website for docs (#8)

* add sample vignette and artificial dataset

* pkgdown workflow

---------

Co-authored-by: Fersoil <Fersoil>

.github/workflows/pkgdown.yaml

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+# 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
+    # 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/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

inst/extdata/artificial_plate.csv

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+Program,xPONENT,,MAGPIX,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Build,3.1.871.0,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Date,01/07/2024,00:00,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+SN,PvSTATEM1234,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Batch,test_plate,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Version,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Operator,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+ComputerName,test,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Country Code,616,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+ProtocolName,test,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+ProtocolVersion,1,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Most Recent Calibration and Verification Results:,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Last VER Calibration,Passed 01/07/2024 00:00:00,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Last CAL Calibration,Passed 01/07/2024 00:00:00,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Last Fluidics Test,Passed 01/07/2024 00:00:00,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+CALInfo:,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Calibrator,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Lot,ExpirationDate,CalibrationTime,DDTemp,CL1Temp,CL2Temp,DDVolts,CL1Volts,CL2Volts,DDRVal,CL1RVal,CL2RVal,Result,MachineSerialNo,,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Samples,8,Min Events,50,Per Bead,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Results,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+DataType:,Median,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Location,Sample,Etramp5_ag1,Etramp4_ag1,AMA1
+1(1,A1),BLANK,20, 21, 23
+2(1,B1),test1,1292,1389,1414
+3(1,C1),test2,1430,1435, 867
+4(1,D1),test3,657,2031,1300
+5(1,E1),CP3 1/50,1486,1437,1893
+6(1,F1),CP3 1/250,130,87,90
+7(1,G1),CP3 1/1250,78,67,64
+8(1,H1),CP3 1/6250, 65,60,64
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+DataType:,Count,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Location,Sample,Etramp5_ag1,Etramp4_ag1,AMA1
+1(1,A1),BLANK,100,121,143
+2(1,B1),test1,102,104,105
+3(1,C1),test2,130,135, 67
+4(1,D1),test3,57,231,100
+5(1,E1),CP3 1/50,86,37,193
+6(1,F1),CP3 1/250,130,87,90
+7(1,G1),CP3 1/1250,53,47,65
+8(1,H1),CP3 1/6250, 85,50,54
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+DataType:,Per Bead Count,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Alyte:,Etramp5_ag1,Etramp4_ag1,AMA1
+BeadID:,73,75,34
+Per Bead:,50,50,50,
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+DataType:,Audit Logs,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+UserId,Date,Message,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+DataType:,Warnings/Errors,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+Location,Status,Message,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+-- CRC --,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+CRC32: 85C2BFCD,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

vignettes/example_script.Rmd

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+---
+title: "Simple example of basic PvSTATEM package pre-release version functionalities"
+author: "Tymoteusz Kwieciński"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_document
+vignette: >
+  %\VignetteIndexEntry{Simple example of basic PvSTATEM package pre-release version functionalities}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(
+  collapse = FALSE,
+  comment = "#>",
+  warning = FALSE,
+  message = FALSE
+)
+```
+
+# Introduction
+The basic functionality of the `PvSTATEM` package is reading raw MBA data. To present the functionalities of the package, we created a simple, artificial `csv` file, which is pre-loaded into the package.
+
+```{r}
+library(PvSTATEM)
+
+plate_filepath <- system.file("extdata", "artificial_plate.csv", package = "PvSTATEM", mustWork = TRUE) # get the filepath of the csv dataset
+
+
+plate <- read_data(plate_filepath) # read the data
+
+```
+
+After the plate is successfully loaded, we can look into some basic information about the plate.
+
+```{r}
+
+
+plate$summary()
+
+plate$get_sample(1)
+plate$get_sample_by_type("POSITIVE CONTROL")[[1]]
+
+plate$sample_names
+plate$analyte_names
+```
+
+
+
+## Warnings
+Our scripts are designed to catch potential errors in the data. If there are any warnings, they will be stored in the `warnings` field of the plate object. The warnings can be accessed by the `$warnings` field of the plate object or by the `$warnings` field of the sample object.
+
+```{r}
+```{r}
+## warnings ----------------------------------------------------------------
+
+plate$warnings
+
+plate$get_sample(1)$warnings
+
+plate$get(analyte = "AMA1", sample = 1)
+
+plate$get_sample_by_type("POSITIVE CONTROL")[[1]]$warnings
+```
+
+
+
+## simple standard curve plotting
+```{r}
+plot_standard_curve_antibody(plate, antibody_name = "AMA1")
+
+plate$blank_adjustment()
+
+plot_standard_curve_antibody(plate, antibody_name = "AMA1")
+
+
+```