DSsim: Distance Sampling Simulations

Performs distance sampling simulations. It repeatedly generates instances of a user defined population within a given survey region, generates realisations of a survey design (currently these must be generated using Distance software in advance <http://distancesampling.org/>) and simulates the detection process. The data are then analysed so that the results can be compared for accuracy and precision across all replications. This will allow users to select survey designs which will give them the best accuracy and precision given their expectations about population distribution. Any uncertainty in population distribution or population parameters can be included by running the different survey designs for a number of different population descriptions. An example simulation can be found in the help file for make.simulation.

AuthorLaura Marshall <lhm@st-and.ac.uk>
Date of publication2016-11-07 17:21:58
MaintainerLaura Marshall <lhm@st-and.ac.uk>
LicenseGPL (>= 2)
Version1.0.8

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Man pages

add.hotspot-methods: S4 generic method to add a hotspot to the density grid

create.bins: Create bins from a set of binned distances and a set of...

create.region.table-methods: S4 generic method to generate a region table

create.sample.table-methods: S4 generic method to generate a sample table

create.survey.results-methods: S4 generic method to simulate a survey

data.for.distance: data.for.distance

DDF.Analysis-class: Class "DDF.Analysis"

DDF.Data-class: Class "DDF.Data"

Density-class: Class "Density"

description.summary: Provides a description of the summary object/output Prints a...

Design.Summary-class: S4 Class "Design.Summary"

Detectability-class: S4 Class "Detectability"

generate.population-methods: S4 generic method to generate an instance of a population

generate.transects-methods: S4 generic method to generate an instance of a design

get.area-methods: Returns the area of the region

get.distance.data-methods: S4 generic method to extract distance data

get.N-methods: S4 generic method to return N

histogram.N.ests-methods: histogram.N.ests

Line.Transect-class: S4 Class "Line.Transect"

LT.Design-class: Virtual Class "LT.Design" extends Class "Survey.Design"

LT.Survey-class: Virtual Class "LT.Survey" extends class "Survey"

LT.Survey.Results-class: S4 Class "LT.Survey.Results"

make.ddf.analysis.list: Creates a list of DDF.Analysis objects

make.density: Creates a Density object

make.design: Creates a Survey.Design object

make.detectability: Creates a Detectablility object

make.population.description: Creates a Population.Description object

make.region: Creates a Region object

make.simulation: Creates a Simulation object

Obs.Table-class: Class "Obs.Table"

plot.DDF.Data-methods: Plot

plot.Density-methods: Plot

plot.Line.Transect-methods: Plot

plot.LT.Survey.Results-methods: Plot

plot.Point.Transect-methods: Plot

plot.Population-methods: Plot

plot.Region-methods: Plot

plot.Survey.Results-methods: Plot

Point.Transect-class: S4 Class "Point.Transect"

Populatin.Summary-class: S4 Class "Population.Summary"

Population-class: Class "Population"

Population.Description-class: Class "Population.Description"

PT.Design-class: Virtual Class "PT.Design" extends Class "Survey.Design"

PT.Survey-class: Virtual Class "PT.Survey" extends class "Survey"

Region-class: Class "Region"

Region.Table-class: S4 Class "Region.Table"

rename.duplicates: Renumbers the object IDs for the duplicate observations...

run.analysis-methods: S4 generic method to run analyses

run-methods: S4 generic method to run a simulation

Sample.Table-class: Class "Sample.Table"

save.sim.results-methods: save.sim.results

show.Simulation-methods: show

show.Simulation.Summary-methods: show

Simulation-class: Class "Simulation"

Simulation.Summary-class: Class "Simulation.Summary"

Single.Obs.DDF.Data-class: S4 Class "Single.Obs.DDF.Data"

Single.Obs.LT.Survey-class: Class "Single.Obs.LT.Survey"

summary.Simulation-methods: summary

Survey-class: Virtual Class "Survey"

Survey.Design-class: S4 Class "Survey.Design"

Survey.Results-class: S4 Class "Survey.Results"

Transect-class: S4 Virtual Class "Transect"

transects: Shapefile describing the transects

Files in this package

DSsim
DSsim/tests
DSsim/tests/test-that.R
DSsim/tests/testthat
DSsim/tests/testthat/test-Intersections.r
DSsim/tests/testthat/test-Constructors.r
DSsim/tests/testthat/test-UserInput.r
DSsim/tests/testthat/test-BasicLineSimulations.r
DSsim/NAMESPACE
DSsim/NEWS
DSsim/data
DSsim/data/transects.shp.rda
DSsim/R
DSsim/R/calc.poss.detect.dists.lines.R DSsim/R/Survey.Design.R DSsim/R/get.bound.box.R DSsim/R/Density.R DSsim/R/Population.Summary.R DSsim/R/Simulation.Summary.R DSsim/R/is.gap.R DSsim/R/get.ave.density.R DSsim/R/in.polygons.R DSsim/R/Transect.R DSsim/R/get.surface.gam.R DSsim/R/LT.Random.Design.R DSsim/R/data.for.distance.R DSsim/R/Sample.Table.R DSsim/R/LT.SegmentedGrid.Design.R DSsim/R/add.dist.error.R DSsim/R/uf.detect.R DSsim/R/LT.Survey.Results.R DSsim/R/calc.area.R DSsim/R/DDF.Data.R DSsim/R/Survey.R DSsim/R/Region.Table.R DSsim/R/single.simulation.loop.R DSsim/R/get.line.sampler.info.R DSsim/R/Design.Summary.R DSsim/R/simulate.detections.R DSsim/R/get.surface.constant.R DSsim/R/get.point.sampler.info.R DSsim/R/Survey.Results.R DSsim/R/LT.SegmentedTrack.Design.R DSsim/R/LT.Systematic.Design.R DSsim/R/PT.Random.Design.R DSsim/R/Obs.Table.R DSsim/R/generate.pop.D.R DSsim/R/DSM.Analysis.R DSsim/R/rename.duplicates.R DSsim/R/LT.Design.R DSsim/R/modify.strata.for.analysis.R DSsim/R/hn.detect.R DSsim/R/calc.poss.detect.dists.points.R DSsim/R/LT.EqSpace.ZZ.Design.R DSsim/R/generate.pop.N.R DSsim/R/check.intersection.R DSsim/R/DS.Analysis.R DSsim/R/description.summary.R DSsim/R/Single.Obs.DDF.Data.R DSsim/R/Simulation.R DSsim/R/Population.Description.R DSsim/R/check.shapefile.R DSsim/R/hr.detect.R DSsim/R/Single.Obs.LT.Survey.R DSsim/R/Detectability.R DSsim/R/add.summary.results.R DSsim/R/PT.Survey.R DSsim/R/coords.from.shapefile.R DSsim/R/Population.R DSsim/R/store.ddf.results.R DSsim/R/LT.EqAngle.ZZ.Design.R DSsim/R/accumulate.PP.results.R DSsim/R/check.LinkID.order.R DSsim/R/generic.functions.R DSsim/R/store.dht.results.R DSsim/R/save.sim.results.R DSsim/R/LT.User.Specified.Design.R DSsim/R/PT.Systematic.Design.R DSsim/R/LT.Survey.R DSsim/R/Region.R DSsim/R/create.bins.R DSsim/R/extract.spat.poly.coords.R DSsim/R/Class.Constructors.R DSsim/R/Single.Obs.PT.Survey.R DSsim/R/PT.Design.R DSsim/R/Line.Transect.R DSsim/R/Point.Transect.R DSsim/R/DDF.Analysis.R DSsim/R/get.shapefile.names.R
DSsim/MD5
DSsim/DESCRIPTION
DSsim/man
DSsim/man/LT.Design-class.Rd DSsim/man/plot.Point.Transect-methods.Rd DSsim/man/Region-class.Rd DSsim/man/get.area-methods.Rd DSsim/man/show.Simulation.Summary-methods.Rd DSsim/man/plot.DDF.Data-methods.Rd DSsim/man/make.detectability.Rd DSsim/man/generate.population-methods.Rd DSsim/man/Population.Description-class.Rd DSsim/man/Survey.Design-class.Rd DSsim/man/Single.Obs.LT.Survey-class.Rd DSsim/man/LT.Survey-class.Rd DSsim/man/make.simulation.Rd DSsim/man/DDF.Analysis-class.Rd DSsim/man/Region.Table-class.Rd DSsim/man/show.Simulation-methods.Rd DSsim/man/run-methods.Rd DSsim/man/plot.Region-methods.Rd DSsim/man/Single.Obs.DDF.Data-class.Rd DSsim/man/make.ddf.analysis.list.Rd DSsim/man/DDF.Data-class.Rd DSsim/man/create.sample.table-methods.Rd DSsim/man/PT.Survey-class.Rd DSsim/man/generate.transects-methods.Rd DSsim/man/Line.Transect-class.Rd DSsim/man/Survey-class.Rd DSsim/man/summary.Simulation-methods.Rd DSsim/man/Population-class.Rd DSsim/man/Density-class.Rd DSsim/man/make.region.Rd DSsim/man/Point.Transect-class.Rd DSsim/man/rename.duplicates.Rd DSsim/man/plot.LT.Survey.Results-methods.Rd DSsim/man/run.analysis-methods.Rd DSsim/man/create.bins.Rd DSsim/man/description.summary.Rd DSsim/man/Detectability-class.Rd DSsim/man/Survey.Results-class.Rd DSsim/man/plot.Population-methods.Rd DSsim/man/Sample.Table-class.Rd DSsim/man/Obs.Table-class.Rd DSsim/man/Simulation-class.Rd DSsim/man/get.N-methods.Rd DSsim/man/Transect-class.Rd DSsim/man/create.region.table-methods.Rd DSsim/man/plot.Line.Transect-methods.Rd DSsim/man/add.hotspot-methods.Rd DSsim/man/Populatin.Summary-class.Rd DSsim/man/create.survey.results-methods.Rd DSsim/man/make.population.description.Rd DSsim/man/Design.Summary-class.Rd DSsim/man/transects.Rd DSsim/man/LT.Survey.Results-class.Rd DSsim/man/make.design.Rd DSsim/man/save.sim.results-methods.Rd DSsim/man/histogram.N.ests-methods.Rd DSsim/man/get.distance.data-methods.Rd DSsim/man/data.for.distance.Rd DSsim/man/PT.Design-class.Rd DSsim/man/Simulation.Summary-class.Rd DSsim/man/plot.Survey.Results-methods.Rd DSsim/man/plot.Density-methods.Rd DSsim/man/make.density.Rd

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