Data Package Metadata   View Summary

Forest structural diversity at NEON sites in the continuous USA that experienced recent moderate disturbance

General Information
Data Package:
Local Identifier:edi.448.1
Title:Forest structural diversity at NEON sites in the continuous USA that experienced recent moderate disturbance
Alternate Identifier:DOI PLACE HOLDER
Abstract:

Disturbances can change the structural diversity of forests through time, which can be measured from three-dimensional data provided by LiDAR. Discrete-return LiDAR was used to measure a suite of 19 structural diversity metrics that describe the height, cover and openness, vegetation density, and internal and external heterogeneity of forest vegetation at NEON base plots. Discrete-return LiDAR point clouds from the NEON Aerial Observation Platform (DP1.30003.001) were downloaded September of 2020 and used to estimate the metrics within 40 x 40 m base plots. Metrics were estimated from base plots at 15 NEON forested sites from provisional LiDAR data available from 2014 to 2020. The workflow that produced the data was developed in the program R.

Publication Date:2021-09-07

Time Period
Begin:
2014-01-01
End:
2020-01-01

People and Organizations
Contact:Hardiman, Brady S (Purdue University) [  email ]
Creator:Hardiman, Brady S (Purdue University)
Creator:LaRue, Elizabeth A (Purdue University, University of Texas at El Paso)
Creator:Foster, Jane R (University of Vermont)
Creator:Fahey, Robert (University of Connecticut)
Creator:Hatala Matthes, Jaclyn (Wellesley College)
Organization:National Ecological Observatory Network (NEON)

Data Entities
Data Table Name:
check_outliers_04132021
Description:
Supporting file for running the code to obtain the output
Data Table Name:
disturbance_structural_diversity_data
Description:
disturbance_structural_diversity_data.csv
Data Table Name:
NEON_Base_Plot_Centroid
Description:
Supporting file for running the code to obtain the output
Other Name:
01_process_NEON_lidar_baseplots_04072021
Description:
This code was used to download NEON 1 km2 tiles from the NEON data portal, clip a buffer, remove outliers within 6 SD of the Z mean and with the VFI algorithm, and correct the data for elevation for each of the 15 site by year combinations of NEON base plots (40 x 40 m). It is necessary to run the code separately for each site x year combo. A file for each plot and year was created and then copied to a new folder containing all 15 site x year x plots. Supporting data file includes coordinates of base plot centers.
Other Name:
02_FSD_metrics_loops_04082021
Description:
The second step of the workflow is to create the structural diversity metric table that is provided in the EDI. The code contains the portion of the workflow that measures the FSD metrics from the .las file (named as site_plot_year.las). There were 2,291 of these files. Plots that had a maxZ (maximum point height) of greater than 50 m were visually checked for atmospheric outlier points. If so, they were removed in a step added to the beginning of the workflow (step 02) and then the whole step was rerun to fix these.
Detailed Metadata

Data Entities


Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/448/1/2404f177155672820679b0931b613e11
Name:check_outliers_04132021
Description:Supporting file for running the code to obtain the output
Number of Records:74
Number of Columns:4

Table Structure
Object Name:check_outliers_04132021.csv
Size:2195 bytes
Authentication:0f0ab198871230a97c20dba21b1fc1c0 Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,

Table Column Descriptions
 
Column Name:filename  
maxZ  
outlier  
filter  
Definition:plotID LIDAR file name; Name of the processed and clipped LiDAR file used to get FSD metricsMaximum point height (m)Outlier visually observed in 40 x 40 m baseplot point cloud (yes or no)The numeric value for which to filter outlier points above true vegetation visually observed in plots that had an atmospheric outlier
Storage Type:string  
float  
string  
float  
Measurement Type:nominalrationominalratio
Measurement Values Domain:
DefinitionplotID LIDAR file name; Name of the processed and clipped LiDAR file used to get FSD metrics
UnitmeterSquared
Typereal
Min50.03 
Max65.14 
Allowed Values and Definitions
Enumerated Domain 
Code Definition
Codeno
Definitionno there was no outlier
Source
Code Definition
Codeyes
Definitionyes there was an outlier
Source
Unitdimensionless
Typenatural
Min40 
Max40 
Missing Value Code:        
Accuracy Report:        
Accuracy Assessment:        
Coverage:        
Methods:        

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/448/1/eb35af7919d757f2857dd887db2a60e1
Name:disturbance_structural_diversity_data
Description:disturbance_structural_diversity_data.csv
Number of Records:2291
Number of Columns:28

Table Structure
Object Name:disturbance_structural_diversity_data.csv
Size:645464 bytes
Authentication:ebe5de970116eaf6b35d6758c6e3cabd Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,

Table Column Descriptions
 
Column Name:site  
plotID  
year  
plotID_year  
filename  
plot_area_ground  
den  
maxZ  
rumple  
deepgap.fraction  
mean.max.canopy.ht  
max.canopy.ht  
top.rugosity  
vert.sd  
sd.sd  
GFP  
VAI  
VCI  
vertCV  
q0  
q25  
q50  
q75  
q100  
fhd  
gini  
LAI  
LAI_subcanopy  
Definition:NEON site; Standard NEON four letter site codeNEON site and base plot ID; Unique plot ID that contains the standard NEON four letter site code and three number base plot IDYear that LiDAR data was collected by NEONPlot ID and LiDAR year collected; Unique NEON base plot ID and LiDAR year collectedplotID LIDAR file name; Name of the processed and clipped LiDAR file used to get FSD metricsPlot area: area of the plot (should be close to 1600 m2) including ground pointsPoint density of LiDAR (pt/m2): point cloud density of LiDAR (pt/m2)Maximum point height (m)Rumple: Area of canopy surface relative to plot area (unitless ratio)DGF (deep gap fraction): Fraction of 1 m2 canopy gaps in the plot (unitless)MOCH (mean outer canopy height): Mean of maximum height (m) in 1m2 grid of plotMaximum canopy height (m)Top rugosity: Standard deviation of outer canopy heights in 1 m2 of plot (m)SD(ht): Standard deviation of heights within the plot (m)SD(SD(ht)): Plot level- standard deviation of the standard deviation of heights within 9 m2 voxels in the plot area (m)GFP (gap fraction profile): Distribution of gaps in the point cloud 0.5 m above the ground (unitless)VAI (vegetation area index): Sum of the 1 m horizontal slices (starting 0.5 m above the ground) of leaf area density with the plot (m2/m3)VCI (vertical complexity index): Normalization of diversity and evenness (entropy) of 1 m height bins within the plot (unitless)CV(ht): Coefficient of variation of heights within the plot (unitless)Q0: 0th quantile of height (m)Q25: 25th quantile of height (m)Q50: 50th quantile of height (m)Q75: 75th quantile of height (m)Q100: 100th quantile of height (m)FHD (foliage height diversity): Calculated from the point abundances as per voxel relative LAD values; described in MacArthur R and MacArthur J. 1961. On Bird Species Diversity. Ecology 42: 594�8.Gini index: Calculates the Gini coefficient (GC) from unvoxelized LIDAR returns (equivalent to Gini) in Valbuena R., Maltamo M., Meht�talo L., Packalen P. (2017) Key structural features of Boreal forests may be detected directly using L-moments from airborne lidar data. Remote Sensing of Environment. 194: 437�446. https://doi.org/10.1016/j.rse.2016.10.024LAI (leaf area index): LAI of vegetation in canopy from 1 m above ground (units leaf area over plot area m2/m2)LAI of subcanopy: LAI of the points from 1 to 5 m above the ground (units leaf area over plot area m2/m2)
Storage Type:string  
string  
date  
string  
string  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
float  
Measurement Type:nominalnominaldateTimenominalnominalratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratio
Measurement Values Domain:
DefinitionNEON site; Standard NEON four letter site code
DefinitionNEON site and base plot ID; Unique plot ID that contains the standard NEON four letter site code and three number base plot ID
FormatYYYY
Precision
DefinitionPlot ID and LiDAR year collected; Unique NEON base plot ID and LiDAR year collected
DefinitionplotID LIDAR file name; Name of the processed and clipped LiDAR file used to get FSD metrics
UnitmeterSquared
Typereal
Min1500.1722 
Max1599.448318 
UnitpointPerSquareMeter
Typereal
Min1.313265486 
Max54.79093992 
UnitmeterSquared
Typereal
Min2.07 
Max65.14 
Unitdimensionless
Typereal
Min
Max13.42370534 
Unitdimensionless
Typereal
Min
Max
Unitmeter
Typereal
Min0.789019608 
Max45.2294756 
Unitmeter
Typereal
Min2.07 
Max65.14 
Unitmeter
Typereal
Min0.326680668 
Max18.0834024 
Unitmeter
Typereal
Min0.293961895 
Max17.59262603 
Unitmeter
Typereal
Min0.107996835 
Max6.790072136 
Unitdimensionless
Typereal
Min0.672495824 
Max0.999277457 
UnitmeterSquaredPerMeterCubed
Typereal
Min
Max17.35624171 
Unitdimensionless
Typereal
Min0.107861374 
Max0.881182483 
Unitdimensionless
Typereal
Min0.130402842 
Max1.681063657 
Unitmeter
Typereal
Min0.5 
Max5.01 
Unitmeter
Typereal
Min0.56 
Max32.4425 
Unitmeter
Typereal
Min0.66 
Max37.6835 
Unitmeter
Typereal
Min0.83 
Max42.465 
Unitmeter
Typereal
Min2.07 
Max65.14 
Unitdimensionless
Typereal
Min0.038585127 
Max3.855102109 
Unitdimensionless
Typereal
Min0.058136844 
Max0.682909663 
UnitmeterSquaredPerMeterSquared
Typereal
Min0.000563224 
Max5.078740502 
UnitmeterSquaredPerMeterSquared
Typereal
Min
Max2.490773638 
Missing Value Code:                                                        
Accuracy Report:                                                        
Accuracy Assessment:                                                        
Coverage:                                                        
Methods:                                                        

Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/448/1/27685fbc5555928bb1e8c7afd14cbbf3
Name:NEON_Base_Plot_Centroid
Description:Supporting file for running the code to obtain the output
Number of Records:670
Number of Columns:5

Table Structure
Object Name:NEON_Base_Plot_Centroid.csv
Size:28034 bytes
Authentication:caf521c2e9ddd0ca3e0390885e1be55f Calculated By MD5
Text Format:
Number of Header Lines:1
Record Delimiter:\r\n
Orientation:column
Simple Delimited:
Field Delimiter:,

Table Column Descriptions
 
Column Name:siteID  
plotID  
utmZone  
easting  
northing  
Definition:NEON site; Standard NEON four letter site codeNEON site and base plot ID; Unique plot ID that contains the standard NEON four letter site code and three number base plot IDUTM Zone; Standard UTM zone codesEasting coordinateNorthing coordinate
Storage Type:string  
string  
string  
float  
float  
Measurement Type:nominalnominalnominalratioratio
Measurement Values Domain:
DefinitionNEON site; Standard NEON four letter site code
DefinitionNEON site and base plot ID; Unique plot ID that contains the standard NEON four letter site code and three number base plot ID
DefinitionUTM Zone; Standard UTM zone codes
Unitdimensionless
Typereal
Min242767.665 
Max753360.691 
Unitdimensionless
Typereal
Min1986086.733 
Max5125885.357 
Missing Value Code:          
Accuracy Report:          
Accuracy Assessment:          
Coverage:          
Methods:          

Non-Categorized Data Resource

Name:01_process_NEON_lidar_baseplots_04072021
Entity Type:unknown
Description:This code was used to download NEON 1 km2 tiles from the NEON data portal, clip a buffer, remove outliers within 6 SD of the Z mean and with the VFI algorithm, and correct the data for elevation for each of the 15 site by year combinations of NEON base plots (40 x 40 m). It is necessary to run the code separately for each site x year combo. A file for each plot and year was created and then copied to a new folder containing all 15 site x year x plots. Supporting data file includes coordinates of base plot centers.
Physical Structure Description:
Object Name:01_process_NEON_lidar_baseplots_04072021.R
Size:13643 bytes
Authentication:ea7abe5f2fc7d6a73735c969f35ef41a Calculated By MD5
Externally Defined Format:
Format Name:text/plain
Data:https://pasta-s.lternet.edu/package/data/eml/edi/448/1/cf8e973f411fafb3a42ecdb5ea3d5151

Non-Categorized Data Resource

Name:02_FSD_metrics_loops_04082021
Entity Type:unknown
Description:The second step of the workflow is to create the structural diversity metric table that is provided in the EDI. The code contains the portion of the workflow that measures the FSD metrics from the .las file (named as site_plot_year.las). There were 2,291 of these files. Plots that had a maxZ (maximum point height) of greater than 50 m were visually checked for atmospheric outlier points. If so, they were removed in a step added to the beginning of the workflow (step 02) and then the whole step was rerun to fix these.
Physical Structure Description:
Object Name:02_FSD_metrics_loops_04082021.R
Size:9994 bytes
Authentication:c3b3c586ff2dbb4ecd4a8468119f2f4e Calculated By MD5
Externally Defined Format:
Format Name:text/plain
Data:https://pasta-s.lternet.edu/package/data/eml/edi/448/1/b314ae5f7cfcd48bdbb2f00dc6c26a2f

Data Package Usage Rights

This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

Keywords

By Thesaurus:
(No thesaurus)Canopy structural complexity, forest structure, NEON, structural diversity, National Ecological Observatory Network
LTER Controlled Vocabularyforest disturbance

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:

Structural diversity metrics were derived from discrete return LiDAR point clouds from the NEON data portal. Tiles were obtained for geographic locations at forested base plots from fifteen NEON sites: ABBY (2017-2019), BART (2014, 2016-2019), BLAN (2016, 2017, 2019), GRSM (2015-2018), GUAN (2018), HARV (2014, 2017-2019), JERC (2014, 2016-2019), OSBS (2017-2019), SCBI (2016, 2017, 2019), SOAP (2013, 2017-2019), STEI (2016, 2017, 2019, 2020), TALL (2015-2019), TEAK (2013, 2017-2019), UKFS (2017-2020), UNDE (2016, 2017, 2020). An R workflow was used to process the point clouds and derive 19 structural diversity metrics. The workflow is provided as an attached R script with two supporting .csv files (coordinates - NEON_Base_Plot_Centroid.csv and outlier fixes - check_outliers_04132021.csv). No LiDAR data (raw or intermediate) are provided; the workflow generates these files.

NEON (National Ecological Observatory Network). Discrete return LiDAR point cloud (DP1.30003.001). https://data.neonscience.org (accessed September 30, 2020)

Description:

This method step describes provenance-based metadata

This provenance metadata does not contain entity specific information.

Data Source
Discrete return LiDAR point cloud (DP1.30003.001)

People and Organizations

Publishers:
Organization:Environmental Data Initiative
Email Address:
info@environmentaldatainitiative.org
Web Address:
https://environmentaldatainitiative.org
Creators:
Individual: Brady S Hardiman
Organization:Purdue University
Email Address:
bhardima@purdue.edu
Id:https://orcid.org/0000-0001-6833-9404
Individual: Elizabeth A LaRue
Organization:Purdue University, University of Texas at El Paso
Email Address:
elarue@purdue.edu
Id:https://orcid.org/0000-0002-9535-0630
Individual: Jane R Foster
Organization:University of Vermont
Email Address:
jane.foster@uvm.edu
Id:https://orcid.org/0000-0002-5997-0269
Individual: Robert Fahey
Organization:University of Connecticut
Email Address:
robert.fahey@uconn.edu
Id:https://orcid.org/0000-0001-7246-8292
Individual: Jaclyn Hatala Matthes
Organization:Wellesley College
Email Address:
jmatthes@wellesley.edu
Id:https://orcid.org/0000-0001-8999-8062
Contacts:
Individual: Brady S Hardiman
Organization:Purdue University
Email Address:
bhardima@purdue.edu
Id:https://orcid.org/0000-0001-6833-9404
Associated Parties:
Organization:National Ecological Observatory Network (NEON)
Role:Data Provider

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2014-01-01
End:
2020-01-01
Sampling Site: 
Description:Abby Road NEON | ABBY | https://www.neonscience.org/field-sites/ABBY
Site Coordinates:
Longitude (degree): -122.330317Latitude (degree): 45.762439
Sampling Site: 
Description:Bartlett Experimental Forest NEON | BART | https://www.neonscience.org/field-sites/BART
Site Coordinates:
Longitude (degree): -71.287375Latitude (degree): 44.063889
Sampling Site: 
Description:Blandy Experimental Farm NEON | BLAN | https://www.neonscience.org/field-sites/BLAN
Site Coordinates:
Longitude (degree): -78.041788Latitude (degree): 39.033698
Sampling Site: 
Description:Great Smoky Mountains National Park NEON | GRSM | https://www.neonscience.org/field-sites/GRSM
Site Coordinates:
Longitude (degree): -83.50195Latitude (degree): 35.68896
Sampling Site: 
Description:Guanica Forest NEON | GUAN | https://www.neonscience.org/field-sites/GUAN
Site Coordinates:
Longitude (degree): -66.8687Latitude (degree): 17.96955
Sampling Site: 
Description:Harvard Forest & Quabbin Watershed NEON | HARV | https://www.neonscience.org/field-sites/HARV
Site Coordinates:
Longitude (degree): -72.17265Latitude (degree): 42.53691
Sampling Site: 
Description:The Jones Center At Ichauway NEON | JERC | https://www.neonscience.org/field-sites/JERC
Site Coordinates:
Longitude (degree): -84.468623Latitude (degree): 31.194839
Sampling Site: 
Description:Ordway-Swisher Biological Station NEON | OSBS | https://www.neonscience.org/field-sites/OSBS
Site Coordinates:
Longitude (degree): -81.993431Latitude (degree): 29.689282
Sampling Site: 
Description:Smithsonian Conservation Biology Institute NEON | SCBI | https://www.neonscience.org/field-sites/SCBI
Site Coordinates:
Longitude (degree): -78.139494Latitude (degree): 38.892925
Sampling Site: 
Description:Soaproot Saddle NEON | SOAP | https://www.neonscience.org/field-sites/SOAP
Site Coordinates:
Longitude (degree): -119.26219Latitude (degree): 37.03337
Sampling Site: 
Description:Steigerwaldt-Chequamegon NEON | STEI | https://www.neonscience.org/field-sites/STEI
Site Coordinates:
Longitude (degree): -89.58637Latitude (degree): 45.50894
Sampling Site: 
Description:Talladega National Forest NEON | TALL | https://www.neonscience.org/field-sites/TALL
Site Coordinates:
Longitude (degree): -87.393259Latitude (degree): 32.95047
Sampling Site: 
Description:Lower Teakettle NEON | TEAK | https://www.neonscience.org/field-sites/TEAK
Site Coordinates:
Longitude (degree): -119.00602Latitude (degree): 37.00583
Sampling Site: 
Description:KU Field Station NEON | UKFS | https://www.neonscience.org/field-sites/UKFS
Site Coordinates:
Longitude (degree): -95.19215Latitude (degree): 39.040431
Sampling Site: 
Description:University of Notre Dame Environmental Research Center NEON | UNDE | https://www.neonscience.org/field-sites/UNDE
Site Coordinates:
Longitude (degree): -89.537254Latitude (degree): 46.23391

Project

Parent Project Information:

Title:Collaborative Research: MSA: Incorporating canopy structural complexity to improve model forecasts of functional effects of forest disturbance
Personnel:
Individual: Brady S Hardiman
Organization:Purdue University
Email Address:
bhardima@purdue.edu
Id:https://orcid.org/0000-0001-6833-9404
Role:Principal Investigator
Funding: National Science Foundation, Division of Environmental Biology #1926538

Maintenance

Maintenance:
Description:2014-2020 from NEON AOP
Frequency:
Other Metadata

Additional Metadata

additionalMetadata
        |___text '\n    '
        |___element 'metadata'
        |     |___text '\n      '
        |     |___element 'unitList'
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'meterSquaredPerMeterCubed'
        |     |     |     |  \___attribute 'multiplierToSI' = ''
        |     |     |     |  \___attribute 'name' = 'meterSquaredPerMeterCubed'
        |     |     |     |  \___attribute 'parentSI' = ''
        |     |     |     |  \___attribute 'unitType' = 'ratio'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'meter squared per meter cubed'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'meterSquaredPerMeterSquared'
        |     |     |     |  \___attribute 'multiplierToSI' = '1'
        |     |     |     |  \___attribute 'name' = 'meterSquaredPerMeterSquared'
        |     |     |     |  \___attribute 'parentSI' = 'meterSquaredPerMeterSquared'
        |     |     |     |  \___attribute 'unitType' = 'ratio'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'meter squared per meter squared'
        |     |     |     |___text '\n        '
        |     |     |___text '\n        '
        |     |     |___element 'unit'
        |     |     |     |  \___attribute 'id' = 'pointPerSquareMeter'
        |     |     |     |  \___attribute 'multiplierToSI' = ''
        |     |     |     |  \___attribute 'name' = 'pointPerSquareMeter'
        |     |     |     |  \___attribute 'parentSI' = ''
        |     |     |     |  \___attribute 'unitType' = 'pointCloudDensity'
        |     |     |     |___text '\n          '
        |     |     |     |___element 'description'
        |     |     |     |     |___text 'point per square meter'
        |     |     |     |___text '\n        '
        |     |     |___text '\n      '
        |     |___text '\n    '
        |___text '\n  '

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

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