Recruitment analaysis .

This function computes the likelihood associated to a specific set of parameters. The specification of parameters determines the ecological processes involved.

recuitmentAnalysis(site, year, tree, age, mat_par, path = "./",
  zero_infl = FALSE, disp = FALSE, favo = FALSE, neigh = FALSE,
  clip = NULL, kernel = "kern_lognormal", mxt = 100, quiet = TRUE,
  record = NULL)

launchIt(iter, simu = NULL, mxt = 100, record = "test.txt",
  quiet = TRUE, path = "output/")

Arguments

site	site name.
year	year (2015 or 2016) name.
tree	abbreviation of the tree species names of the species.
age	age of the species (1 or 2).
mat_par	a matrix of parameters (see getParameters).
path	a character string giving the path to access the data.
zero_infl	logical. If TRUE then a zero-inflated poisson distribution is used, otherwise a poisson distribution is used.
disp	a logical. If TRUE, then dispersal parameters are used.
favo	a logical. If TRUE, then favorability parameters are used.
neigh	a logical. If TRUE, then neighborhood effect parameter is used.
clip	a numeric vector of standardized DBH (Diameter at breast heights).
kernel	a character string indicating which kernel should be used (either kern_lognormal or kern_exponential_power). See kernels for further details.
mxt	a numeric. Maximum running time in seconds (see GenSA).
quiet	logical. If TRUE details about the state of simulations are printed.
record	a connection, or a character string naming the file to print to. If NULL, the default values, no record is done.
iter	a integer identifying the iteration.
simu	a data frame describing the simulation.

Value

The log-likelihood values associated to a given set of parameters.

Details

The parameter pz have a value even if it is not included in the analysis (meaning a poisson distribution is used).

Functions

• launchIt: Launch the analysis for a given row of the simulation data frame or file.