dataOrganize: R6 class to assist in reformatting the data to be used in...

In PhilipMostert/inlabruSDMs: Fit Models Derived from Point Processes to Species Distributions using 'inlabru'

R6 class to assist in reformatting the data to be used in dataSDM.

Description

Internal functions used to temporarily store data and other information before adding to dataSDM.

Methods

Public methods

• dataOrganize$makeData()

• dataOrganize$makeSpecies()

• dataOrganize$makeMultinom()

• dataOrganize$makeFormulas()

• dataOrganize$makeComponents()

• dataOrganize$makeLhoods()

• dataOrganize$clone()

---

Method makeData()

Usage

dataOrganize$makeData(
  datapoints,
  datanames,
  coords,
  proj,
  marktrialname,
  paresp,
  countsresp,
  trialname,
  speciesname,
  marks,
  pointcovnames,
  markfamily,
  temporalvar,
  offsetname
)

---

Method makeSpecies()

Usage

dataOrganize$makeSpecies(speciesname, repl = FALSE)

---

Method makeMultinom()

Usage

dataOrganize$makeMultinom(multinomVars, return, oldVars, repl = FALSE)

---

Method makeFormulas()

Usage

dataOrganize$makeFormulas(
  spatcovs,
  speciesname,
  paresp,
  countresp,
  marks,
  marksspatial,
  speciesintercept,
  speciesenvironment,
  spatial,
  intercept,
  temporalname,
  speciesindependent,
  markintercept,
  pointcovs,
  speciesspatial,
  biasformula,
  covariateformula
)

---

Method makeComponents()

Usage

dataOrganize$makeComponents(
  spatial,
  intercepts,
  datanames,
  marks,
  speciesname,
  multinomnames,
  pointcovariates,
  covariatenames,
  covariateclass,
  marksspatial,
  marksintercept,
  temporalname,
  speciesspatial,
  speciesenvironment,
  speciesintercept,
  numtime,
  temporalmodel,
  offsetname,
  copymodel,
  speciesindependent,
  biasformula,
  covariateformula,
  marksCopy
)

---

Method makeLhoods()

Usage

dataOrganize$makeLhoods(
  mesh,
  ips,
  paresp,
  ntrialsvar,
  markstrialsvar,
  speciesname
)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

dataOrganize$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

PhilipMostert/inlabruSDMs documentation built on April 14, 2025, 11:39 a.m.