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index.Rmd
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---
title: 'Data From: TERRA-REF, An Open Reference Data Set From High Resolution Genomics,
Phenomics, and Imaging Sensors'
author:
- David S. LeBauer^[University of Arizona, orcid:0000-0001-7228-053X]
- Maxwell A. Burnette^[NCSA, University of Illinois at Urbana-Champaign, orcid:0000-0002-1786-3676]
- Jeffrey Demieville^[University of Arizona, orcid:0000-0002-7725-7379]
- Noah Fahlgren^[Donald Danforth Plant Science Center, orcid:0000-0002-5597-4537]
- Andrew N. French^[USDA Agricultural Research Service, orcid:0000-0002-4018-1817]
- Roman Garnett^[Washington University in St. Louis, orcid:0000-0002-0152-5453]
- Zhenbin Hu^[Kansas State University, orcid:0000-0002-1500-1255]
- Kimberly Huynh^[University of Arizona, orcid:0000-0003-3360-4073]
- Rob Kooper^[NCSA, University of Illinois at Urbana-Champaign, orcid:0000-0002-5781-7287]
- Zongyang Li^[Donald Danforth Plant Science Center, orcid:0000-0002-8601-378X]
- Maitiniyazi Maimaitijiang^[Saint Louis University, orcid:0000-0001-6153-1583]
- Jerome Mao^[University of California at Irvine, current:Case Western Reserve University orcid:0000-0003-2505-8666]
- Todd C. Mockler^[Donald Danforth Plant Science Center, orcid:0000-0002-0462-5775]
- Geoffrey Morris^[Kansas State University, orcid:0000-0002-3067-3359]
- Maria Newcomb^[University of Arizona, current:USDA Forest Service, orcid:0000-0003-2974-9149]
- Michael J. Ottman^[University of Arizona, orcid:0000-0003-0763-3073]
- Philip Ozersky^[Danforth Plant Science Center, orcid:0000-0002-8942-0524]
- Sidike Paheding^[Saint Louis University, orcid:0000-0003-4712-9672]
- Duke Pauli^[University of Arizona, orcid:0000-0002-8292-2388]
- Robert Pless^[George Washington University, orcid:0000-0001-5775-8216]
- Wei Qin^[University of Illinois at Urbana-Champaign, current:Amazon.com, Inc, orcid:0000-0003-4816-6336]
- Kristina Riemer^[University of Arizona, orcid:0000-0003-3802-3331]
- Gareth Scott Rohde^[University of Illinois at Urbana-Champaign, orcid:0000-0001-9030-0936]
- William L. Rooney^[Texas A&M University, orcid:0000-0001-7953-1856]
- Vasit Sagan^[Saint Louis University, orcid:0000-0003-4375-2096]
- Nadia Shakoor^[Donald Danforth Plant Science Center, orcid:0000-0002-2035-7117]
- Abby Stylianou^[Saint Louis University, orcid:0000-0002-4387-028X]
- Kelly Thorp^[USDA Agricultural Research Service, orcid:0000-0001-9168-875X]
- Richard Ward^[University of Arizona, current:unaffiliated , orcid:0000-0003-4436-0019]
- Jeffrey W White^[USDA Agricultural Research Service, current:University of Florida, orcid:0000-0002-2051-4645]
- Craig Willis^[University of Illinois at Urbana-Champaign, orcid:0000-0002-6148-7196]
- Charles S Zender^[University of California, Irvine, orcid:0000-0003-0129-8024]
date: "`r Sys.Date()`"
bibliography:
- book.bib
- packages.bib
description: This describes the TERRA REF public data release
documentclass: book
geometry: margin=1in
link-citations: yes
site: bookdown::bookdown_site
biblio-style: apalike
urlcolor: blue
linkcolor: blue
classoption: openany
---
```{r include = FALSE}
knitr::opts_chunk$set(
echo = FALSE,
include = FALSE,
cache = TRUE,
message = FALSE)#,
#root.dir = normalizePath("../book")))
library(dplyr)
library(stringr)
library(ggplot2)
#Setting up traits package
#library(traits)
#options(betydb_url = "https://terraref.ncsa.illinois.edu/bety/",
# betydb_api_version = 'v1',
# betydb_key = readLines('~/.betykey', warn = FALSE))
# to query the database either use
# ssh -Nf -L 5432:localhost:5432 bety6.ncsa.illinois.edu
# to mount the database
try(
bety_src <- src_postgres(dbname = "bety",
password = 'DelchevskoOro',
host = 'localhost',
user = 'viewer',
port = 5432)
, silent = TRUE)
# for use with publication: after making data public
# cd code/betydb_docker
# docker-compose up -d postgres
# docker-compose run --rm bety initialize
# docker-compose run --rm bety sync
# bety_src <- src_postgres(dbname = "bety",
# password = 'bety',
# host = 'localhost',
# user = 'bety',
# port = 5433)
```
```{r include=FALSE}
# automatically create a bib database for R packages
knitr::write_bib(c(
.packages(), 'bookdown', 'knitr', 'rmarkdown'
), 'packages.bib')
```