Function reference • matreex

Main package documentation.

matreex: matreex

Working with IPMs

Function used to create and modify IPMs

make_IPM(): Build IPM for a given species and climate

get_step_IPM(): Extract an IPM matrix

make_mu_gr(): Build IPM for a given species and climate

Species functions

Functions for building species object, default functions used for initiation of population, harvesting and disturbance.

species(): Create a new species for simulation

def_init(): Default population initialization

def_initBA(): Init population at BA

def_init_even(): Default even population initialization

def_init_k(): Init population with precise distribution

def_harv(): Default population harvest

def_disturb(): Default disturbance function

Running a simulation.

Takes a forest class object to run a simulation.

forest(): Create a new forest for simulation

sim_deter_forest(): Deterministic Tree population simulation

Harvesting

Function for harvesting models during simulations.

Uneven_harv(): Perform the harvest Uneven

Even_harv(): Perform the harvest Even

sim_rdikg(): Compute RDI and Kg from simulations output

Disturbance

Function for disturbance models during simulations.

disturb_fun(): Disturbance function

disturb_fun_mixt(): Disturbance function

Example dataset

Species vital traits models and various datasets.

fit_species lag_species fit_Abies_alba fit_Acer_campestre fit_Acer_pseudoplatanus fit_Alnus_glutinosa fit_Betula fit_Carpinus_betulus 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: Species fited models dataset.

tree_type: Species type.

disturb_coef: Species disturbance parameters.

rdi_coef: Species Rdi intercept and slope.

climate_species: Species climate optimum dataset.

Loading old objects

IPMs have been build with the functions before creating {matreex}. These functions allow to load them and format them into the recent classes.

old_fit2fit(): load old fitted models

old_ipm2species(): Dev function to read old ipm

old_ipm2forest(): Dev function to read old ipm

Misc

fit_sgr(): Create a new fitted models from

delay(): Add delay states to a system

correction(): Add correction states to a system

QMD(): get Quadratic Mean Diameter

get_maxdbh(): Get the max_dbh of a fitted species

climatic(): Get climatic values in matreex class object

sp_name(): List the species in matreex class object

Deprecated Functions

tree_format(): tree_format generic