Package: BIOMASS 3.0

Dominique Lamonica

BIOMASS: Estimating Aboveground Biomass and Its Uncertainty in Tropical Forests

Contains functions for estimating above-ground biomass/carbon and its uncertainty in tropical forests. These functions allow to (1) retrieve and correct taxonomy, (2) estimate wood density and its uncertainty, (3) build height-diameter models, (4) manage tree and plot coordinates, (5) estimate above-ground biomass/carbon at stand level with associated uncertainty. To cite ‘BIOMASS’, please use citation(‘BIOMASS’). For more information, see Réjou-Méchain et al. (2017) <doi:10.1111/2041-210X.12753>.

Authors:Dominique Lamonica [aut, cre], Maxime Réjou-Méchain [aut, dtc], Arthur Bailly [aut], Guillaume Cornu [aut], John Godlee [ctb], Fabian Fischer [ctb], Jerome Chave [ctb], Arthur Pere [aut], Ariane Tanguy [aut], Camille Piponiot [aut], Bruno Hérault [aut], Philippe Verley [ctb], Ted Feldpausch [dtc]

BIOMASS_3.0.tar.gz
BIOMASS_3.0.zip(r-4.7)BIOMASS_3.0.zip(r-4.6)BIOMASS_3.0.zip(r-4.5)
BIOMASS_3.0.tgz(r-4.6-any)BIOMASS_3.0.tgz(r-4.5-any)
BIOMASS_3.0.tar.gz(r-4.7-any)BIOMASS_3.0.tar.gz(r-4.6-any)
BIOMASS_3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BIOMASS/json (API)

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

Bug tracker:https://github.com/umr-amap/biomass/issues

Pkgdown/docs site:https://umr-amap.github.io

Datasets:

On CRAN:

Conda:

10.54 score 35 stars 1 packages 98 scripts 1.1k downloads 40 mentions 28 exports 39 dependencies

Last updated from:a6fced4d7a. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK332
source / vignettesOK340
linux-release-x86_64OK341
macos-release-arm64OK296
macos-oldrel-arm64OK252
windows-develOK306
windows-releaseOK281
windows-oldrelOK289
wasm-releaseOK214

Exports:AGBmonteCarloattributeTreeattributeTreeCoordbilinear_interpolationcacheManagercachePathcalibrate_modelcheck_plot_coordclearCachecomputeAGBcomputeEcomputeFeldRegioncorrectCoordGPScorrectTaxocreateCachecutPlotdivide_plotgetBioclimParamgetWoodDensitylatlong2UTMmodelHDnumberCornerpredict_mappredictHeightretrieveHsubPatternsubplot_summarysummaryByPlot

Dependencies:classclassIntclicpp11data.tableDBIe1071farverggnewscaleggplot2gluegtableisobandKernSmoothlabelinglifecyclemagrittrMASSminpack.lmproj4proxyR6rappdirsRColorBrewerRcpprlangs2S7scalessfstringdiststringistringrterraunitsvctrsviridisLitewithrwk

Estimate stand biomass
Complete BIOMASS workflow and vignette organisation | General workflow and required data | Wood density | Checking and retrieving tree taxonomy | Getting wood density | Height | Building a local H-D model | Using the continent- or region-specific H–D model (Feldpausch) | Using the generic H–D model based on a bioclimatic predictor (Chave) | Estimate AGB | Propagate AGB errors | Diameter measurement error | Wood density error | Height error | All together and AGB visualisation of plots | Some tricks | Mixing measured and estimated height values | Building bayesian Height-Diameter models | Add your tricks
Rendered fromVignette_BIOMASS.Rmdusingknitr::rmarkdown

Last update: 2026-04-30
Started: 2025-01-31

Predict maps of AGBD based on inventory and LiDAR data
Overview | Mathematical modelling | Warning on vignette example | Previous steps | Load inventory, plot coordinates and LiDAR data | Compute AGBD | Spatialize AGBD | Spatialize LiDAR metric | Calibrate model | Predict AGBD map on the LiDAR footprint | Run prediction in parallel | What about validation ?
Rendered fromVignette_predict_map_AGBD.Rmdusingknitr::rmarkdown

Last update: 2026-04-27
Started: 2026-02-13

Spatialize trees and forest stand metrics with BIOMASS
Overview | Required data | Checking plot's coordinates | Checking the corners of the plot | If we rely on the GPS coordinates of the corners: | If we rely on the shape of the plot measured on the field: | Recovering reference corner coordinates and the associated polygon(s) | Visualising and retrieving projected tree coordinates | Integrating LiDAR data | Checking multiple plots at once | Dividing plots | Summarising metrics at subplot level | Summarising tree metrics | Summarising the AGBD and its uncertainties | Summarising LiDAR metrics | All at once | Customizing the ggplot
Rendered fromVignette_spatialized_trees_and_forest_stand_metrics.Rmdusingknitr::rmarkdown

Last update: 2026-04-13
Started: 2025-01-31

Readme and manuals

Help Manual

Help pageTopics
Propagating above ground biomass (AGB) or carbon (AGC) errors to the stand levelAGBmonteCarlo
Attribute trees to subplotsattributeTree
Attribute GPS coordinates to treesattributeTreeCoord
Generalized bilinear interpolation of coordinatesbilinear_interpolation
Function that return a possibly cached file, transparently downloading it if missingcacheManager
Function used to build a file path based on a cache foldercachePath
Calibrate a bayesian model to fit log(AGBD) ~ log(raster metric)calibrate_model
Check coordinates of plot corners and treescheck_plot_coord
Function to clear cache content and possibly remove itclearCache
Computing tree above ground biomass (AGB)computeAGB
Retrieving Feldpausch regionscomputeFeldRegion
Correct the GPS coordinatescorrectCoordGPS
Correct and match taxonomic names to the World Flora Online databasecorrectTaxo
Function used to create or activate a permanent cache.createCache
Divides one or more plots into subplotscutPlot
Divides one ore more plots into subplotsdivide_plot
Estimating wood density and associated uncertaintiesgetWoodDensity
HDmethodsHDmethods loglogFunction michaelisFunction weibullFunction
Translate the long lat coordinate in UTM coordinatelatlong2UTM
Fitting height-diameter modelsmodelHD
Nouragues plot coordinatesNouraguesCoords
Height-Diameter dataNouraguesHD
Nouragues plot 201 coordinatesNouraguesPlot201
Nouragues forest datasetNouraguesTrees
Get the UTM coordinates with the corner of the plotnumberCorner
Predict map of AGBD and associated uncertaintypredict_map
Tree height predictionspredictHeight
Procrust analysisprocrust
Retrieving tree height from modelsretrieveH
Common taxonomic name substitutionssubPattern
Summarise and display tree information by subplotsubplot_summary
Summarise by plot the posterior distribution of AGB valuessummaryByPlot