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.

Author
Laura Marshall <lhm@st-and.ac.uk>
Date of publication
2016-11-07 17:21:58
Maintainer
Laura Marshall <lhm@st-and.ac.uk>
License
GPL (>= 2)
Version
1.0.8

View on CRAN

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