Accessing Jornada data in EDI

Introduction

This lesson will teach you several methods for accessing Jornada data at the Environmental Data Initiative (EDI) repository. EDI has recently become more strict about data access and now requires authentication for downloading data files.

1. Downloading from the portal

The EDI Portal (portal.edirepository.org) is the main graphical interface to the repository. It provides a search interface and landing pages for all datasets, and provides a way to download the files published as a part of any dataset.

Downloading data requires “authentication” - i.e. you have to be logged in with a non-anonymous account. EDI makes it easy to use your pre-existing Google or GitHub account to authenticate.

2. EDIutils

The EDIutils R package is a wrapper around the EDI repository’s API. It provides functions to search and access the data published in EDI from the comfort of your R scripts

# Access Jornada data from the EDI repository

library('tidyverse')
library('EDIutils')

# Data access at EDI requires authentication. The easiest way is to create
# an API key at https://auth.edirepository.org. Once you have that, place 
# it in your script.
mykey <- "<my EDI API key>"

# Log in to EDI rogrammatically with an API key
EDIutils::login(key = mykey)

# Set the dataset ID
datasetID <- "knb-lter-jrn.210011003.106"


# Read the list of "entities" in the dataset
ents <- read_data_entity_names(datasetID)

# Read the raw entity data
raw <- read_data_entity(datasetID, ents[1, "entityId"])

# Now read the raw data as a CSV
df <- readr::read_csv(file = raw)

# Explore the data a little
head(df)
unique(df$site)
length(unique(df$site))


# Now make a simple plot
g <- ggplot(data=df, aes(x=year, y=npp_g_m2, col=site)) + 
  geom_line()

# Show it
g

# Now lets subset and plot site==IBPE
df_ibpe <- df |> filter(site=="IBPE")
g2 <- ggplot(data=df_ibpe, aes(x=year, y=npp_g_m2, col=site)) + 
  geom_line()

g2