README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# ctreesR

<!-- badges: start -->
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
<!-- badges: end -->

A thin reticulate-backed wrapper for reading the CTrees aboveground
biomass Zarr cube from Arraylake into a `terra::SpatRaster`. **Note this is not the best way to use these data we should work towards arraylake R bindings, but this is a stopgap for now.**

## Installation

```r
# install.packages("pak")
pak::pak("belian-earth/ctreesR")
```

The Arraylake repository must be supplied: pass it as
`session_auth(repo = "org/repo")`, set `options(ctreesR.repo = ...)`,
or set the `CTREES_REPO` environment variable (e.g. in `~/.Renviron`).
The package does not ship a default repo.

Arraylake credentials are resolved in this order:

1. The `token` argument to `session_auth()` (an Earthmover account API
   key, e.g. `session_auth(token = "ema_...")`).
2. The `EARTHMOVER_KEY` environment variable. Use this in
   non-interactive deployments (containers, Shiny apps) where no
   browser is available.
3. The OAuth token cached at `~/.arraylake/token.json` by
   `arraylake auth login`. This is the default for interactive use.

## Usage

```{r usage}
library(ctreesR)

session <- session_auth()
ctrees  <- open_ctrees(session)

bbx <- c( -73.2,-8.0, -72.1, -7.1)
bzr <- read_ctrees(ctrees, bbox = bbx, year_start = 2025, year_end = 2025)
terra::plot(bzr, range=c(0, 350), fill_range=TRUE)
```