---
title: "Installation Guide"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Installation Guide}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment  = "#>",
  eval     = FALSE
)
```

## Overview

`ukbflow` is an R package for UK Biobank data analysis and visualization, designed to work natively with the [UK Biobank Research Analysis Platform (RAP)](https://ukbiobank.dnanexus.com). It supports two working modes:

- **Local → RAP**: Run R locally, authenticate with DNAnexus, submit jobs, and download summary results.
- **RAP → RAP**: Run R directly inside the RAP cloud environment, where authentication is handled automatically.

> **UK Biobank Data Policy (2024+)**: Individual-level phenotype and genotype data must remain within the RAP environment and cannot be downloaded locally. Only summary-level outputs (aggregated statistics, plots, reports) may be exported.

---

## Quick Install

### From CRAN *(recommended)*

```{r cran-install}
install.packages("ukbflow")
```

### From GitHub *(latest development version)*

```{r github-install}
# Using pak (faster)
install.packages("pak")
pak::pkg_install("evanbio/ukbflow")

# Using remotes
install.packages("remotes")
remotes::install_github("evanbio/ukbflow")
```

---

## System Requirements

- **R Version**: >= 4.1
- **Operating Systems**: Windows, macOS, Linux
- **dxpy**: Required for local → RAP authentication and job submission (see below)
- **RAP Account**: A valid UK Biobank RAP account and API token

---

## Dependencies

`ukbflow` dependencies are installed automatically with the package.

### Core Dependencies

- **data.table** — Fast in-memory data processing
- **cli** — Progress messages and user feedback
- **processx** — Reliable system command execution with robust error handling (used by auth and job functions)
- **jsonlite** — JSON parsing for RAP API responses
- **curl** — File downloads

### Analysis Dependencies

- **gtsummary** — Table 1 generation
- **gt** — Publication-quality table rendering
- **survival** — Survival analysis
- **dplyr** / **tidyselect** / **rlang** — Data manipulation

### Visualization Dependencies

- **forestploter** — Forest plot generation

### Optional Dependencies

These packages are not installed automatically. Install them only if you need the corresponding features:

```{r optional-deps}
# PDF export from plot_tableone() (requires Chrome / Chromium)
install.packages("pagedown")

# PNG export from plot_tableone()
install.packages("webshot2")
```

---

## Install dxpy (Local Mode Only)

The `auth_*` and `job_*` functions rely on the `dx` command-line tool from [dxpy](https://documentation.dnanexus.com/downloads). Required only when running locally.

```{bash install-dxpy}
pip install dxpy
```

Verify:

```{bash verify-dx}
dx --version
```

> Skip this step if you are running entirely within the RAP RStudio environment.

---

## Authentication Setup

### Local → RAP

Obtain your API token from the DNAnexus platform under **Account Settings > API Tokens**. Store it in your `.Renviron` file (never in your script):

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

Then authenticate:

```{r 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
```

> For full details on token management, project selection, and both authentication modes, see `vignette("auth")`.

### RAP → RAP

Authentication is automatic inside the RAP environment. Verify the session with:

```{r auth-rap}
library(ukbflow)

auth_status()  # confirms user and active project
```

---

## Verify Installation

```{r verify}
library(ukbflow)

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

---

## Update ukbflow

### From GitHub

```{r update-github}
remotes::install_github("evanbio/ukbflow", force = TRUE)
```

### From CRAN

```{r update-cran}
update.packages("ukbflow")
```

---

## Troubleshooting

### `dx` not found

**Solution**: Ensure dxpy is installed and on your PATH:

```{bash dx-path}
pip install dxpy
which dx   # macOS/Linux
where dx   # Windows
```

### Token expired or session lost

DNAnexus API tokens have a limited validity period. If authentication fails, generate a new token from the DNAnexus platform and log in again:

```{r fix-token}
auth_login("your_new_token_here")
```

### Installation fails on Windows

**Solution**: Install [Rtools](https://cran.r-project.org/bin/windows/Rtools/) for packages that require compilation.

### Network / Firewall issues

**Solution**: Configure a proxy before installing:

```{r proxy}
Sys.setenv(http_proxy  = "http://your-proxy:port")
Sys.setenv(https_proxy = "https://your-proxy:port")
```

---

## Uninstall

```{r uninstall}
remove.packages("ukbflow")
```

---

## Getting Help

- **Documentation**: <https://evanbio.github.io/ukbflow/>
- **Issues**: [GitHub Issues](https://github.com/evanbio/ukbflow/issues)

---

## Next Steps

After installation:

1. Read the [Getting Started](https://evanbio.github.io/ukbflow/articles/get-started.html) guide
2. Browse the [Function Reference](https://evanbio.github.io/ukbflow/reference/)
