Introduction to working with PhenoCam Images

Overview

Phenology—the study of how nature changes seasonally—is a core focus of research enabled by NEON data and infrastructure. NEON gathers phenological data at its field sites through various methods including field sampling of specific plants and insects, flyovers to collect remote sensing data and in situ phenocams that collect phenology image data. These data are hosted by PhenoCam Network  and also accessible via the NEON data portal as NEON Data Products DP1.00033.001, DP1.00042.001,  and DP1.20002.001. 

The tutorials in this series were developed in close collaboration with Phenocam Network scientists.  

This series provides instruction on how to work with the photographs from the PhenoCam Network to extract the day you want for phenology or time-series analyses. 

Learning Objectives

After completing the series, you will be able to:

  • Access and download raw and processed data from the PhenoCam network
  • Extract time-series data from any stack of digital images, including but not limited to the images of the PhenoCam network
  • Quantitatively remove data obtained from bad weather conditions (such as presence fog and cloud, camera field of view shifts)
  • Analyze the extracted time-series to address environmental questions

Things You’ll Need To Complete This Series

Install R & Set up RStudio

To complete the tutorial series, you will need an updated version of R (version 3.4 or later) and, preferably, RStudio installed on your computer.

R is a programming language that specializes in statistical computing. It is a powerful tool for exploratory data analysis. To interact with R, we strongly recommend RStudio, an interactive development environment (IDE).

Install R Packages

You can chose to install packages with each lesson or you can download all of the necessary R packages now. You can install the necessary R packages by running the code below

 install.packages('rgdal')
 utils::install.packages('devtools', repos = "http://cran.us.r-project.org" )
 install.packages('hazer')
 install.packages('jpeg')
 install.packages('lubridate')
 install.packages('hazer')
 install.packages('data.table')
 install.packages('phenocamapi')
 install.packages('phenocamr')
 install.packages('xROI')
 devtools::install_github('khufkens/phenor')
 install.packages('daymetr')
 install.packages('tidyverse')
 install.packages('shiny')
 install.packages('xaringan')
 install.packages('maps')
 install.packages('raster')
 install.packages('sp')

More on Packages in R – Adapted from Software Carpentry.

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