In FCACollin/ClinAD: ClinAD: Standard Management of Clinical Data

This documents in a draft for keeping track of instruction which were necessary to shape, build, test, document, check the package.

https://bookdown.org/rdpeng/RProgDA/data-within-a-package.html

Create the package structure

# TODO https://rmflight.github.io/posts/2014/07/vignetteAnalysis.html
options(
  usethis.description = list(
    `Authors@R` = 'person(
    given  = "François",
    family = "Collin",
    email  = "[e-mail]",
    role   = c("aut", "cre", "cph"),
    comment = c(
      ORCID = "0000-0003-0524-5755"
    )
    )',
  URL      = "https://FCACollin.github.io/Latarnia",
  License  = "CC BY-NC-ND 4.0",
  Language =  "en",
  LazyData = "true",
  Version  = numeric_version("0.1.0-1"),
  Title    = "ClinAD: Standard Management of Clinical Data",
  Description = paste(
    "A S4-base class for handling clinical data in a standardise way."
  )
)
)
devtools::create(".")

devtools::test()
usethis::use_git()
usethis::use_pkgdown()
usethis::use_lifecycle()

Append DESCRIPION file

usethis::use_package("testthat", type = "Suggests") 
usethis::use_package("lintr", type = "Suggests") 
usethis::use_package("methods") 
usethis::use_package("Rdpack")
# usethis::use_package("knitr", type = "Suggests") 
# usethis::use_package("rmarkdown", type = "Suggests") 
# usethis::use_package("lme4", type = "Suggests") 
# usethis::use_package("emmeans", type = "Suggests") 
# usethis::use_package("Hmisc") 
# usethis::use_package("corrplot") 
# # usethis::use_package("viridis") 
# usethis::use_package("car") 
# # usethis::use_package("multcompView") 
# usethis::use_package("multcomp") 
# usethis::use_package("tidyr") 
# usethis::use_package("FactoMineR") 
# usethis::use_package("kableExtra") 
# usethis::use_package("reshape2") 
# usethis::use_package("missMDA") 
# usethis::use_package("ggplot2") 
# usethis::use_package("styler")
# # usethis::use_package("ggthemr", type = "Suggests")
# # usethis::use_package("shiny")
# # usethis::use_package("shinydashboard")
# usethis::use_package("dplyr", type = "Suggests")

# usethis::use_package("ggplot2", type = "Suggests") 
# usethis::use_vignette("demographics")
##  <https://community.rstudio.com/t/devtools-check-error-with-vignette-but-vignette-can-be-knitted-without-problem/55962/2>

usethis::use_data_raw(name = "sdtm")
source("data-raw/sdtm.R")

Document

devtools::document()
rmarkdown::render("README.Rmd")
pkgdown::build_site()

Testing

rm(list = ls())
devtools::document()
devtools::test()
devtools::check()
pkgdown::build_site()

devtools::load_all()

Usual checks before commit.

devtools::test()
devtools::check()
pkgdown::build_site()
devtools::build_vignettes() 
devtools::install(build_vignettes = FALSE, upgrade = "never")
devtools::install(build_vignettes = TRUE, upgrade = "never")
devtools::build()

library(ClinAD)
# usethis::use_vignette("dm")
vignette("dm", package = "RPack.Diabete.microRNA")

# Test Rdpack
install.packages("Rdpack")
# Applied:
# https://geobosh.github.io/Rdpack/
vignette("Inserting_bibtex_references", package = "Rdpack")

devtools::build(binary = TRUE)

library(RPack.Diabete.microRNA)
sdtm
adsl
adlb
advs
SDTM
labelling

FCACollin/ClinAD documentation built on Feb. 1, 2021, 12:22 a.m.