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add quarto website config and homepage
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_publish.yml

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- source: project
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gh-pages:
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- url: https://PecanProject.github.io/betydata/

_quarto.yml

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project:
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type: website
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output-dir: _site
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preview:
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watch-inputs: true
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render:
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- index.qmd
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- vignettes/*.qmd
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website:
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title: "betydata"
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search: true
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sidebar:
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style: docked
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collapse-level: 1
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contents:
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- href: index.qmd
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text: Home
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- section: Guides
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contents:
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- href: vignettes/getting_started.qmd
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text: Getting Started
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- href: vignettes/common_analyses.qmd
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text: Common Analyses
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- section: Advanced
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contents:
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- href: vignettes/pfts-priors.qmd
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text: PFTs & Priors
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- href: vignettes/manuscript.qmd
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text: Manuscript Reproduction
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tools:
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- icon: github
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href: https://github.com/PecanProject/betydata
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format:
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html:
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theme: cosmo
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toc: true
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self-contained: false
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df-print: paged
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execute:
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echo: true
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warning: false
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message: false
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freeze: auto
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author: "David LeBauer and Akash B V"
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date: today

index.qmd

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---
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title: "betydata"
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subtitle: "Public Data from the BETYdb Database"
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---
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```{r}
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#| echo: false
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library(betydata)
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library(dplyr)
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```
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**betydata** is an R data package providing offline access to public data from [BETYdb](https://betydb.org) (Biofuel Ecophysiological Traits and Yields database). It enables reproducible analyses of plant traits, crop yields, and supporting metadata without requiring database connectivity.
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## At a Glance
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```{r}
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#| echo: false
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#| label: tbl-overview
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#| tbl-cap: "Dataset summary"
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tibble::tibble(
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Metric = c(
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"Total observations", "Unique traits", "Plant species",
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"Research sites", "Literature citations", "Tables"
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),
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Value = c(
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format(nrow(traitsview), big.mark = ","),
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n_distinct(traitsview$trait),
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format(nrow(species), big.mark = ","),
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nrow(sites),
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nrow(citations),
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16
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)
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) |> knitr::kable()
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```
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## Installation
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```r
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# install.packages("remotes")
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remotes::install_github("PecanProject/betydata")
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```
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## Quick Start
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```{r}
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library(betydata)
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library(dplyr)
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# The primary table -- key columns first, IDs last
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traitsview
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# Bioenergy crop observations
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bioenergy_genera <- c("Miscanthus", "Panicum", "Populus", "Salix", "Saccharum")
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traitsview |>
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filter(genus %in% bioenergy_genera) |>
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count(genus, sort = TRUE)
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```
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## Guides
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| Guide | Description |
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|-------|-------------|
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| [Getting Started](vignettes/getting_started.qmd) | Package overview, data model, and key concepts |
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| [Common Analyses](vignettes/common_analyses.qmd) | Practical analysis patterns with dplyr |
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| [PFTs & Priors](vignettes/pfts-priors.qmd) | Plant Functional Types and Bayesian prior distributions |
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| [Manuscript Reproduction](vignettes/manuscript.qmd) | Reproduce key analyses from LeBauer et al. (2018) |
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## Data License
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Data: [ODC-By-1.0](https://opendatacommons.org/licenses/by/1-0/)
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| Code: [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause)
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## Citation
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LeBauer, D. S., et al. (2018). BETYdb: a yield, trait, and ecosystem service database applied to second-generation bioenergy feedstock production. *GCB Bioenergy*. [doi:10.1111/gcbb.12420](https://doi.org/10.1111/gcbb.12420)

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