Package: forestr 2.1.0

forestr: Ecosystem and Canopy Structural Complexity Metrics from LiDAR

Provides a toolkit for calculating forest and canopy structural complexity metrics from terrestrial LiDAR (light detection and ranging). References: Atkins et al. 2018 <doi:10.1111/2041-210X.13061>; Hardiman et al. 2013 <doi:10.3390/f4030537>; Parker et al. 2004 <doi:10.1111/j.0021-8901.2004.00925.x>.

Authors:Jeff Atkins [aut, cre], Gil Bohrer [aut], Robert Fahey [aut], Brady Hardiman [aut], Chrisopher Gough [aut], Timothy Morin [aut], Atticus Stovall [aut], Naupaka Zimmerman [ctb, aut], Chris Black [ctb]

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forestr.pdf |forestr.html✨
forestr/json (API)

# Install 'forestr' in R:
install.packages('forestr', repos = c('https://atkinsjeff.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/atkinsjeff/forestr/issues

Datasets:
  • osbs - PCL transect from Ordway-Swisher Biological Station, Florida, US.
  • pcl_adjusted - A data frame LiDAR returns that have been split to x and z position and coded and adjusted for user height
  • pcl_coded - A data frame LiDAR returns that have been split to x and z position and coded
  • pcl_data - PCL transect from the University of Virginia
  • pcl_matrix - A LiDAR hit density by x, z position
  • pcl_norm - A data frame of normalized LiDAR return density
  • pcl_split - A data frame LiDAR returns that have been split to x and z position
  • pcl_summary - Summary matrix
  • pcl_vai - A data frame of vegetation area index
  • red_pine - PCL transect from a red pine plantation in Northern Michigan, US.

On CRAN:

4.92 score 27 stars 31 scripts 169 downloads 29 exports 41 dependencies

Last updated 12 months agofrom:1ddce0d514. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-winNOTEOct 25 2024
R-4.5-linuxNOTEOct 25 2024
R-4.4-winNOTEOct 25 2024
R-4.4-macNOTEOct 25 2024
R-4.3-winNOTEOct 25 2024
R-4.3-macNOTEOct 25 2024

Exports:adjust_by_usercalc_enlcalc_fhdcalc_gap_fractioncalc_ginicalc_intensitycalc_rugositycalc_rumplecalc_tls_mean_leaf_htcalc_vaicode_hitscsc_metricsget_transect_lengthmake_matrixmake_summary_matrixnormalize_pclnormalize_pcl_mhpcl_diagnostic_plotplot_hit_gridplot_pavdprocess_multi_pclprocess_pclprocess_tlsread_pclread_pcl_multisplit_transects_from_pclwrite_hit_matrix_to_csvwrite_pcl_to_csvwrite_summary_matrix_to_csv

Dependencies:clicolorspacecpp11dplyrfansifarvergenericsggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmomentsmunsellnlmepillarpkgconfigplyrpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
'read_pcl' imports PCL or portable canopy LiDAR files into the workspace and formats them.%>% read_pcl read_pcl_multi
Adjust by user heightadjust_by_user
Calculate rugosity and other higher level complexity metricscalc_enl
foliar height diversitycalc_fhd
Calculate gap fractioncalc_gap_fraction
Gini coefficientcalc_gini
Intensity Statisticscalc_intensity
Calculate rugosity and other higher level complexity metricscalc_rugosity
Calculates rumplecalc_rumple
Calculates rumplecalc_tls_csc
Process single PCL transects.calc_tls_mean_leaf_ht
Calculate vegetation area index (VAI) from normalized PCL data matrixcalc_vai
Code hitscode_hits
Canopy cover and sky fraction estimatescsc_metrics
Get transect length of PCL transect (in meters)get_transect_length
Make PCL matrix for higher level complexity measuresmake_matrix
Make PCL matrix part onemake_matrix_part_one
Make PCL matrix part twomake_matrix_part_two
Creates summary matrixmake_summary_matrix
Normalize PCL data based on light saturation and attenuationnormalize_pcl
Normalize PCL data based on light saturation and attenuationnormalize_pcl_mh
PCL transect from Ordway-Swisher Biological Station, Florida, US.osbs
a data frame LiDAR returns that have been split to x and z position and coded and adjusted for user heightpcl_adjusted
a data frame LiDAR returns that have been split to x and z position and codedpcl_coded
PCL transect from the University of Virginiapcl_data
PCL diagnostic plotpcl_diagnostic_plot
a LiDAR hit density by x, z positionpcl_matrix
a data frame of normalized LiDAR return densitypcl_norm
a data frame LiDAR returns that have been split to x and z positionpcl_split
summary matrixpcl_summary
a data frame of vegetation area index (VAI)pcl_vai
Plots LiDAR hit grids of VAIplot_hit_grid
Graphs Plant Area Volume Density Profilesplot_pavd
Process multiple PCL transects.process_multi_pcl
Process single PCL transects.process_pcl
Process single PCL transects.process_tls
PCL transect from a red pine plantation in Northern Michigan, US.red_pine
Split transects from PCLsplit_transects_from_pcl
Writes hit matrix to csv for further analysiswrite_hit_matrix_to_csv
Writes csc metrics and output variables to .csvwrite_pcl_to_csv
Writes csc metrics and output variables to .csvwrite_summary_matrix_to_csv