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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 the wood density and its uncertainty;
  3. constructing height-diameter models;
  4. estimating the above ground biomass/carbon at the stand level with the associated uncertainty;
  5. managing tree and plot coordinates.

For more information, see the paper of 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

871

Version

2.2.3

License

GPL-2

Issues

Pull Requests

Stars

Forks

Maintainer

Dominique Lamonica

Last Published

February 24th, 2025

Functions in BIOMASS (2.2.3)

NouraguesHD

Height-Diameter data
HDmethods

HDmethods
bilinear_interpolation

Generalized bilinear interpolation of coordinates
computeFeldRegion

Retrieving Feldpausch regions
BIOMASS-package

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

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

Retrieving Chave's environmental index
attributeTreeCoord

Attribute GPS coordinates to trees
attributeTree

Attribute trees to subplots
cacheManager

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

Divides one ore more plots into subplots
feldCoef

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

Retrieve trees taxonomy
getWoodDensity

Estimating wood density
correctTaxo

Correct trees taxonomy
correctCoordGPS

Correct the GPS coordinates
cachePath

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

Check coordinates of plot corners and trees
cutPlot

Divides one or more plots into subplots
numberCorner

Get the UTM coordinates with the corner of the plot
summaryByPlot

Summarise by plot the posterior distribution of AGB values
createCache

Function used to create or activate a permanent cache.
modelHD

Fitting height-diameter models
NouraguesTrees

Nouragues forest dataset
NouraguesCoords

Nouragues plot coordinates
clearCache

Function to clear cache content and possibly remove it
latlong2UTM

Translate the long lat coordinate in UTM coordinate
genusFamily

Genus Family database
getBioclimParam

Retrieving bioclimatic parameters
computeAGB

Computing tree above ground biomass (AGB)
apgFamilies

Angiosperm Phylogeny Group (APG III) dataset
wdData

The global wood density database
param_4

Posterior distribution of Chave et al.'s 2014 equation 4 parameters
param_7

Posterior distribution of parameters associated with the equation 7 by Chave et al. 2014.
sd_10

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

Summarise and display tree information by subplot
predictHeight

Tree height predictions
retrieveH

Retrieving tree height from models
procrust

Procrust analysis
NouraguesPlot201

Nouragues plot 201 coordinates