Data release for phenocam analysis subset associated with the journal article "Solar and sensor geometry, not vegetation response, drive satellite NDVI phenology in widespread ecosystems of the western United States"

This dataset provides calculated camera-NDVI data for individual regions-of-interest (ROI's) for the phenocam named 'GRCA1PJ'  (part of the Phenocam Network, https://phenocam.sr.unh.edu/webcam/). The GRCA1PJ phenocam is within a pinyon-juniper woodland in Grand Canyon National Park. Camera-NDVI refers to a modified version of NDVI calculated by the phenopix package (Filippa et al., 2016). The camera-calculated NDVI data are in the folder FinalOutput. File attributes within that folder are described in detail in the entity and attribute information section of this metadata. 
It should be possible for the user to use only the ROI definitions, image data downloaded from the phenocam network, and the phenopix R-package to reproduce the final NDVI dataset. However, the dataset also contains scripts and intermediate files that may be helpful in reproducing or extending the processing, but are not essential to reproducing the data.
The complete dataset release includes
1) A workflow spreadsheet file that describes the processing steps, associated scripts, and output filenames (filename:Workflow_With_Filenames.ods).
2) R-code script files used in processing (folder:'Code').
3) ROI boundary files and jpg images for the ROIs presented in the linked publication. (folder:"Phenocamdata/grca1pj/ROI")
4)  Ancillary files used to create the NDVI dataset; these include exposure coordinates and training files (folder:'Phenocamdata/grca1pj/Ancillary').
5) Files listing exposures for individual photos within the initial processing time period (folder:'Exposures').
6) Screening parameters for cloud and poor-light-condition screening of photos, as well as a list of photos that meet the cloud-screening standards (folder:'Phenocamdata/grca1pj/BlueSkyScreening').
7) Vegetation index files produced by the phenopix package, organized by ROI and month-year group (folder:"Phenocamdata/grca1pj/VI_Tables").
8) Supplemental R-project and packrat files that allow the user to apply the workflow by opening a project that will use the same package versions used in this study (eg, .folders Rproj.user, and packrat, and files .RData, and PhenocamPR.Rproj). 
9) The graphic 'Fig_4_ROIWithLabels.jpg' shows the phenocam field of view with labelled ROIs. outline colors correspond to juniper (red), pinyon (blue), 238 and other species (yellow). Labels correspond to NDVI curves in 'Fig_7_PhenocamCurves.JPG', (also included in this data release).  The composite area comprises the field of view beneath the approximate horizon line labelled ‘J’ (gray). This image corresponds to Figure 4 in the associated journal article.
10)  The graphic 'Fig_7_PhenocamCurves.JPG' shows NDVI curves derived from phenocam images from September 2017 - December 2018 for individual regions of interest (ROIs). Letter designations correspond to ROI labels in Fig_4_ROIWithLabels.jpg (also included in this data release). Data were screened to remove cloudy photos during Aqua and Terra flyover hours. Black ellipses indicate times when the ROI target vegetation was shaded. Red ellipses indicate times when the background of the ROI was shaded. To improve visibility, the Y axis is restricted and excludes 37 extreme values out of a total of 6698 values. The exposure adjustment method used by the phenopix package produces NDVI values that have a strong linear correlation with spectroradiometer-derived NDVI but are negatively shifted so that vegetated areas often have NDVI values below zero. This image corresponds to Figure 7 in the associated journal article.
The file types .Rdata or .rds are commonly used in this release because these are the types created by the phenopix processing package, and these files will be needed (or the user will need to recreate new versions) for further processing. The scripts enable the user to replicate processing or to extend it to different times or areas of interest; however, these scripts require as additional input phenocam imagery that the user must download.
To successfully use the packrat information to replicate the exact processing steps that were used, the user should refer to packrat documentation available at https://cran.r-project.org/web/packages/packrat/index.html and at https://www.rdocumentation.org/packages/packrat/versions/0.5.0. Alternatively, the user may also use the descriptive documentation phenopix package documentation, and description/references provided in the associated journal article to process the data to achieve the same results using newer packages or other software programs.
Species-specific phenological curves included in the NDVI output section this dataset: Juniperus osteosperma,  Pinus edulis, Purshia stansburiana, Artemisia tridentata, and Chamaebatiaria millefolium

Tags: arizona, biota, grand-canyon, ndvi, phenocam, usgs-5e94eaab82ce172707f036c2
Organization: Department of the Interior