PvSTATEM 0.0.2 (#37)

* bug: standard curve sample type (#13)

* simple README with overview and installation (#7)

* website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

* added STANDARD CURVE type, added option to reverse the xaxis of MFI plot, plots in ggplot2, log scales

* docs

* plate name detection based on filepath

* changed the default log scale into `all`

---------

Co-authored-by: Fersoil <Fersoil>

* Add tests and setup GHA (#18)

* simple README with overview and installation (#7)

* website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

* Add .gitignore

* Add sample files and adequate tests

* Setup package workflow

* Style code (GHA)

* Export remaining objects

* Move dots down

* Add missing usage description

* Disable lint error

* Fix missing import ggplot2

---------

Co-authored-by: Tymoteusz Kwieciński <[email protected]>
Co-authored-by: ZetrextJG <[email protected]>

* Add dev to GHA for R check and test coverage (#19)

* Add codecov (#26)

* bug fixes #16, #24  (#32)

* simple README with overview and installation (#7)

* website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

* bug: standard curve sample type (#13)

* simple README with overview and installation (#7)

* website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

* added STANDARD CURVE type, added option to reverse the xaxis of MFI plot, plots in ggplot2, log scales

* docs

* plate name detection based on filepath

* changed the default log scale into `all`

---------

Co-authored-by: Fersoil <Fersoil>

* Add tests and setup GHA (#18)

* simple README with overview and installation (#7)

* website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

* Add .gitignore

* Add sample files and adequate tests

* Setup package workflow

* Style code (GHA)

* Export remaining objects

* Move dots down

* Add missing usage description

* Disable lint error

* Fix missing import ggplot2

---------

Co-authored-by: Tymoteusz Kwieciński <[email protected]>
Co-authored-by: ZetrextJG <[email protected]>

* Add dev to GHA for R check and test coverage (#19)

* fixed sample type recognition; added standard curve to summary

* updated example script with Covid OISE dataset

* updated example script

---------

Co-authored-by: Jakub Grzywaczewski <[email protected]>
Co-authored-by: ZetrextJG <[email protected]>
Co-authored-by: Fersoil <Fersoil>

* Covid OISE datasets & external data (#34)

* Add covid and external data

* Rename file and add a second plate from Covid OISE

* description of available datasets

---------

Co-authored-by: Fersoil <Fersoil>

* Standard curves - normalization & plotting (#36)

* simple README with overview and installation (#7)

* website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

* added simple nplr model

* standard curve as plate attribute; simple plot of fitted model

* standard curve model fitting

* enchanced standard curve fitting, fixed reading Covid oise files, added docs

* expanded example script with Covid oise dataset and curve fitting

* predictions in example script

* minor fixes of predictions script

* covid oise datasets

* add `nplr` to `DESCRIPTION`

* vignette engine fixes

* added `ggplot2` import

* error fixes

* add imports to vignettes

* add docs

* CMD check fixes

* CMD check warning fixes

* correct license formatting

* datasets description

* add covid oise layout file

* restore `qpdf` import

---------

Co-authored-by: Fersoil <Fersoil>

* Style code (GHA)

* update package version

---------

Co-authored-by: Jakub Grzywaczewski <[email protected]>
Co-authored-by: ZetrextJG <[email protected]>
Co-authored-by: Fersoil <Fersoil>
Co-authored-by: Fersoil <[email protected]>

.Rbuildignore

@@ -1,2 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^LICENSE\.md$
+^\.github$

.github/.gitignore

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

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

@@ -0,0 +1,52 @@
+# 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, dev]
+  pull_request:
+    branches: [main, dev]
+
+name: R-CMD-check
+
+permissions: read-all
+
+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@v4
+
+      - 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
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/lint.yaml

@@ -0,0 +1,34 @@
+# 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, dev]
+  pull_request:
+    branches: [main, dev]
+
+name: lint
+
+permissions: read-all
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: false

.github/workflows/pkgdown.yaml

@@ -13,6 +13,56 @@ name: pkgdown
 
 permissions: read-all
 
+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@v4
+
+      - 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
+# 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]
+  pull_request:
+    branches: [main]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest

.github/workflows/style.yaml

@@ -0,0 +1,78 @@
+# 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:
+    paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown", "**.[rR]nw", "**.[rR]profile"]
+    branches: [main, dev]
+
+name: Style
+
+permissions: read-all
+
+jobs:
+  style:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::styler, any::roxygen2
+          needs: styler
+
+      - name: Enable styler cache
+        run: styler::cache_activate()
+        shell: Rscript {0}
+
+      - name: Determine cache location
+        id: styler-location
+        run: |
+          cat(
+            "location=",
+            styler::cache_info(format = "tabular")$location,
+            "\n",
+            file = Sys.getenv("GITHUB_OUTPUT"),
+            append = TRUE,
+            sep = ""
+          )
+        shell: Rscript {0}
+
+      - name: Cache styler
+        uses: actions/cache@v4
+        with:
+          path: ${{ steps.styler-location.outputs.location }}
+          key: ${{ runner.os }}-styler-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-styler-
+            ${{ runner.os }}-
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          if FILES_TO_COMMIT=($(git diff-index --name-only ${{ github.sha }} \
+              | egrep --ignore-case '\.(R|[qR]md|Rmarkdown|Rnw|Rprofile)$'))
+          then
+            git config --local user.name "$GITHUB_ACTOR"
+            git config --local user.email "[email protected]"
+            git commit ${FILES_TO_COMMIT[*]} -m "Style code (GHA)"
+            git pull --ff-only
+            git push origin
+          else
+            echo "No changes to commit."
+          fi

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# 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, dev]
+  pull_request:
+    branches: [main, dev]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - 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, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -0,0 +1,5 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+inst/doc

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+
+-   repo: local
+    hooks:
+    -   id: styler
+        name: Style R code with styler
+        entry: Rscript -e "errors <- styler::style_pkg(); print(errors); quit(save = 'no', status = sum(errors[[2]]))"
+        language: system
+        files: '\.Rproj$'
+        always_run: true

DESCRIPTION

@@ -1,17 +1,25 @@
 Package: PvSTATEM
 Type: Package
 Title: Reading, quality control and preprocessin of MBA assay data
-Version: 0.0.1
+Description: Reading, quality control and preprocessin of MBA assay data.
+Version: 0.0.2
 Authors@R: person("Tymoteusz", "Kwiecinski", email = "[email protected]", role = c("aut", "cre"))
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports:
     dplyr,
     R6,
     tools,
+    qpdf,
     readxl,
-    RColorBrewer
-Suggests: 
+    RColorBrewer,
+    knitr,
+    rmarkdown,
+    ggplot2,
+    nplr,
+Suggests:
     testthat (>= 3.0.0)
-Config/testthat/edition: 3
+Config/testfhat/edition: 3
 Roxygen: list(markdown = TRUE, r6 = TRUE)
+License: BSD_3_clause
+VignetteBuilder: knitr

LICENSE → LICENSE.md

@@ -26,3 +26,4 @@ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+

NAMESPACE

@@ -1,5 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
+export(Analyte)
 export(Plate)
+export(Sample)
+export(SampleLocation)
+export(SampleType)
+export(create_standard_curve_model_antibody)
 export(plot_standard_curve_antibody)
+export(plot_standard_curve_antibody_with_model)
+export(predict_dilutions)
 export(read_data)
+import(ggplot2)
+import(nplr)