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Build IPM for a given species and climate

Source: R/class_mu_gr.R
make_mu_gr.Rd

Integrate IPM for growth and survival function at a specific climate for a species on a basal area variation.

Usage

make_mu_gr(
  species,
  fit,
  climate = NULL,
  mesh = c(m = 700, L = 90, U = 1500),
  BA = 0:200,
  correction = c("none", "constant", "ceiling", "sizeExtremes"),
  stepMu = 0.001,
  level = c(3, 140),
  diag_tresh = 50,
  midbin_tresh = 25,
  mid_level = 5,
  year_delta = 1,
  IsSurv = TRUE,
  verbose = FALSE
)

Arguments

species

The species names to be registered in the object

fit

Fitted model for growth and survival of the species and climate given. Functions will depend on size and basal area.

climate

Climate table for the species. Optionnal if the species is defined in the package. The format is climatic variable in column and different climate by row. An example is in the package with cliamte_species.

mesh

vector of mesh variables. m is the number of bins, L is the minimum size and U the maximum size. h will be defined in the function as \(h <- (U - L) / m\).

BA

Vector of basal area to integrate on. Integrating on 0 is important so use it. Integrating above 200 is absurd.

correction

Correction to apply to the IPM matrix for eviction. Choices constant (default), ceiling, sizeExtremes and none.

stepMu

Step between each mu in the species range. This value has effect simulation. Default is 1e-3. Values below 1e-5 takes longer than classical matrix integration.

level

Number of point to use for integration in a cell during Gauss-Legendre integration. This value will be divided by 3 since size t is integrated at level = 3 and size t+1 at level = level/3. single int (default 420).

diag_tresh

Threshold for Gauss-Legendre integration, which a distance to the diagonal. Number of cell integrated is the number of cell for which size t+1 - size t is inferior to this threshold. single dbl (default 50).

midbin_tresh

Number of cells external to the GL integration to integrate with the mid bin method.

mid_level

Number of point to use for integration in a cell during mid bin integration.

year_delta

Number of year between 2 obersavtion when using this model. default 1, single int. NOTE : value for dev usage only !

IsSurv

Adding survival to the IPM. Set to FALSE is useful to test for eviction of the model. TRUE by default.

verbose

Print message. FALSE by defaul

Details

The check between climate variables and fitted variable will assert if all variables in the model are provided expect variables derived from "size" (size, size2, logsize), "intercept" and "BATOTcomp". An error will be triggered if the climate variable is missing.

One can desactivate each kind of integration with some treshold values. A negative value in diag_tresh (ex: -1) will cancel the Gauss-Legendre integration and a midbin_tresh null value (ex: 0) will cancel the midbin integration.

This is a working function to test faster integration but it integrate a ba value