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Merge branch 'develop' into lemireg-add_quartiles-pairwise_test_cont
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‎.Rbuildignore‎

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CONTRIBUTING.md
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^\.github$
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data-raw/
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^_pkgdown\.yml$
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^docs$
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^pkgdown$

‎.github/workflows/R-CMD-check.yaml‎

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fancyhdr colortbl soul setspace relsize makecell threeparttable
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threeparttablex environ trimspaces
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- uses: r-lib/actions/setup-r@v2
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- name: Setup recent R
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uses: r-lib/actions/setup-r@v2
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if: ${{ matrix.config.r != '4.0.4' }}
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- name: Install statsrv packages
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- name: Setup R 4.0.4
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uses: r-lib/actions/setup-r@v2
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if: ${{ matrix.config.r == '4.0.4' }}
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run: |
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sudo apt install -y libx11-dev make libgit2-dev libssh2-1-dev libssl-dev zlib1g-dev libicu-dev libpng-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev libxml2-dev libcurl4-openssl-dev
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R -q -e 'utils::install.packages("remotes")'
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R -q -e 'remotes::install_version("htmlTable", "2.4.1")'
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R -q -e 'remotes::install_version("scales", "1.3.0")'
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R -q -e 'remotes::install_version("Hmisc", "4.5-0")'
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R -q -e 'remotes::install_version("svglite", "2.1.3")'
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R -q -e 'remotes::install_github("FredHutch/VISCfunctions", dependencies = TRUE)'
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R -q -e 'utils::install.packages("rcmdcheck")'
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with:
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r-version: ${{ matrix.config.r }}
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cran: 'https://packagemanager.posit.co/cran/__linux__/noble/2024-04-19'
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- uses: r-lib/actions/setup-r-dependencies@v2
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if: ${{ matrix.config.r != '4.0.4' }}
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with:
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extra-packages: any::rcmdcheck
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needs: check

‎.github/workflows/pkgdown.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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release:
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types: [published]
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workflow_dispatch:
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name: pkgdown.yaml
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permissions: read-all
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jobs:
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pkgdown:
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runs-on: ubuntu-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::pkgdown, local::.
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needs: website
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- name: Build site
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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- name: Deploy to GitHub pages 🚀
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if: github.event_name != 'pull_request'
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uses: JamesIves/github-pages-deploy-action@v4.5.0
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with:
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clean: false
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branch: gh-pages
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folder: docs

‎.gitignore‎

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Meta
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/doc/
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/Meta/
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docs

‎DESCRIPTION‎

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Package: VISCfunctions
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Type: Package
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Package: VISCfunctions
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Title: VISC STP/SRA functions
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Version: 1.3.0
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Authors@R: c(person("Bryan", "Mayer", ,"bmayer@fredhutch.org", "aut"),
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person("Monica", "Gerber", ,"mgerber@fredhutch.org", "aut"),
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person("Celia", "Mahoney", ,"cmahoney@fredhutch.org", "aut"),
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person("Ellis", "Hughes", ,"ehhughes@fredhutch.org", "aut"),
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person("Heather", "Bouzek", ,"hbouzek@fredhutch.org", "aut"),
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person("Jimmy", "Fulp", ,"wfulp@fredhutch.org", c("aut", "cre"))
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)
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Description: Statistical, data processing, and annotation functions for VISC.
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Version: 1.3.0.9000
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Authors@R: c(
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person("Bryan", "Mayer", , "bmayer@fredhutch.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2258-5276")),
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person("Dave", "Slager", , "dslager@fredhutch.org", role = "aut", comment = c(ORCID = "0000-0003-2525-2039")),
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person("Kellie", "MacPhee", , "kmacphee@fredhutch.org", role = "aut", comment = c(ORCID = "0009-0008-0993-4009")),
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person("Gabrielle", "Lemire", , "glemire@fredhutch.org", role = "aut"),
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person("Claudio", "Yurdadon", , "cyurdado@fredhutch.org", role = "aut", comment = c(ORCID = "0000-0002-4928-2737")),
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person("Monica", "Gerber", , , role = "aut"),
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person("Celia", "Mahoney", , , role = "aut"),
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person("Ellis", "Hughes", , , role = "aut", comment = c(ORCID = "0000-0003-0637-4436")),
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person("Heather", "Bouzek", , , role = "aut"),
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person("Jimmy", "Fulp", , , role = "aut")
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)
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Description:
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Statistical, data processing, and annotation functions for VISC.
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License: MIT + file LICENSE
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Depends: R (>= 2.10)
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Depends:
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R (>= 3.5)
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Imports:
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binom,
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coin (>= 1.3-1),
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coin,
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Exact,
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kableExtra,
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knitr,
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lifecycle,
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purrr,
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sessioninfo,
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survival,
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withr
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Suggests:
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ggplot2,
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dplyr,
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tidyr,
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ggplot2,
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pracma,
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rmarkdown,
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testthat,
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stringr,
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tibble
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tidyr
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VignetteBuilder:
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knitr
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 7.3.2
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.3
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URL: https://fredhutch.github.io/VISCfunctions/

‎NEWS.md‎

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# VISCfunctions (development version)
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* Maintenance of package and CI (#114)
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* Add B cell example dataset from G001 flow and sequencing file (#108)
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# VISCfunctions 1.3.0
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* Fix bug in `pairwise_test_bin()` and `pairwise_test_cont()` (#111)

‎R/data.R‎

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#' }
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#' @source \url{https://dataspace.cavd.org}
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"CAVD812_mAB"
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#' @title Example B-cell flow-and-summary file derived from G001
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#' @description Example B-cell flow-and-summary file derived from G001
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#' @format A data frame with 3995 rows and 22 variables:
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#' \describe{
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#' \item{\code{pubid}}{character COLUMN_DESCRIPTION}
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#' \item{\code{group}}{integer COLUMN_DESCRIPTION}
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#' \item{\code{treatment}}{character COLUMN_DESCRIPTION}
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#' \item{\code{dose}}{double COLUMN_DESCRIPTION}
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#' \item{\code{dose_unit}}{character COLUMN_DESCRIPTION}
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#' \item{\code{visitno}}{character COLUMN_DESCRIPTION}
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#' \item{\code{visit}}{integer COLUMN_DESCRIPTION}
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#' \item{\code{visit_units}}{character COLUMN_DESCRIPTION}
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#' \item{\code{sample_type}}{character COLUMN_DESCRIPTION}
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#' \item{\code{probeset}}{character COLUMN_DESCRIPTION}
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#' \item{\code{source_assay}}{character COLUMN_DESCRIPTION}
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#' \item{\code{endpoint}}{character COLUMN_DESCRIPTION}
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#' \item{\code{endpoint_value}}{double COLUMN_DESCRIPTION}
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#' \item{\code{endpoint_value_type}}{character COLUMN_DESCRIPTION}
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#' \item{\code{endpoint_value_imputed}}{character COLUMN_DESCRIPTION}
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#' \item{\code{bcell_population}}{character COLUMN_DESCRIPTION}
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#' \item{\code{percent_denominator}}{character COLUMN_DESCRIPTION}
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#' \item{\code{igx_type}}{character COLUMN_DESCRIPTION}
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#' \item{\code{antigen_specificity}}{character COLUMN_DESCRIPTION}
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#' \item{\code{epitope_specificity}}{character COLUMN_DESCRIPTION}
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#' \item{\code{bnab_class}}{character COLUMN_DESCRIPTION}
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#' \item{\code{source_file}}{character COLUMN_DESCRIPTION}
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#'}
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#' @details Example B-cell flow-and-summary file derived from G001
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#' @source \url{https://github.com/SchiefLab/G001/raw/main/data/figures/flow_summary/flow_and_sequences.csv.gz}
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"G001_Bcell_flow_seq_PBMC"

‎R/pairwise_comparisons.R‎

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#' ## Group Comparison
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#'group_testing_tibble <- exampleData_BAMA %>%
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#' group_by(antigen, visitno) %>%
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#' summarise(pairwise_test_cont(x = magnitude,
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#' group = group,
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#' paired = FALSE,
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#' method = 'wilcox',
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#' alternative = "less",
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#' sorted_group = c(1,2),
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#' digits = 3,
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#' num_needed_for_test = 3,
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#' verbose = TRUE),
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#' .groups = "keep")
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#' reframe(pairwise_test_cont(x = magnitude,
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#' group = group,
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#' paired = FALSE,
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#' method = 'wilcox',
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#' alternative = "less",
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#' sorted_group = c(1,2),
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#' digits = 3,
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#' num_needed_for_test = 3,
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#' verbose = TRUE))
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#'
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#'
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#' ## Timepoint Comparison
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#'timepoint_testing_dt <- exampleData_BAMA %>%
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#' group_by(antigen, group) %>%
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#' summarise(pairwise_test_cont(x = magnitude,
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#' group = visitno,
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#' paired = TRUE,
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#' id = pubID,
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#' method = 'wilcox',
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#' sorted_group = c(0,1,2),
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#' alternative = 'less',
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#' num_needed_for_test = 3,
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#' digits = 3,
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#' trailing_zeros = TRUE,
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#' sep_val = ' vs. ',
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#' verbose = TRUE),
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#' .groups = "keep")
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#' reframe(pairwise_test_cont(x = magnitude,
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#' group = visitno,
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#' paired = TRUE,
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#' id = pubID,
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#' method = 'wilcox',
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#' sorted_group = c(0,1,2),
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#' alternative = 'less',
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#' num_needed_for_test = 3,
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#' digits = 3,
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#' trailing_zeros = TRUE,
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#' sep_val = ' vs. ',
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#' verbose = TRUE))
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#'
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#'
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#' # ICS Assay Data Example
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#' # using dplyr
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#'exampleData_ICS %>%
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#'group_by(Stim, Parent, Population, Visit) %>%
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#'summarise(pairwise_test_cont(x = PercentCellNet,
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#' group = Group,
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#' paired = FALSE,
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#' method = 'wilcox',
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#' alternative = 'less',
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#' sorted_group = c(1,2,3,4),
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#' num_needed_for_test = 3,
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#' digits = 4,
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#' trailing_zeros = TRUE,
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#' sep_val = ' vs. ',
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#' verbose = TRUE),
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#' .groups = "keep")
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#'reframe(pairwise_test_cont(x = PercentCellNet,
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#' group = Group,
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#' paired = FALSE,
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#' method = 'wilcox',
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#' alternative = 'less',
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#' sorted_group = c(1,2,3,4),
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#' num_needed_for_test = 3,
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#' digits = 4,
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#' trailing_zeros = TRUE,
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#' sep_val = ' vs. ',
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#' verbose = TRUE))
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#'
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#' # Timepoint Comparison
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#'timepoint_testing_dt <- exampleData_ICS %>%
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#' group_by(Stim, Parent, Population, Group) %>%
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#' summarise(pairwise_test_cont(x = PercentCellNet,
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#' group = Visit,
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#' paired = TRUE,
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#' id = pubID,
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#' method = 'wilcox',
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#' sorted_group = c(0,1,2),
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#' alternative = 'less',
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#' num_needed_for_test = 3,
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#' digits = 4,
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#' trailing_zeros = TRUE,
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#' sep_val = ' vs. ',
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#' verbose = TRUE),
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#' .groups = "keep")
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#' reframe(pairwise_test_cont(x = PercentCellNet,
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#' group = Visit,
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#' paired = TRUE,
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#' id = pubID,
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#' method = 'wilcox',
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#' sorted_group = c(0,1,2),
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#' alternative = 'less',
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#' num_needed_for_test = 3,
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#' digits = 4,
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#' trailing_zeros = TRUE,
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#' sep_val = ' vs. ',
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#' verbose = TRUE))
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#'
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#'
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#'@export
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#' cor_test_pairs(x = magnitude, pair = antigen, id = pubID,
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#' method = 'spearman', n_distinct_value = 3, digits = 1, verbose = TRUE),
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#' .groups = 'drop'
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#' )
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#' )
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#'
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#' @export
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‎R/pretty_output_functions.R‎

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#'
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#' descriptive_stats_by_group <- exampleData_BAMA %>%
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#' group_by(visitno,antigen) %>%
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#' summarise(
49+
#' reframe(
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#' Group1 = unique(group[group == 1]), Group2 = unique(group[group == 2]),
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#' Group1_n = length(magnitude[group == 1]), Group2_n = length(magnitude[group == 2]),
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#' Group1_mean = mean(magnitude[group == 1]), Group2_mean = mean(magnitude[group == 2]),
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#' Group1_sd = sd(magnitude[group == 1]), Group2_sd = sd(magnitude[group == 2]),
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#' Group1_median = median(magnitude[group == 1]), Group2_median = median(magnitude[group == 2]),
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#' Group1_min = min(magnitude[group == 1]), Group2_min = min(magnitude[group == 2]),
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#' Group1_max = max(magnitude[group == 1]), Group2_max = max(magnitude[group == 2]),
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#' .groups = 'drop'
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#' Group1_max = max(magnitude[group == 1]), Group2_max = max(magnitude[group == 2])
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#' )
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#'
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#' paste_tbl_grp(data = descriptive_stats_by_group, vars_to_paste = 'all', first_name = 'Group1',
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#'exampleData_BAMA %>%
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#' mutate(group = paste0("Group", group)) %>%
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#' group_by(group, visitno, antigen) %>%
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#' summarise(N = n(), mean = mean(magnitude), sd = sd(magnitude),
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#' median = median(magnitude), min = min(magnitude),
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#' max = max(magnitude), q95_fun = quantile(magnitude, 0.95),
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#' .groups = 'drop') %>%
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#' reframe(N = n(), mean = mean(magnitude), sd = sd(magnitude),
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#' median = median(magnitude), min = min(magnitude),
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#' max = max(magnitude), q95_fun = quantile(magnitude, 0.95)) %>%
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#' pivot_longer(-(group:antigen)) %>% # these three chains create a wide dataset
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#' unite(temp, group, name) %>%
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#' pivot_wider(names_from = temp, values_from = value) %>%

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