## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment  = "#>",
  eval     = FALSE
)

## ----github-install-----------------------------------------------------------
# # Using remotes
# install.packages("remotes")
# remotes::install_github("evanbio/ukbflow")
# 
# # Using pak (faster, recommended)
# install.packages("pak")
# pak::pkg_install("evanbio/ukbflow")

## ----cran-install-------------------------------------------------------------
# # CRAN submission planned after GitHub MVP is stable
# # install.packages("ukbflow")

## ----optional-deps------------------------------------------------------------
# # PDF export from plot_tableone() (requires Chrome / Chromium)
# install.packages("pagedown")
# 
# # PNG export from plot_tableone()
# install.packages("webshot2")

## ----auth-renviron------------------------------------------------------------
# usethis::edit_r_environ()
# # Add the following line, then save and restart R:
# # DX_API_TOKEN=your_token_here

## ----auth-local---------------------------------------------------------------
# library(ukbflow)
# 
# auth_login()                                 # reads DX_API_TOKEN automatically
# auth_status()                                # confirm user and active project
# auth_list_projects()                         # find your project ID
# auth_select_project("project-XXXXXXXXXXXX")  # switch to your UKB project

## ----auth-rap-----------------------------------------------------------------
# library(ukbflow)
# 
# auth_status()  # confirms user and active project

## ----verify-------------------------------------------------------------------
# library(ukbflow)
# 
# packageVersion("ukbflow")
# ops_setup()   # checks R version, dxpy, DX_API_TOKEN, and key package versions

## ----update-github------------------------------------------------------------
# remotes::install_github("evanbio/ukbflow", force = TRUE)

## ----update-cran--------------------------------------------------------------
# update.packages("ukbflow")

## ----fix-token----------------------------------------------------------------
# auth_login("your_new_token_here")

## ----proxy--------------------------------------------------------------------
# Sys.setenv(http_proxy  = "http://your-proxy:port")
# Sys.setenv(https_proxy = "https://your-proxy:port")

## ----uninstall----------------------------------------------------------------
# remove.packages("ukbflow")