data-raw/devstuffs.R

In kapsner/rBiasCorrection: Correct Bias in DNA Methylation Analyses

# nolint start
packagename <- "rBiasCorrection"

# remove existing description object
unlink("DESCRIPTION")
# Create a new description object
my_desc <- desc::description$new("!new")
# Set your package name
my_desc$set("Package", packagename)
#Set your name
my_desc$set_authors(c(
  person("Lorenz A.", "Kapsner", email = "lorenz.kapsner@gmail.com", role = c('cre', 'aut', 'cph'),
         comment = c(ORCID = "0000-0003-1866-860X")),
  person("Evgeny A.", "Moskalev", role = "aut")))
# Remove some author fields
my_desc$del("Maintainer")
# Set the version
my_desc$set_version("0.3.5")
# The title of your package
my_desc$set(Title = "Correct Bias in DNA Methylation Analyses")
# The description of your package
my_desc$set(Description = paste0(
  "Implementation of the algorithms (with minor modifications) to correct ",
  "bias in quantitative DNA methylation analyses as described by ",
  "Moskalev et al. (2011) <doi:10.1093/nar/gkr213>. ",
  "Publication: Kapsner et al. (2021) <doi:10.1002/ijc.33681>."
))
# The description of your package
my_desc$set("Date/Publication" = paste(as.character(Sys.time()), "UTC"))
# The urls
my_desc$set("URL", "https://github.com/kapsner/rBiasCorrection")
my_desc$set("BugReports",
            "https://github.com/kapsner/rBiasCorrection/issues")

# Vignette Builder
my_desc$set("VignetteBuilder" = "quarto")

# Testthat stuff
my_desc$set("Config/testthat/parallel" = "false")
my_desc$set("Config/testthat/edition" = "3")
# Roxygen
my_desc$set("Roxygen" = "list(markdown = TRUE)")
# load data
my_desc$set("LazyData" = "true")

# License
my_desc$set("License" = "GPL (>= 3)")

# Save everyting
my_desc$write(file = "DESCRIPTION")

# License
#usethis::use_gpl3_license(name="Lorenz Kapsner")

# Depends
usethis::use_package("R", min_version = "3.6", type = "Depends")

# Imports
# https://cran.r-project.org/web/packages/data.table/vignettes/datatable-importing.html
usethis::use_package("data.table", type="Imports")
usethis::use_package("ggplot2", type="Imports")
usethis::use_package("magrittr", type="Imports")
usethis::use_package("polynom", type="Imports")
usethis::use_package("nls2", type="Imports")
usethis::use_package("stats", type="Imports")
usethis::use_package("future.apply", type="Imports")
usethis::use_package("future", type = "Imports")
usethis::use_package("utils", type = "Imports")
usethis::use_package("minpack.lm", type = "Imports")

# Suggests
usethis::use_package("testthat", type = "Suggests", min_version = "3.0.1")
usethis::use_package("lintr", type = "Suggests")
usethis::use_package("quarto", type = "Suggests")
usethis::use_package("knitr", type = "Suggests")
usethis::use_package("microbenchmark", type = "Suggests")
usethis::use_package("ggpubr", type = "Suggests")


# dev packages
# tag <- "master"
# devtools::install_github(repo = "r-lib/testthat", ref = tag, upgrade = "always")
# # https://cran.r-project.org/web/packages/devtools/vignettes/dependencies.html
# desc::desc_set_remotes(paste0("github::r-lib/testthat@", tag), file = usethis::proj_get())


# gitignore
usethis::use_git_ignore("/*")
usethis::use_git_ignore("/*/")
usethis::use_git_ignore("*.log")
usethis::use_git_ignore("!/.gitignore")
usethis::use_git_ignore("!/.Rbuildignore")
usethis::use_git_ignore("!/.gitlab-ci.yml")
usethis::use_git_ignore("!/data-raw/")
usethis::use_git_ignore("!/data/")
usethis::use_git_ignore("!/inst/")
usethis::use_git_ignore("/data-raw/*")
usethis::use_git_ignore("!/data-raw/devstuffs.R")
usethis::use_git_ignore("!/DESCRIPTION")
usethis::use_git_ignore("!/FAQ.md")
usethis::use_git_ignore("!/NEWS.md")
usethis::use_git_ignore("!/LICENSE.md")
usethis::use_git_ignore("!/cran-comments.md")
usethis::use_git_ignore("!/man/")
usethis::use_git_ignore("!NAMESPACE")
usethis::use_git_ignore("!/R/")
usethis::use_git_ignore("!/README.md")
usethis::use_git_ignore("!/README.qmd")
usethis::use_git_ignore("!/vignettes/")
usethis::use_git_ignore("!/tests/")
usethis::use_git_ignore("/tests/*")
usethis::use_git_ignore("!/tests/testthat/")
usethis::use_git_ignore("/tests/testthat/*")
usethis::use_git_ignore("!/tests/testthat/_snaps/")
usethis::use_git_ignore("/tests/testthat/_snaps/*")
usethis::use_git_ignore("!/tests/testthat/_snaps/*.md")
usethis::use_git_ignore("!/tests/testthat/test-*.R")
usethis::use_git_ignore("!/tests/testthat.R")
usethis::use_git_ignore("/tests/testthat/testdata/")
usethis::use_git_ignore("/.Rhistory")
usethis::use_git_ignore("!/*.Rproj")
usethis::use_git_ignore("/.Rproj*")
usethis::use_git_ignore("/.RData")
usethis::use_git_ignore("/.vscode")
usethis::use_git_ignore("!/.lintr")
usethis::use_git_ignore("!/.github/")
usethis::use_git_ignore("!/tic.R")

usethis::use_build_ignore("csvdir")
usethis::use_build_ignore("plotdir")
usethis::use_build_ignore("log.txt")
usethis::use_build_ignore("vignettes/log.txt")
usethis::use_build_ignore("cran-comments.md")
usethis::use_build_ignore("revdep")
usethis::use_build_ignore("FAQ.md")
usethis::use_build_ignore("FAQ.html")
usethis::use_build_ignore("tests/testthat/csvdir")
usethis::use_build_ignore("tests/testthat/plotdir")
usethis::use_build_ignore("tests/testthat/log.txt")
usethis::use_build_ignore(".vscode")
usethis::use_build_ignore(".lintr")
usethis::use_build_ignore("tic.R")
usethis::use_build_ignore(".github")
usethis::use_build_ignore("README.md")
usethis::use_build_ignore("README.qmd")
usethis::use_build_ignore("NEWS.md")


# experimental = "../19_PCR-bias/data/example_data/type1/example_data_type1_experimentaldata.csv"
# calibration = "../19_PCR-bias/data/example_data/type1/example_data_type1_calibrationdata.csv"
# data
example.data_experimental <- data.table::fread("./tests/testthat/testdata/exp_type_1.csv")
example.data_calibration <- data.table::fread("./tests/testthat/testdata/cal_type_1.csv")

# vec <- colnames(example.data_experimental)
# vec <- vec[2:length(vec)]
# example.data_experimental[, (vec) := lapply(.SD, function(x) {
#   as.numeric(gsub("\\,", ".", x))
#   }), .SDcols=vec]
#
# data.table::fwrite(example.data_experimental, "./tests/testthat/testdata/exp_type_1.csv")
#
# vec <- colnames(example.data_calibration)
# example.data_calibration[, (vec) := lapply(.SD, function(x) {
#   as.numeric(gsub("\\,", ".", x))
# }), .SDcols=vec]
#
# data.table::fwrite(example.data_calibration, "./tests/testthat/testdata/cal_type_1.csv")

example.data_experimental <- rBiasCorrection::clean_dt(example.data_experimental,
                                                       "experimental",
                                                       1,
                                                       "./logfile.txt")
example.data_calibration <- rBiasCorrection::clean_dt(example.data_calibration,
                                                      "calibration",
                                                      1,
                                                      "./logfile.txt")
file.remove("./logfile.txt")

example._plot.df_agg <- rBiasCorrection:::create_agg_df(
  datatable = example.data_calibration$dat,
  index = "CpG#1"
)

usethis::use_data(example.data_experimental, example.data_calibration,
                  example._plot.df_agg,
                  internal = F,
                  overwrite = F)


# BiasCorrection(experimental = "../19_PCR-bias/data/example_data/type1/example_data_type1_experimentaldata.csv", calibration = "../19_PCR-bias/data/example_data/type1/example_data_type1_calibrationdata.csv", samplelocusname = "Test")
#covr::package_coverage()
#lintr::lint_package()
#styler::style_pkg()

usethis::use_tidy_description()

quarto::quarto_render(input = "README.qmd")

# create NEWS.md using the python-package "auto-changelog" (must be installed)
# https://www.conventionalcommits.org/en/v1.0.0/
# build|ci|docs|feat|fix|perf|refactor|test
an <- autonewsmd::autonewsmd$new(repo_name = packagename)
an$generate()
an$write(force = TRUE)

# nolint end