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VEZYVEZY
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Add github actions + rename package biomech + add description + add readme
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Diff for: ‎.Rbuildignore

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^codecov\.yml$
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^bin$
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^tmp$
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^\.github$

Diff for: ‎.github/.gitignore

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*.html

Diff for: ‎.github/workflows/R-CMD-check.yaml

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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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- master
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pull_request:
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branches:
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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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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@master
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with:
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r-version: ${{ matrix.config.r }}
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- uses: r-lib/actions/setup-pandoc@master
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$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@v1
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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

Diff for: ‎.github/workflows/pkgdown.yaml

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on:
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push:
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branches: master
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name: pkgdown
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jobs:
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pkgdown:
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runs-on: macOS-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-r@master
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- uses: r-lib/actions/setup-pandoc@master
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$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@v1
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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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remotes::install_deps(dependencies = TRUE)
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install.packages("pkgdown")
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shell: Rscript {0}
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- name: Install package
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run: R CMD INSTALL .
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- name: Deploy package
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run: |
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git config --local user.email "[email protected]"
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git config --local user.name "GitHub Actions"
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Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

Diff for: ‎.github/workflows/render-readme.yaml

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on:
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push:
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paths:
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- README.Rmd
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name: Render README
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jobs:
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render:
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name: Render README
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runs-on: macOS-latest
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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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- uses: r-lib/actions/setup-pandoc@v1
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- name: Install rmarkdown, remotes, and the local package
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run: |
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install.packages("remotes")
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remotes::install_local(".")
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remotes::install_cran("rmarkdown")
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shell: Rscript {0}
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- name: Render README
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run: Rscript -e 'rmarkdown::render("README.Rmd")'
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- name: Commit results
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run: |
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git config --local user.email "[email protected]"
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git config --local user.name "GitHub Actions"
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git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit"
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git push origin || echo "No changes to commit"

Diff for: ‎DESCRIPTION

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Package: deformation
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Package: biomech
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Type: Package
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Title: What the Package Does (Title Case)
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Title: Compute Beam Bending and Torsion
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Version: 0.1.0
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Author: Who wrote it
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Maintainer: The package maintainer <[email protected]>
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Description: More about what it does (maybe more than one line)
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Use four spaces when indenting paragraphs within the Description.
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License: What license is it under?
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Authors@R: c(person(given = "Remi", family = "Vezy", email = "[email protected]", role = c("aut","cre"),comment = c(ORCID = "0000-0002-0808-1461")),
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person(given = "Loic", family = "Brancheriau", email = "[email protected]", role = c("aut")),
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person(given = "Raphael", family = "Perez", email = "[email protected]", role = c("aut")),
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person(given = "Jean", family = "Dauzat", email = "[email protected]", role = c("aut")))
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Description: Compute bending and torsion of beams following the Euler-Bernoulli beam theory. It is specifically designed to be applied on
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tree branches (or e.g. palm leaves), but is available for any other beam-shaped structure.
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License: GPL-3
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Encoding: UTF-8
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LazyData: true
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.1.1
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Suggests:
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testthat
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Config/testthat/edition: 3
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Imports:
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data.table

Diff for: ‎R/Agl_Vers_XYZ.R

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#' @param vAngle_XY Angle between the segment and the XY plane (radian)
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#' @param vAngle_XZ Angle between the segment and the XZ plane (radian)
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#'
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#' @return
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#' @return Point coordinates
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#' @export
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#'
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Agl_Vers_XYZ = function(dist_P2P1, vAngle_XY, vAngle_XZ){

Diff for: ‎R/InterpPoints.R

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vAngle_XZ = XYZ_Agl$vAngle_XZ
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distLineique = cumsum(vDist_P2P1)
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distTotale = tail(distLineique,1)
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distTotale = utils::tail(distLineique,1)
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# Les distances des segments ne peuvent pas etre nulles
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# Le point origine (0,0,0) ne peut etre dans matPoints

Diff for: ‎R/XYZ_Vers_Agl.R

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#' @export
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#'
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#' @examples
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#' library(data.table)
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#' filepath = system.file("extdata/6_EW01.22_17_kanan.txt", package = "deformation")
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#' filepath = system.file("extdata/6_EW01.22_17_kanan.txt", package = "biomech")
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#' df = read_mat(filepath)
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#' df = unbend(2000,400,df)
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#' XYZ_Vers_Agl(df[1,],df[2,],df[3,])
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#' XYZ_Vers_Agl(df$x,df$y,df$z)
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#'
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XYZ_Vers_Agl = function(vecX, vecY, vecZ){
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N = length(vecX)

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