Built in tandem with a manuscript entitled "Characterizing individual tree-level snags using airborne lidar-derived forest canopy gaps within closed-canopy conifer forests"; submitted to Methods in Ecology & Evolution (MEE), 2021.
Corresponding author: Jess M. Stitt Email: jessmstitt [at] gmail.com
This repository contains all files related to a project investigating forest canopy gap dynamics around individual standing dead trees (snags) vs. live trees in a closed-canopy conifer forest.
- Determine if forest canopy gaps can be used to improve snag detection / prediction in forests
- Focus on two aspects:
- height in canopy where gaps occur & gap size for snags vs. live trees
- extent of footprint size around all individual trees
Canopy gaps are those areas in the overstory where trees are absent - often times they are created by treefalls, but may also represent still-standing dead trees, with the gap primarily composed of the area previously taken up by the live canopy of the now-dead snag (yet still containing the standing dead trunk and possibly some branches).
The files for this project are organized into folders, grouped into four (4) subfolders:
Within this folder are the raw data used for this project, including:
- 01_csv = spreadsheets (.csv) for plots, snags, and subplots
- 02_las = airborne lidar data (not included in this repository)
- 03_gis = all files for spatial information, further subdivided:
- 00_shp = shapefiles (.shp) for the study sites and survey plots
- 01:07 folders = raster processing steps; only step included here is
- 02_asc_chm-r50m = 50m-radius clips of pit-free canopy height models (chm) around each survey plot (n=53), at 0.5m resolution
Within this folder are the four (4) R scripts (named following a template of ORDER_PROJECT_FUNCTION):
- 01_snag-gaps_als-proc.R = processing raw lidar data into chm for each plot
- 02_snag-gaps_itd-qaqc.R = individual tree detection (itd) accuracy tests
- 03_snag-gaps_fcgap-calc.R = individual tree-level gap detection & analyses
- 04_snag-gaps_graphics.R = generation of figures based on fc gap results
Within this folder are all results from processing done within the project:
- 01_tables = csv files including the itd-generated live tree locations, gap statistics, and full itd accuracy test datasets
- 02_gis = any shapefiles of gap boundaries (not currently included)
- 03_las-metrics = lidar-derived metrics at the plot & tree level
- 04_figures = graphics generated based on the fc gap results
Within this folder are any larger "reports" including R Markdown files, maps created within QGIS, and additional figures
Data were collected in large part by USFS RMRS, which provided the airborne lidar data of the Idaho Panhandle National Forests and conducted the subplot surveys across both sites.
Much of the code contained within this project derives from the ForestGapR github page and other sources online, such as the lidR package book and a Quantitative Ecology tutorial.