Package: matreex 0.4.0

Maxime Jaunatre

matreex: matreex: Simulation IPM for forest dynamic depending on climatic variables from Kunstler et al (2020)

The goal of this package is to run integrated projection models of tree species in single or multi-specific density dependence context. The simulations return the size distribution dynamics along time. These models can be completed with different harvest and disturbance models and be runned untile equilibrium.

Authors:Maxime Jaunatre [aut, cre, trl], Julien Barrere [aut], Thomas Cordonnier [aut], Arnaud Guyennon [aut], Bjoern Reineking [aut], Laura Touzot [aut], INRAE [cph], Georges Kunstler [aut]

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manual.pdf |manual.html✨
card.svg |card.png
matreex/json (API)
NEWS

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

Bug tracker:https://github.com/gowachin/matreex/issues

Datasets:

On CRAN:

Conda:

3.18 score 34 exports 27 dependencies

Last updated from:3b685b6fd1. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK177
source / vignettesOK497
linux-release-x86_64OK170
macos-release-arm64OK111
macos-oldrel-arm64OK95
windows-develOK153
windows-releaseOK122
windows-oldrelOK120
wasm-releaseOK118

Exports:climaticcorrectiondef_disturbdef_harvdef_initdef_init_evendef_init_kdef_initBAdelaydisturb_fundisturb_fun_mixtEven_harvfit_sgrforestget_maxdbhget_step_IPMgetRangemumake_IPMmake_mu_grnew_fit_sgrnew_forestnew_mu_grnew_speciesold_fit2fitold_ipm2forestold_ipm2speciesQMDsim_deter_forestsim_rdikgsp_namesp_recspeciestree_formatUneven_harv

Dependencies:backportscheckmateclicpp11dplyrgenericsglueherelatticelifecyclemagrittrMatrixpillarpkgconfigpurrrR6rlangrprojrootstatmodstringistringrtibbletidyrtidyselectutf8vctrswithr

Basic functions and examples

Rendered frommatreex.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2024-03-04
Started: 2023-01-10

Disturbance models

Rendered fromDisturbance.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2023-12-05
Started: 2023-10-05

Harvesting models

Rendered fromHarvesting.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2024-02-02
Started: 2023-01-10

Readme and manuals

Help Manual

Help pageTopics
Species climate optimum dataset.climate_species
Get climatic values in matreex class objectclimatic
Add correction states to a systemcorrection
Default disturbance functiondef_disturb
Default population harvestdef_harv
Default population initializationdef_init
Default even population initializationdef_init_even
Init population with precise distributiondef_init_k
Init population at BAdef_initBA
Add delay states to a systemdelay
Delay dgCMatrixdelay.dgCMatrix
Delay dsCMatrixdelay.dsCMatrix
Delay dtCMatrixdelay.dtCMatrix
Species disturbance parameters.disturb_coef
Disturbance functiondisturb_fun
Disturbance functiondisturb_fun_mixt
Perform the harvest EvenEven_harv
Species fited models dataset.fit_Abies_alba fit_Acer_campestre fit_Acer_pseudoplatanus fit_Alnus_glutinosa fit_Betula fit_Carpinus_betulus fit_data fit_Fagus_sylvatica fit_Fraxinus_excelsior fit_Juniperus_thurifera fit_Larix_decidua fit_Picea_abies fit_Pinus_halepensis fit_Pinus_nigra fit_Pinus_pinaster fit_Pinus_pinea fit_Pinus_sylvestris fit_Pinus_uncinata fit_Populus_tremula fit_Prunus_padus fit_Quercus_faginea fit_Quercus_ilex fit_Quercus_petraea fit_Quercus_pubescens fit_Quercus_pyrenaica fit_Quercus_robur fit_Quercus_suber fit_Salix_caprea fit_species lag_species
Create a new fitted models fromfit_sgr
Create a new forest for simulationforest
Get the max_dbh of a fitted speciesget_maxdbh
Extract an IPM matrixget_step_IPM
Build IPM for a given species and climatemake_IPM
Build IPM for a given species and climatemake_mu_gr
matreexmatreex
load old fitted modelsold_fit2fit
Dev function to read old ipmold_ipm2forest
Dev function to read old ipmold_ipm2species
get Quadratic Mean DiameterQMD
Species Rdi intercept and slope.rdi_coef
Deterministic Tree population simulationsim_deter_forest
Compute RDI and Kg from simulations outputsim_rdikg
List the species in matreex class objectsp_name
sp recruitsp_rec
Create a new species for simulationharvest_fun init_pop recruit_fun species
IPM summarysummary.ipm
mu_gr summarysummary.mu_gr
species summarysummary.species
Species type.tree_type
Perform the harvest UnevenUneven_harv