Installation and Configuration Guide

The ciecl package is designed to work with ICD-10 and ICD-11 classifications in the Chilean clinical context. This guide covers the recommended installation, system requirements, and the configuration of external credentials.

Basic Installation

The easiest way to install ciecl is using the pak package, which automatically manages system dependencies and R package requirements.

From CRAN (Stable Version)

# Install pak if you don't have it
if (!requireNamespace("pak", quietly = TRUE)) install.packages("pak")

# Install ciecl
pak::pkg_install("ciecl")

From GitHub (Development Version)

To use the latest features from the rev-ropensci branch:

pak::pkg_install("RodoTasso/ciecl@rev-ropensci")

Installation with Optional Dependencies

The package has minimal dependencies for core functionality. To enable all features, including comorbidity indices and interactive tables:

# Full installation with all optional packages
pak::pkg_install("RodoTasso/ciecl", dependencies = TRUE)

Dependencies by Feature

Feature Required Package Installation
Charlson/Elixhauser Comorbidities comorbidity install.packages("comorbidity")
Interactive GT Tables gt install.packages("gt")
WHO ICD-11 API httr2 install.packages("httr2")
Read MINSAL Excel Files readxl install.packages("readxl")

System Requirements

The package uses a local SQLite database to ensure high performance in vectorized searches.

Windows

No additional configuration needed. The installation works out of the box.

macOS

Install the Xcode Command Line Tools if you plan to compile from source:

xcode-select --install

Linux (Ubuntu/Debian)

Execute the following to install system requirements:

sudo apt-get update
sudo apt-get install -y \
  r-base-dev \
  libcurl4-openssl-dev \
  libssl-dev \
  libxml2-dev

Linux (Fedora/RHEL/CentOS)

sudo dnf install -y \
  R-devel \
  libcurl-devel \
  openssl-devel \
  libxml2-devel

ICD-11 API Configuration (Optional)

To use cie11_search() and access the WHO ICD-11 international classification, you need free credentials.

  1. Register at icd.who.int/icdapi.
  2. Obtain your Client ID and Client Secret.

Credential Management

Option A: Using keyring (Recommended)

The keyring package stores secrets in the OS native keychain (macOS Keychain, Windows Credential Store, Linux Secret Service), avoiding plain text secrets in your environment files.

# Store credentials once (it will prompt for them)
# Format: "client_id:client_secret"
keyring::key_set("ciecl_icd11")

# Use them in your session
Sys.setenv(ICD_API_KEY = keyring::key_get("ciecl_icd11"))

Option B: Using .Renviron File

Add the following line to your ~/.Renviron file (you can use usethis::edit_r_environ()):

ICD_API_KEY=your_client_id:your_client_secret

Restart R for the changes to take effect. Ensure .Renviron is not tracked by Git.

Verify Installation

library(ciecl)

# Check package version
packageVersion("ciecl")

# Verify catalog access
nrow(cie10_cl) # Should return ~39,873 records

# Test basic lookup
cie_lookup("E11.0")

# Test fuzzy search
cie_search("diabetes")

Troubleshooting

Connection to Local Database

If you encounter errors related to the database connection or corrupt data, force a rebuild of the local cache:

ciecl::cie10_clear_cache()

Manual Proxy Configuration

If you are behind a corporate proxy, configure your R environment before using the WHO API:

Sys.setenv(https_proxy = "http://your-proxy-url:port")