DSsim (version 1.1.4)

Simulation-class: Class "Simulation"

Description

Class "Simulation" is an S4 class containing descriptions of the region, population, survey design and analyses the user wishes to investigate. Once the simulation has been run the N.D.Estimates will contain multiple estimates of abundance and density obtained by repeatedly generating populations, simulating the survey and completing the analyses.

Slots

reps

Object of class "numeric"; the number of times the simulation should be repeated.

single.transect.set

Object of class "logical"; if TRUE the same set of transects are used in each repetition.

double.observer

Object of class "logical"; whether a double observer protocol is being used. Not currently implemented.

region

Object of class "Region"; the survey region.

design

Object of class "Survey.Design"; the survey design.

population.description

Object of class "Population.Description"; the population.description.

detectability

Object of class "Detectability"; a description of the detectability of the population.

ddf.analyses

Object of class "list"; a list of objects of class DDF.Analysis. These are fitted and the one with the minimum criteria is selected and used in predicting N and D.

dsm.analysis

Object of class "DSM.Analysis"; Not yet implemented.

ddf.param.ests

Object of class "array"; stores the parameters associated with the detection function.

results

A "list" of "arrays"; stores the estimated of abundance and density as well as other measures of interest.

warnings

A "list" to store warnings and error messages encountered during runtime.

Methods

add.hotspot

signature=(object = "Simulation"): adds a hotspot based on a gaussian decay to the density surface.

summary

signature=(object = "Simulation"): produces a summary of the simulation and its results.

generate.population

signature = (object = "Simulation"): generates a single instance of a population.

generate.transects

signature = (object = "Simulation"): generates a single set of transects.

create.survey.results

signature = (object = "Simulation"): carries out the simulation process as far as generating the distance data and returns an object containing the population, transects and data.

run.analysis

signature = c(object = "Simulation", data = "LT.Survey.Results"): returns the ddf analysis results from the models in the simulation fitted to the data in the LT.Survey.Results object.

run.analysis

signature = c(object = "Simulation", data = "DDF.Data"): returns the ddf analysis results from the models in the simulation fitted to the data in the DDF.Data object.

run

signature = (object = "Simulation"): runs the whole simulation for the specified number of repetitions.

See Also

make.simulation