downloads")
 ```
 
 For more information on the `anomalize` methods and the inner workings, please see ["Anomalize Methods" Vignette](https://business-science.github.io/anomalize/articles/anomalize_methods.html). 

README.md

@@ -1,8 +1,22 @@
 
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
 # Anomalize is being Superceded by Timetk:
 
+# anomalize <img src="man/figures/anomalize-logo.png" width="147" height="170" align="right" />
+
+<!-- badges: start -->
+
+[![R-CMD-check](https://github.com/business-science/anomalize/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/business-science/anomalize/actions/workflows/R-CMD-check.yaml)
+[![Lifecycle
+Status](https://img.shields.io/badge/lifecycle-superceded-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)
+[![Coverage
+status](https://codecov.io/gh/business-science/anomalize/branch/master/graph/badge.svg)](https://app.codecov.io/github/business-science/anomalize?branch=master)
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/anomalize)](https://cran.r-project.org/package=anomalize)
+![](http://cranlogs.r-pkg.org/badges/anomalize?color=brightgreen)
+![](http://cranlogs.r-pkg.org/badges/grand-total/anomalize?color=brightgreen)
+<!-- badges: end -->
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
 The `anomalize` package functionality has been superceded by `timetk`.
 We suggest you begin to use the `timetk::anomalize()` to benefit from
 enhanced functionality to get improvements going forward. [Learn more
@@ -24,16 +38,6 @@ plot_anomalies <- anomalize::plot_anomalies
 
 <!-- # anomalize -->
 
-# anomalize <img src="man/figures/anomalize-logo.png" width="147" height="170" align="right" />
-
-[![Lifecycle
-Status](https://img.shields.io/badge/lifecycle-superceded-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)
-[![Coverage
-status](https://codecov.io/gh/business-science/anomalize/branch/master/graph/badge.svg)](https://app.codecov.io/github/business-science/anomalize?branch=master)
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/anomalize)](https://cran.r-project.org/package=anomalize)
-![](http://cranlogs.r-pkg.org/badges/anomalize?color=brightgreen)
-![](http://cranlogs.r-pkg.org/badges/grand-total/anomalize?color=brightgreen)
-
 > Tidy anomaly detection
 
 `anomalize` enables a tidy workflow for detecting anomalies in data. The
@@ -98,14 +102,15 @@ anomalous. It’s as easy as using the three main functions
 visualization function, `plot_anomalies()`.
 
 ``` r
+library(magrittr)
 tidyverse_cran_downloads %>%
     # Data Manipulation / Anomaly Detection
     time_decompose(count, method = "stl") %>%
     anomalize(remainder, method = "iqr") %>%
     time_recompose() %>%
     # Anomaly Visualization
     plot_anomalies(time_recomposed = TRUE, ncol = 3, alpha_dots = 0.25) +
-    labs(title = "Tidyverse Anomalies", subtitle = "STL + IQR Methods") 
+    ggplot2::labs(title = "Tidyverse Anomalies", subtitle = "STL + IQR Methods") 
 ```
 
 <img src="man/figures/README-tidyverse_anoms_1-1.png" width="100%" />
@@ -122,16 +127,16 @@ Anomalies](https://business-science.github.io/anomalize/articles/forecasting_wit
 
 ``` r
 tidyverse_cran_downloads %>%
-    filter(package == "lubridate") %>%
-    ungroup() %>%
+    dplyr::filter(package == "lubridate") %>%
+    dplyr::ungroup() %>%
     time_decompose(count) %>%
     anomalize(remainder) %>%
 
     # New function that cleans & repairs anomalies!
     clean_anomalies() %>%
 
-    select(date, anomaly, observed, observed_cleaned) %>%
-    filter(anomaly == "Yes")
+    dplyr::select(date, anomaly, observed, observed_cleaned) %>%
+    dplyr::filter(anomaly == "Yes")
 #> # A time tibble: 19 × 4
 #> # Index:         date
 #>    date       anomaly  observed observed_cleaned
@@ -166,12 +171,12 @@ There are a several extra capabilities:
 
 ``` r
 tidyverse_cran_downloads %>%
-    filter(package == "lubridate") %>%
-    ungroup() %>%
+    dplyr::filter(package == "lubridate") %>%
+    dplyr::ungroup() %>%
     time_decompose(count) %>%
     anomalize(remainder) %>%
     plot_anomaly_decomposition() +
-    labs(title = "Decomposition of Anomalized Lubridate Downloads")
+    ggplot2::labs(title = "Decomposition of Anomalized Lubridate Downloads")
 ```
 
 <img src="man/figures/README-unnamed-chunk-3-1.png" width="100%" />