3 Package setup

The DESCRIPTION file is created using this code.

usethis::create_package(
  path = ".",
  fields = list(
    Package = params$package_name,
    Version = "0.0.0.9000",
    Title = "flowtrend",
    Description = "Time-smooth mixture modeling for flow cytometry data (Hyun et al. 2025).",
    `Authors@R` = c(
        person(
            given = "Sangwon",
            family = "Hyun",
            email = "sangwonh@ucsc.edu",
            role = c("aut", "cre")),
        person(
            given = "Tim",
            family = "Coleman",
            email = "tscoleman226@gmail.com",
            role = c("aut")
        ),
        person(
            given = "Francois",
            family = "Ribalet",
            email = "ribalet@uw.edu",
            role = c("aut")
        ),
        person(
            given = "Jacob",
            family = "Bien",
            email = "jbien@usc.edu",
            role = c("aut")
        )
    )
  )
)
usethis::use_mit_license(copyright_holder = "Sangwon Hyun")

The following is what will show up when someone types package?flowtrend in the console.

#' flowtrend
#'
#' This package implements the `flowtrend` method for automatic gating of flow cytometry data using trend filtering.
#' It was proposed in <https://arxiv.org/abs/2504.12287>.  To learn
#' more about this package, please visit its website
#' <https://sangwon-hyun/flowtrend-project>.
#' 
#' @docType package

This package will have some dependancies:

library(tidyverse)
library(ggplot2)
usethis::use_package("tidyverse", type = "depends") 
usethis::use_package("ggplot2")
usethis::use_pipe()
usethis::use_package("glmnet")
usethis::use_package("clue")

The figures from this bookdown will be stored here:

## knitr::opts_chunk$set(fig.path = "docs/create/_main_files/figure-html")  ## let's see if we actually even need this.