DSsim: Distance Sampling Simulations
Version 1.1.1

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 ) 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 publication2017-02-21 16:46:17
MaintainerLaura Marshall <lhm@st-and.ac.uk>
LicenseGPL (>= 2)
Version1.1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DSsim")

Getting started

Distance Sampling Simulations

Popular man pages

covmod_summary: Covariate Truncation Simulation Summaries
create.region.table-methods: S4 generic method to generate a region table
create.survey.results-methods: S4 generic method to simulate a survey
data.for.distance: data.for.distance
DDF.Data-class: S4 Class "DDF.Data"
histogram.N.ests-methods: histogram.N.ests
make.ddf.analysis.list: Creates a list of DDF.Analysis objects
See all...

All man pages Function index File listing

Man pages

add.hotspot-methods: S4 generic method to add a hotspot to the density grid
check.sim.setup: check.sim.setup
covmod_summary: Covariate Truncation Simulation Summaries
cov_param: Parameter Estimates from Covariate Simulation
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: S4 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.Detectability-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"
Population-class: Class "Population"
Population.Description-class: Class "Population.Description"
Population.Summary-class: S4 Class "Population.Summary"
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...
rtpois: Ramdonly generates values from a zero-truncated Poisson...
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
trunc_cov_summary: Covariate Truncation Simulation Summaries
trunc_summary: Truncation Simulation Summaries

Functions

DDF.Analysis-class Man page
DDF.Data-class Man page
Density-class Man page
Design.Summary-class Man page
Detectability-class Man page
LT.Design-class Man page
LT.Survey-class Man page
LT.Survey.Results-class Man page
Line.Transect-class Man page
Obs.Table-class Man page
PT.Design-class Man page
PT.Survey-class Man page
Point.Transect-class Man page
Population-class Man page
Population.Description-class Man page
Population.Summary-class Man page
Region-class Man page
Region.Table-class Man page
Sample.Table-class Man page
Simulation-class Man page
Simulation.Summary-class Man page
Single.Obs.DDF.Data-class Man page
Single.Obs.LT.Survey-class Man page
Survey-class Man page
Survey.Design-class Man page
Survey.Results-class Man page
Transect-class Man page
accumulate.PP.results Source code
add.covariate.values Source code
add.dist.error Source code
add.hotspot Man page
add.hotspot,Density-method Man page
add.miss.dists Source code
add.summary.results Source code
calc.area Source code
calc.poss.detect.dists.lines Source code
calc.poss.detect.dists.points Source code
calculate.fitted Source code
calculate.scale.param Source code
check.LinkID.order Source code
check.covariates Source code
check.intersection Source code
check.shapefile Source code
check.sim.setup Man page Source code
coords.from.shapefile Source code
cov.summary.list Man page
covmod.summary.list Man page
create.bins Man page Source code
create.region.table Man page
create.region.table,Survey-method Man page
create.sample.table Man page
create.sample.table,Survey-method Man page
create.survey.results Man page
create.survey.results,Simulation-method Man page
create.survey.results,Single.Obs.LT.Survey-method Man page
create.survey.results,Single.Obs.PT.Survey-method Man page
data.for.distance Man page Source code
description.summary Man page Source code
extract.spat.poly.coords Source code
generate.pop.D Source code
generate.pop.N Source code
generate.population Man page
generate.population,Population.Description-method Man page
generate.population,Simulation-method Man page
generate.transects Man page
generate.transects,LT.Design-method Man page
generate.transects,LT.Systematic.Design-method Man page
generate.transects,PT.Design-method Man page
generate.transects,PT.Nested.Design-method Man page
generate.transects,PT.Systematic.Design-method Man page
generate.transects,Simulation-method Man page
get.N Man page
get.N,Population.Description-method Man page
get.area Man page
get.area,Region-method Man page
get.ave.density Source code
get.bound.box Source code
get.distance.data Man page
get.distance.data,LT.Survey.Results-method Man page
get.distance.data,Survey.Results-method Man page
get.line.sampler.info Source code
get.point.sampler.info Source code
get.shapefile.names Source code
get.surface.constant Source code
get.surface.gam Source code
histogram.N.ests Man page Source code
hn.detect Source code
hr.detect Source code
in.polygons Source code
is.gap Source code
make.ddf.analysis.list Man page Source code
make.density Man page Source code
make.design Man page Source code
make.detectability Man page Source code
make.population.description Man page
make.region Man page Source code
make.simulation Man page Source code
modify.strata.for.analysis Source code
param.list Man page
plot,DDF.Data,ANY-method Man page
plot,Density,ANY-method Man page
plot,Detectability,ANY-method Man page
plot,Detectability,Population.Description-method Man page
plot,LT.Survey.Results,ANY-method Man page
plot,Line.Transect,ANY-method Man page
plot,Point.Transect,ANY-method Man page
plot,Population,ANY-method Man page
plot,Region,ANY-method Man page
plot,Survey.Results,ANY-method Man page
rename.duplicates Man page Source code
rtpois Man page Source code
run Man page
run,Simulation-method Man page
run.analysis Man page
run.analysis,DDF.Analysis,DDF.Data-method Man page
run.analysis,Simulation,DDF.Data-method Man page
run.analysis,Simulation,Survey.Results-method Man page
save.sim.results Man page Source code
setcov Source code
show,Design.Summary-method Man page
show,Simulation-method Man page
show,Simulation.Summary-method Man page
simulate.detections Source code
single.simulation.loop Source code
store.ddf.results Source code
store.dht.results Source code
summary,Simulation-method Man page
summary.list Man page
transects.shp Man page

Files

inst
inst/doc
inst/doc/Investigating_Covariates_and_Truncation.Rmd
inst/doc/Investigating_Covariates_and_Truncation.R
inst/doc/Investigating_Covariates_and_Truncation.html
tests
tests/test-that.R
tests/testthat
tests/testthat/test-Intersections.r
tests/testthat/test-Constructors.r
tests/testthat/test-UserInput.r
tests/testthat/test-BasicLineSimulations.r
tests/testthat/test-SystematicDefaultPointSimulations.R
tests/testthat/test-NestedPointSimulations.r
tests/testthat/test-SystematicLineSimulations.r
tests/testthat/test-Covariates.r
NAMESPACE
NEWS
data
data/transects.shp.rda
data/cov_param.rda
data/trunc_cov_summary.rda
data/covmod_summary.rda
data/trunc_summary.rda
R
R/calc.poss.detect.dists.lines.R
R/Survey.Design.R
R/get.bound.box.R
R/Density.R
R/Population.Summary.R
R/Simulation.Summary.R
R/is.gap.R
R/get.ave.density.R
R/in.polygons.R
R/Transect.R
R/PT.Nested.Design.R
R/get.surface.gam.R
R/LT.Random.Design.R
R/data.for.distance.R
R/Sample.Table.R
R/LT.SegmentedGrid.Design.R
R/add.dist.error.R
R/LT.Survey.Results.R
R/calc.area.R
R/DDF.Data.R
R/Survey.R
R/Region.Table.R
R/single.simulation.loop.R
R/calculate.scale.param.R
R/rtpois.R
R/get.line.sampler.info.R
R/Design.Summary.R
R/simulate.detections.R
R/get.surface.constant.R
R/get.point.sampler.info.R
R/Survey.Results.R
R/LT.SegmentedTrack.Design.R
R/LT.Systematic.Design.R
R/PT.Random.Design.R
R/check.sim.setup.R
R/Obs.Table.R
R/generate.pop.D.R
R/calculate.fitted.R
R/DSM.Analysis.R
R/rename.duplicates.R
R/LT.Design.R
R/modify.strata.for.analysis.R
R/hn.detect.R
R/calc.poss.detect.dists.points.R
R/LT.EqSpace.ZZ.Design.R
R/generate.pop.N.R
R/check.intersection.R
R/DS.Analysis.R
R/description.summary.R
R/Single.Obs.DDF.Data.R
R/Simulation.R
R/add.miss.dists.R
R/Population.Description.R
R/check.shapefile.R
R/add.covariate.values.R
R/hr.detect.R
R/Single.Obs.LT.Survey.R
R/Detectability.R
R/check.covariates.R
R/add.summary.results.R
R/PT.Survey.R
R/coords.from.shapefile.R
R/Population.R
R/store.ddf.results.R
R/LT.EqAngle.ZZ.Design.R
R/accumulate.PP.results.R
R/check.LinkID.order.R
R/generic.functions.R
R/store.dht.results.R
R/setcov.R
R/save.sim.results.R
R/LT.User.Specified.Design.R
R/PT.Systematic.Design.R
R/LT.Survey.R
R/Region.R
R/create.bins.R
R/extract.spat.poly.coords.R
R/Class.Constructors.R
R/Single.Obs.PT.Survey.R
R/PT.Design.R
R/Line.Transect.R
R/Point.Transect.R
R/DDF.Analysis.R
R/get.shapefile.names.R
vignettes
vignettes/Investigating_Covariates_and_Truncation.Rmd
vignettes/refs.bib
vignettes/images
vignettes/images/SimulationDiagram.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/LT.Design-class.Rd
man/plot.Point.Transect-methods.Rd
man/Region-class.Rd
man/get.area-methods.Rd
man/show.Simulation.Summary-methods.Rd
man/plot.DDF.Data-methods.Rd
man/make.detectability.Rd
man/trunc_summary.Rd
man/generate.population-methods.Rd
man/Population.Description-class.Rd
man/Survey.Design-class.Rd
man/Single.Obs.LT.Survey-class.Rd
man/LT.Survey-class.Rd
man/make.simulation.Rd
man/DDF.Analysis-class.Rd
man/Region.Table-class.Rd
man/show.Simulation-methods.Rd
man/run-methods.Rd
man/plot.Region-methods.Rd
man/trunc_cov_summary.Rd
man/Single.Obs.DDF.Data-class.Rd
man/rtpois.Rd
man/make.ddf.analysis.list.Rd
man/DDF.Data-class.Rd
man/cov_param.Rd
man/create.sample.table-methods.Rd
man/PT.Survey-class.Rd
man/generate.transects-methods.Rd
man/Line.Transect-class.Rd
man/Survey-class.Rd
man/summary.Simulation-methods.Rd
man/Population-class.Rd
man/Density-class.Rd
man/make.region.Rd
man/Point.Transect-class.Rd
man/rename.duplicates.Rd
man/plot.LT.Survey.Results-methods.Rd
man/run.analysis-methods.Rd
man/create.bins.Rd
man/description.summary.Rd
man/Detectability-class.Rd
man/Survey.Results-class.Rd
man/plot.Population-methods.Rd
man/Sample.Table-class.Rd
man/Obs.Table-class.Rd
man/Simulation-class.Rd
man/get.N-methods.Rd
man/Population.Summary-class.Rd
man/Transect-class.Rd
man/create.region.table-methods.Rd
man/plot.Line.Transect-methods.Rd
man/plot.Detectability-methods.Rd
man/add.hotspot-methods.Rd
man/create.survey.results-methods.Rd
man/make.population.description.Rd
man/Design.Summary-class.Rd
man/transects.Rd
man/LT.Survey.Results-class.Rd
man/make.design.Rd
man/covmod_summary.Rd
man/save.sim.results-methods.Rd
man/histogram.N.ests-methods.Rd
man/get.distance.data-methods.Rd
man/check.sim.setup.Rd
man/data.for.distance.Rd
man/PT.Design-class.Rd
man/Simulation.Summary-class.Rd
man/plot.Survey.Results-methods.Rd
man/plot.Density-methods.Rd
man/make.density.Rd
DSsim documentation built on May 19, 2017, 8:30 a.m.

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