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.

Install the latest version of this package by entering the following in R:
install.packages("DSsim")
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

View on CRAN

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

add.hotspot Man page
add.hotspot,Density-method Man page
check.sim.setup Man page
covmod.summary.list Man page
cov.summary.list Man page
create.bins Man page
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
DDF.Analysis-class Man page
DDF.Data-class Man page
Density-class Man page
description.summary Man page
Design.Summary-class Man page
Detectability-class Man page
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.area Man page
get.area,Region-method Man page
get.distance.data Man page
get.distance.data,LT.Survey.Results-method Man page
get.distance.data,Survey.Results-method Man page
get.N Man page
get.N,Population.Description-method Man page
histogram.N.ests Man page
Line.Transect-class Man page
LT.Design-class Man page
LT.Survey-class Man page
LT.Survey.Results-class Man page
make.ddf.analysis.list Man page
make.density Man page
make.design Man page
make.detectability Man page
make.population.description Man page
make.region Man page
make.simulation Man page
Obs.Table-class Man page
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,Line.Transect,ANY-method Man page
plot,LT.Survey.Results,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
Point.Transect-class Man page
Population-class Man page
Population.Description-class Man page
Population.Summary-class Man page
PT.Design-class Man page
PT.Survey-class Man page
Region-class Man page
Region.Table-class Man page
rename.duplicates Man page
rtpois Man page
run 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
run,Simulation-method Man page
Sample.Table-class Man page
save.sim.results Man page
show,Design.Summary-method Man page
show,Simulation-method Man page
show,Simulation.Summary-method 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
summary.list Man page
summary,Simulation-method Man page
Survey-class Man page
Survey.Design-class Man page
Survey.Results-class Man page
Transect-class 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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.