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.


News

New Features

  • Now uses a buffer region for generating the density grid rather than jittering the points. Now imports rgeos and sp.

Bug Fixes

  • If present and if the user has not switched the check.LinkID option in make.region off DSsim uses the LinkID attribute to rearrange the survey strata to match the order they would be displayed in Distance. This is important as otherwise the strata ID's for each transect generated by Distance will be wrong.
  • Fixed the bug that meant that DSsim threw an error when the user tried to create a density grid from a gam. Added testing for this feature.
  • Fixed a bug in plotting density object when there are gaps between polygons in the survey region. Now imports fields.

New Features

  • Implements segmented track and segmented grid designs

Bug Fixes

  • Fixed RMSE bug

Notes

  • Objects in a population may be detected from any transect. This means objects can be detected from two or more transects.

New Features

  • Now implemented point transects
  • Now implements AICc and BIC model selection criteria in addition to AIC
  • Stores how many times each model was selected based on information criteria and displays this information in the simulation summary.
  • Stores the delta AIC/AICc/BIC to second best model if there is one (however, not currently displayed in summary)
  • save.sim.results will save simulation replicate results to csv files
  • new function to format data ready to be read into Distance (format.for.distance)

Bug Fixes

  • Contours are now switched off in density plot when density is constant
  • Additional shapefile type checking takes place (for region and transect shapefiles)

Notes

  • Objects in a population may be detected from any transect. This means objects can be detected from two or more transects.

New Features

  • Uniform probability of detection in population detectability
  • Now accepts all types of suitable ESRI shapefiles
  • make.ddf.analysis.list now can optionally take in a data.frame which describes how strata should be grouped for analysis. See ?make.ddf.analysis.list

Bug Fixes

  • Gaps are now allowed to share a common boundary point with the strata / survey region boundary.

Notes

  • Objects in a population may be detected from any transect. This means objects can be detected from two or more transects.
  • Please note that the heat colour have now been inverted by default to be more consistent with normal use. Red is now low and white is high.

New Features

*Better plotting of density surfaces - now displays a grid with contours by default. There is still the option to plot the previous style (points) now with contours option. *There is now the plot option to fill the region polygons and gaps in the polygons with a specified colour.

Notes

  • Please note that currently objects in a population may only be detected from the nearest transect. This can sometimes results in edge-like effects if transects are located close together, e.g. with parallel random designs.

New Features

  • Added ability to save and load data generated from simulations
  • Added ability to run binned analyses
  • It now records the number of failed iterations
  • It now checks to see if there is a file meta.txt in the folder with the transects as this is a more robust way of telling it which transects belong to which strata
  • Now performs more checks on the density grid and makes sure that the required population size has been created
  • You can now provide multiple scale and shape parameters to generate a population with individuals of differing detectability
  • You cannow use adjustment terms in the mrds models
  • Added a glossary of terms for the output

Bug Fixes

  • Now catches ddf failures
  • Fixed bug in plot(density) and plot(region)
  • Fixed the way it checks for non-convergence in ddf
  • Fixed NA/NULL bug when ddf failed
  • Fixed bug when some strata have no indivuduals in them
  • Fixed bug when reps = 1
  • Added check for strata names to make sure they are unique
  • Added a function to fix shapefile generated by Distance
  • Updated the documentation

Reference manual

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install.packages("DSsim")

1.1.2 by Laura Marshall, 4 months ago


Browse source code at https://github.com/cran/DSsim


Authors: Laura Marshall <lhm@st-and.ac.uk>


Documentation:   PDF Manual  


GPL (>= 2) license


Imports graphics, splancs, mgcv, shapefiles, rgeos, fields, sp

Depends on mrds, methods

Suggests testthat, parallel, pbapply, knitr, rmarkdown


See at CRAN