inst/extdata/building_blocks.R

In hmsidwR: Health Metrics and the Spread of Infectious Diseases

## Create a package
## R-Packages - https://r-pkgs.org/
## check the package's name availability
library(available)
available::available("hmsidwR")
suggest(text = "health metrics") # diseasesr
pak::pkg_name_check("hmsidwR")


library(devtools)
library(usethis)
usethis::create_package("~/Documents/R/AAA_packages/hmsidwR")
usethis::use_git()

## Function Documentation
usethis::use_r("lmforecast")
# then position the cursor at the top of the script and
# code-->insert roxygen skeleton

## restart and load the function
devtools::load_all()

## check the package status
devtools::check()

## type ctrl . to access the DESCRIPTION file to customize
## add the licence
# usethis::use_mit_license()

## add documentation of the function
# head over the function file and --> code--> Insert roxygen skeleton
devtools::document()

## Install the package (Cmd + Shift + B)
devtools::install()

## install testthat to check functions
# usethis::use_testthat()
# then fill up the test_that() function with expected output
devtools::test()

## use github
# usethis::use_github()
## use RStudio - this function set all files on the main directory of the prject
usethis::use_rstudio()
usethis::proj_sitrep() # check


## add a readme
# usethis::use_readme_rmd()

## build the readme
# devtools::build_readme()
## then check and install


## Data
## Raw data
usethis::use_data_raw() # create the data_raw/ folder
usethis::use_data_raw("my_pkg_data")

## Data is saved in data/ folder and is usually type .rda
usethis::use_data()
usethis::use_data(my_pkg_data)
# to compress
tools::resaveRdaFiles("data/")
# to check what type of
tools::checkRdaFiles()

## Internal data
usethis::use_data(internal = TRUE) # create R/sysdata.rda
usethis::use_data(internal_this,
                  internal_that,
                  internal = TRUE)


## load packages on DESCRPTION
usethis::use_package("your-package")
# in suggest are packages not absolutely required
# reorder list
usethis::use_tidy_description()

## add a Vignette
usethis::use_vignette("hmsidwR")
# then subsequent vignettes
usethis::use_vignette("sdi90_19")
usethis::use_article("Case Study") # .Rbuildignored
usethis::use_article("Case Study/sdi90_19")
# or
devtools::install(build_vignettes = TRUE)
browseVignettes("hmsidwR")


# Repeat
devtools::load_all()
devtools::check()
devtools::document()
devtools::install()
devtools::build()


## Restyle -package - reshape code
styler::style_pkg()
# add a logo
usethis::use_logo("man/figures/logo.png")

## creates an inst/
usethis::use_rmarkdown_template()
# to add inst/extdata or inst/citation

usethis::use_citation()

## look at the dependencies in the DESCRIPTION file
pak::pkg_deps_tree("tibble")
pak::pkg_deps_explain("tibble", "rlang")

# set up for building the website
usethis::use_github_actions()

# Build a website for the vignette
usethis::use_pkgdown()

pkgdown::build_site()

# publish the website
usethis::use_pkgdown_github_pages()

# build references in the pkg
pkgdown::build_reference_index(pkg = ".")
# link all .rmd files
pkgdown::build_articles()


# Repeat
devtools::load_all()
devtools::document()
devtools::check()
devtools::install()
devtools::build()
pkgdown::build_site()

# install(build_vignettes = TRUE)
# browseVignettes("hmsidwR")
# customization documentation
vignette("pkgdown", package = "pkgdown")

# add the RCheck badge and select (1)
# usethis::use_github_action()

# add NEWs
usethis::use_news_md()

## Submit on CRAN
# devtools::submit_cran()

# mish
# withr::defer()

#####################
## Pushing on CRAN
# https://github.com/Fgazzelloni/hmsidwR/issues/1
usethis::use_release_issue() # first time chosen "minor"
# any time you use this command it will open an issue on github to release a new version, the second time I did it I choose "patch"
# then
usethis::use_cran_comments()
options(timeout = 6000)
urlchecker::url_check()
devtools::build_readme()
devtools::check(remote = TRUE, manual = TRUE)
usethis::use_cran_badge()
devtools::check_win_devel()
git push
#####################
# Submit to CRAN:
# it increment the versions
usethis::use_version('patch')
devtools::submit_cran()

#####################
#Check Your Build Process:
devtools::clean_dll()
devtools::clean_vignettes()
devtools::build(clean = TRUE)  # Rebuild the package with a clean setup
devtools::check(clean = TRUE)  # Run a clean check on the new build

#####################
# remove doc and docs from github
git rm -r doc
git rm -r docs
git commit -m "Remove doc and docs folders to reduce package size"
git push

#####################
# List all files in the 'doc' folder with their sizes
doc_files <- list.files("doc", recursive = TRUE, full.names = TRUE)
file_info <- file.info(doc_files)
file_info[order(file_info$size, decreasing = TRUE), ]

#####################
# Analyze File Sizes in check_package/doc:
pkg <- devtools::build()
utils::untar(pkg, exdir = "check_package")
list.files("check_package/doc", recursive = TRUE)

#####################
# Check the size of a folder
# Define the path to the folder
folder_path <- "~/Documents/R/AAA_packages/hmsidwR_container/hmsidwR/data"
# Get the list of all files in the folder and sub-folders
all_files <- list.files(folder_path,
                        recursive = TRUE,
                        full.names = TRUE)
# Get the size of each file and sum them up
folder_size <- sum(file.info(all_files)$size)
# Convert to MB for readability
folder_size_mb <- folder_size / (1024^2)
folder_size_mb
#####################