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Added new action for CI pipeline (#16)
* Create cran.yml (#15) * Upped version number * Ignore github actions folder * Updated manuals using Roxygen2 * Added virtual deconstructor to prevent memory leak * Cleaned compiler flags * Adjusted testthat catch entrypoint to new definition * Added DS_Store to gitignore * Added DS_Store to gitignore * Create codecov.yml * Added covr, not running all tests yet * LTO warnings - deleted extra ;
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‎.Rbuildignore‎

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^\.travis\.yml$
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^.*\.Rproj$
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^\.Rproj\.user$
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.github
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.covrignore

‎.covrignore‎

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inst

‎.github/workflows/codecov.yml‎

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# This is a basic workflow to help you get started with Actions
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name: codecov
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# Controls when the action will run.
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on:
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# Triggers the workflow on push or pull request events but only for the dev branch
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push:
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branches: [ dev ]
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pull_request:
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branches: [ dev ]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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jobs:
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test-coverage:
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runs-on: macOS-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v1
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install dependencies
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run: |
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install.packages(c("remotes"))
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("covr")
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shell: Rscript {0}
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- name: Test coverage
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run: covr::codecov()
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shell: Rscript {0}

‎.github/workflows/cran.yml‎

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# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
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# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
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on:
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push:
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branches:
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- main
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- master
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pull_request:
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branches:
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- main
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- master
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name: R-CMD-check
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: windows-latest, r: 'release'}
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- {os: macOS-latest, r: 'release'}
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- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@v1
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with:
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r-version: ${{ matrix.config.r }}
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- uses: r-lib/actions/setup-pandoc@v1
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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if: runner.os != 'Windows'
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uses: actions/cache@v2
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install system dependencies
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if: runner.os == 'Linux'
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run: |
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while read -r cmd
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do
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eval sudo $cmd
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done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
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- name: Install dependencies
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run: |
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("rcmdcheck")
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shell: Rscript {0}
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- name: Check
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env:
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_R_CHECK_CRAN_INCOMING_REMOTE_: false
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run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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shell: Rscript {0}
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@main
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with:
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name: ${{ runner.os }}-r${{ matrix.config.r }}-results
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path: check

‎.gitignore‎

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*.o
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*.gcno
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.Rproj.user
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.DS_Store

‎DESCRIPTION‎

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Package: ANN2
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Type: Package
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Title: Artificial Neural Networks for Anomaly Detection
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Version: 2.3.3
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Date: 2020-03-14
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Version: 2.3.4
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Date: 2020-11-29
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Author: Bart Lammers
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Maintainer: Bart Lammers <[email protected]>
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Description: Training of neural networks for classification and regression tasks
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viridisLite (>= 0.3.0), methods
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LinkingTo: Rcpp, RcppArmadillo, testthat
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Suggests: testthat
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RoxygenNote: 6.1.1
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RoxygenNote: 7.1.1

‎R/catch-routine-registration.R‎

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# 'tools::package_native_routine_registration_skeleton()' generates the required
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# registration info for the 'run_testthat_tests' symbol.
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(function() {
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.Call("run_testthat_tests", PACKAGE = "ANN2")
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.Call("run_testthat_tests", FALSE, PACKAGE = "ANN2")
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})

‎R/plotting.R‎

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#' @title Plot training and validation loss
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#' @description \code{plot} Generate plots of the loss against epochs
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#' @details A genereric function for training neural nets
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#' @details A generic function for plot loss of neural net
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#' @method plot ANN
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#' @param x Object of class \code{ANN}
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#' @param max.points Maximum number of points to plot, set to NA, NULL or Inf to
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#' include all points in the plot
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#' @param ... further arguments to be passed to plot
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#' @return Plots
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#' @method plot ANN
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#' @export
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plot.ANN <- function(x, max.points = 1000, ...) {
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‎README.md‎

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[![Licence](https://img.shields.io/badge/licence-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
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[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/ANN2)](https://cran.r-project.org/package=ANN2) ![](http://cranlogs.r-pkg.org/badges/grand-total/ANN2?color=green) ![](http://cranlogs.r-pkg.org/badges/last-week/ANN2?color=green)
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[![Travis build status](https://travis-ci.org/bflammers/ANN2.svg?branch=master)](https://travis-ci.org/bflammers/ANN2)
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[![codecov](https://codecov.io/gh/bflammers/ANN2/branch/master/graph/badge.svg)](https://codecov.io/gh/bflammers/ANN2)
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[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/ANN2)](https://cran.r-project.org/package=ANN2)
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![Monthly downloads](https://cranlogs.r-pkg.org/badges/ANN2)
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![R CMD check](https://github.com/bflammers/ANN2/workflows/R-CMD-check/badge.svg)
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[![codecov](https://codecov.io/gh/bflammers/ANN2/branch/dev/graph/badge.svg)](https://codecov.io/gh/bflammers/ANN2)
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# ANN2
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Artificial Neural Networks package for R

‎man/autoencoder.Rd‎

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