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✨
card.svg |card.png
BIOMASS/json (API)
NEWS

# 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:

10.41 score 35 stars 1 packages 90 scripts 1.0k downloads 40 mentions 28 exports 38 dependencies

Last updated from:8617ac1ce4. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE370
source / vignettesOK353
linux-release-x86_64NOTE319
macos-release-arm64NOTE214
macos-oldrel-arm64NOTE276
windows-develNOTE307
windows-releaseNOTE273
windows-oldrelNOTE306
wasm-releaseOK211

Exports:AGBmonteCarloattributeTreeattributeTreeCoordbilinear_interpolationcacheManagercachePathcalibrate_modelcheck_plot_coordclearCachecomputeAGBcomputeEcomputeFeldRegioncorrectCoordGPScorrectTaxocreateCachecutPlotdivide_plotgetBioclimParamgetWoodDensitylatlong2UTMmodelHDnumberCornerpredict_mappredictHeightretrieveHsubPatternsubplot_summarysummaryByPlot

Dependencies:classclassIntclicpp11data.tableDBIe1071farverggplot2gluegtableisobandKernSmoothlabelinglifecyclemagrittrMASSminpack.lmproj4proxyR6rappdirsRColorBrewerRcpprlangs2S7scalessfstringdiststringistringrterraunitsvctrsviridisLitewithrwk

Predict maps of AGBD based on inventory and LiDAR data

Dominique Lamonica

Rendered fromVignette_predict_map_AGBD.Rmdusingknitr::rmarkdownon May 28 2026.

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

Spatialize trees and forest stand metrics with BIOMASS

Arthur Bailly

Rendered fromVignette_spatialized_trees_and_forest_stand_metrics.Rmdusingknitr::rmarkdownon May 28 2026.

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

Estimate stand biomass

Arthur Bailly

Rendered fromVignette_BIOMASS.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2026-04-30
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