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BIOMASS

The package

The BIOMASS package allows users to estimate above ground biomass/carbon and its uncertainty in tropical forests.

The main implemented steps are as follows :

  1. retrieving and correcting tree taxonomy;
  2. estimating wood density and its uncertainty;
  3. building height-diameter models;
  4. estimating above ground biomass/carbon at stand level with associated uncertainty;
  5. managing tree and plot coordinates.

For more information, see Réjou-Méchain et al. (2017)

Install BIOMASS

The latest released version from CRAN:

install.packages("BIOMASS")

The latest version from Github (in development):

install.packages("remotes")
remotes::install_github('umr-amap/BIOMASS')

To use it :

library("BIOMASS")

Tutorials/Vignettes

Two vignettes are available in the 'Articles' section of the following page : https://umr-amap.github.io/BIOMASS/index.html

Citation

Please cite this package as:

Réjou-Méchain M, Tanguy A, Piponiot C, Chave J, Herault B (2017). “BIOMASS : an R package for estimating above-ground biomass and its uncertainty in tropical forests.” Methods in Ecology and Evolution, 8(9). ISSN 2041210X, doi:10.1111/2041-210X.12753.

Or you can also run

citation("BIOMASS")

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Version

Install

install.packages('BIOMASS')

Monthly Downloads

2,091

Version

2.2.4-1

License

GPL-2

Issues

Pull Requests

Stars

Forks

Maintainer

Dominique Lamonica

Last Published

October 10th, 2025

Functions in BIOMASS (2.2.4-1)

bilinear_interpolation

Generalized bilinear interpolation of coordinates
cachePath

Function used to build a file path based on a cache folder
check_plot_coord

Check coordinates of plot corners and trees
computeFeldRegion

Retrieving Feldpausch regions
correctCoordGPS

Correct the GPS coordinates
cacheManager

Function that return a possibly cached file, transparently downloading it if missing
computeE

Retrieving Chave's environmental index
correctTaxo

Correct trees taxonomy
createCache

Function used to create or activate a permanent cache.
modelHD

Fitting height-diameter models
latlong2UTM

Translate the long lat coordinate in UTM coordinate
feldCoef

Feldpausch et al. 2012 coefficients for generalized height-diameter models
divide_plot

Divides one ore more plots into subplots
clearCache

Function to clear cache content and possibly remove it
getTaxonomy

Retrieve trees taxonomy
numberCorner

Get the UTM coordinates with the corner of the plot
computeAGB

Computing tree above ground biomass (AGB)
getWoodDensity

Estimating wood density
genusFamily

Genus Family database
param_4

Posterior distribution of Chave et al.'s 2014 equation 4 parameters
procrust

Procrust analysis
retrieveH

Retrieving tree height from models
wdData

The global wood density database
cutPlot

Divides one or more plots into subplots
summaryByPlot

Summarise by plot the posterior distribution of AGB values
predictHeight

Tree height predictions
param_7

Posterior distribution of parameters associated with the equation 7 by Chave et al. 2014.
getBioclimParam

Retrieving bioclimatic parameters
subplot_summary

Summarise and display tree information by subplot
sd_10

Mean standard deviation of wood density estimates at different taxonomic levels
attributeTree

Attribute trees to subplots
BIOMASS-package

BIOMASS: Estimating Aboveground Biomass and Its Uncertainty in Tropical Forests
attributeTreeCoord

Attribute GPS coordinates to trees
NouraguesHD

Height-Diameter data
NouraguesPlot201

Nouragues plot 201 coordinates
NouraguesTrees

Nouragues forest dataset
NouraguesCoords

Nouragues plot coordinates
HDmethods

HDmethods
AGBmonteCarlo

Propagating above ground biomass (AGB) or carbon (AGC) errors to the stand level
apgFamilies

Angiosperm Phylogeny Group (APG III) dataset