Package: lidaRtRee 4.0.5

lidaRtRee: Forest Analysis with Airborne Laser Scanning (LiDAR) Data

Provides functions for forest analysis using airborne laser scanning (LiDAR remote sensing) data: tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation; forest parameters estimation and mapping with the area-based approach. It includes complementary steps for forest mapping: co-registration of field plots with LiDAR data (Monnet and Mermin (2014) <doi:10.3390/f5092307>); extraction of both physical (gaps, edges, trees) and statistical features from LiDAR data useful for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>) and forest maturity mapping (Fuhr et al. (2022) <doi:10.1002/rse2.274>); model calibration with ground reference, and maps export.

Authors:Jean-Matthieu Monnet [aut, cre], Pascal Obstétar [ctb]

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

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

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

53 exports 3 stars 0.36 score 130 dependencies 387 downloads

Last updated 1 years agofrom:2c3c1249e2. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 30 2024
R-4.5-winNOTEAug 30 2024
R-4.5-linuxNOTEAug 30 2024
R-4.4-winOKAug 30 2024
R-4.4-macOKAug 30 2024
R-4.3-winOKAug 30 2024
R-4.3-macOKAug 30 2024

Exports:.aba_metricsaa_las_chablais3aba_build_modelaba_combine_strataaba_inferenceaba_metricsaba_plotaba_predictadd_vegetation_indicesboxcox_itrboxcox_itr_bias_corboxcox_trcimg2Rastercircle2Rasterclean_rasterclouds_metricsclouds_tree_metricsconvert_rastercoregistrationcreate_diskdem_filteringedge_detectionellipses4Crowngap_detectionheight_regressionhist_detectionhist_stacklma_checkmaxima_detectionmaxima_selectionplot_matchedplot_tree_inventorypointList2polypoints2DSMpoints2DTMpolar2Projectedraster_chull_maskraster_local_maxraster_metricsraster_xy_maskraster_zonal_statsraster2Cimgrasters_moving_corrasters2Corseg_adjustsegmentationspecies_colorstd_tree_metricsterrain_points_metricstree_detectiontree_extractiontree_matchingtree_segmentation

Dependencies:abindbackportsbase64encBHbmpbootbroombslibcachemcallrcarcarDatacheckmateclassclassIntclicolorspacecowplotcpp11data.tableDBIdensEstBayesDerivdescdigestdistributionaldoBydownloaderdplyre1071evaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegridExtragtablegvlmahighrhtmltoolshtmlwidgetsigraphimagerinlineisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglatticelazyevalleapslidRlifecyclelme4loomagrittrMASSMatrixMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpkgbuildpkgconfigpngposteriorprocessxproxypspurrrquantregQuickJSRR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreadbitmapreldistrglrlangrlasrmarkdownrstanrstantoolss2sassscalessfSparseMStanHeadersstarsstringistringrsurvivaltensorAterratibbletidyrtidyselecttifftinytexunitsutf8vctrsviridisLitewithrwkxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Calibrates and validates area-based modelsaba_build_model
Combines a list of ABA models into a single ABA model objectaba_combine_strata
computes inference from area-based model and predicted valuesaba_inference
Function for area-based metrics computation.aba_metrics aba_metrics
Plots observed VS values predicted in leave one out cross validation of an 'aba_build_model'aba_plot
Mapping of ABA prediction modelsaba_predict
Add vegetation indices on a IRC imageadd_vegetation_indices
Inverse Box-Cox transformationboxcox_itr
Inverse Box-Cox transformation with bias correctionboxcox_itr_bias_cor
Box-Cox Transformationboxcox_tr
Canopy height model (Chablais 3 plot)chm_chablais3
Cimg to SpatRaster conversioncimg2Raster
Raster corresponding to circle extentcircle2Raster
Applies thresholds and mask to a raster objectclean_raster
Computes metrics on list of point cloudsclouds_metrics
Computes metrics on trees detected in list of point clouds.clouds_tree_metrics
Raster format conversionconvert_raster
Tree inventory and canopy height model coregistrationcoregistration
Disk-shaped matrix maskcreate_disk
Image pre-processing (non-linear filtering and Gaussian smoothing)dem_filtering
Edge detection in gap imageedge_detection
Create elliptical polygons from centres and extensions in four directionsellipses4Crown
Gap detection in a Canopy Height Modelgap_detection
Regression of detected heights VS reference heightsheight_regression
Histogram of detectionhist_detection
Stacked histogramhist_stack
las data in France (Chablais 3 plot)las_chablais3
Checks linear model assumptions of a multiple regression modellma_check
Local maxima extraction on imagemaxima_detection
Image maxima selection based on values and neighborhood of local maximamaxima_selection
Plot of matched pairs of detected and reference treesplot_matched
Displays a map of tree inventory dataplot_tree_inventory
Convert a list of points into spatial polygons objectpointList2poly
Digital Surface Modelpoints2DSM
Digital Terrain Modelpoints2DTM
Polar to cartesian coordinates conversionpolar2Projected
Field plot inventory in the Quatre Montagnes area (France)quatre_montagnes
Raster mask of convex hullraster_chull_mask
Statistics of raster local maximumraster_local_max
Computes metrics by aggregating a raster at lower resolution or summarizing attributes based on XY locationsraster_metrics
Raster mask by union of buffers around xy positionsraster_xy_mask
Image statistic in segmentraster_zonal_stats
SpatRaster to Cimg conversionraster2Cimg
Correlation between rasters for different XY translationsrasters_moving_cor
Correlation between two rastersrasters2Cor
Modification of segments based on valuesseg_adjust
Image segmentation by seed-based watershed algorithmsegmentation
Table of species names, abreviations and display colorsspecies_color
Computation of tree metricsstd_tree_metrics
Computation of terrain metricsterrain_points_metrics
Tree detectiontree_detection
Tree extractiontree_extraction
Tree inventory data in France (Chablais 3 plot, July 2010)tree_inventory_chablais3
3D matching of detected tree top positions with reference positionstree_matching
Preprocessing and segmentation of raster image for tree identificationtree_segmentation