make.objective.function: Internal scampr function that uses TMB to make the objective...

In ElliotDovers/scampr: Spatially Correlated, Approximate Modelling of Point patterns in R

Internal scampr function that uses TMB to make the objective function of scampr models

Description

Internal scampr function that uses TMB to make the objective function of scampr models

Usage

make.objective.function(TMB.inputs, maxit = 100)

Arguments

TMB.inputs	a list created by the internal scampr function: get.TMB.data.input.
maxit	a numeric indicating the maximum number of iterations for the optimizer. Default is 100 as this optimization uses gradient information.

Value

a data.frame (sparse or dense depending on parameter bf.matrix.type)

Examples

# Get the flora data for one of the species
dat_po <- flora$po$sp1
dat_pa <- flora$pa

# obtain a sample of 10,000 quadrature points for the point process model
set.seed(1)
quad.pts <- flora$quad[sample(1:nrow(flora$quad), 10000, replace = F), ]
set.seed(NULL)

# Attach the quadrature points to the presence-only data
dat_po <- rbind.data.frame(dat_po, quad.pts)

# Ensure the "response" variable in each data set shares the same name
dat_po$presence <- dat_po$pres
dat_pa$presence <- dat_pa$sp1

# Get the TMB data lists for a combined data model without latent field
tmb.input <- scampr:::get.TMB.data.input(presence ~ MNT, bias.formula ~ D.Main, po.data = dat_po, pa.data = dat_pa)

# create the objective function
obj <- make.objective.function(tmb.input)

ElliotDovers/scampr documentation built on March 17, 2024, 3:27 p.m.