Distance Sampling Detection Function and Abundance Estimation

A simple way of fitting detection functions to distance sampling data for both line and point transects. Adjustment term selection, left and right truncation as well as monotonicity constraints and binning are supported. Abundance and density estimates can also be calculated (via a Horvitz-Thompson-like estimator) if survey area information is provided.


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Distance is a simple way of fitting detection functions to distance sampling data for both line and point transects. Adjustment term selection, left and right truncation as well as monotonicity constraints and binning are supported. Abundance and density estimates can also be calculated (via a Horvitz-Thompson-like estimator) if survey area information is provided.

For more information and examples of use take a look at this preprint.

Getting Distance

The easiest way to ensure you have the latest version of Distance, is to install Hadley Wickham's devtools package:

  install.packages("devtools")

then install Distance from github:

  library(devtools)
  install_github("DistanceDevelopment/Distance")

News

Distance version 0.9.8

  • Includes reference and citation for paper on 'Distance Sampling in R'.
  • AIC now works for multiple models at once (as it does for other model classes) thanks to Tiago Marques and Len Thomas for this suggestion.
  • Added examples to create.bins, ds.gof, gof_ds, summarize_ds_models, logLik.dsmodel and AIC.dsmodel. Thanks to a reviewer of our Journal of Statistical Software paper.
  • Parameters from previous fit are used as starting values for the next fit when AIC is used to select adjustments
  • when distbegin and distend were specified in the data but distance wasn't, checkdata() threw an error. checkdata() now generates the distance column at the midpoint. Thanks to Tom for spotting this.
  • new argument to ds(), max.adjustments gives the maximum number of adjustment terms to add to the model when doing AIC term selection. Thanks to Oscar Dewhurst for the suggestion.

Distance version 0.9.7

  • summarize_ds_models now will only compare models that are allowed by AIC (all binning and truncation must be the same). Thanks to Carolin Tröger and Eric Rextad for highlighting this issue.
  • If there are numerical issues that cause NAs in the Hessian, ds() will not try to run dht() to estimate abundance (as it will fail), instead throws a message and returns only the detection function. Thanks to Steve Ahlswede for bringing this to our attention.

Distance version 0.9.6

  • Coefficients are called coefficients (not a mixture of coefficients and parameters) in summary() results
  • Added gof_ds() for easy access to goodness of fit testing and q-q plotting
  • Checking of truncation distance was checking via is.double rather than is.numeric. Thanks to Tiago Marques for spotting this!
  • Functions AIC() and logLik() now exist for quick extraction of AIC and log-likelihood values. Thanks to Tiago Marques for this suggestion.
  • Added amakihi (point transect) data
  • add extra documentation for objects in obs.table, thanks to Olivier Devineau for spotting this

Distance version 0.9.5

  • Truncation by percentage now works when there are missing distances (i.e. when we are using flatfile). Thanks to Len Thomas for pointing out this bug.

Distance version 0.9.4

  • Object ID uniqueness stopped abundance estimation from working (since NA IDs were "not unique").
  • Check that areas are consistently entered. This was problematic when areas were not entered identically for each region, but unique was used to extract the region table. Thanks to Katy Echave for finding this bug!
  • Monotonicity constraints were not applied during automated model selection. Thanks to Tiago Marques for spotting this.
  • AIC selection of adjustment terms goes up to 5 terms by default, as in DISTANCE. Thanks to Eric Rexstad for suggesting this.

Distance version 0.9.3

  • Updated tests to work with new unique object ID code.
  • Liberally sprinkled tests with suppressMessages()

Distance version 0.9.2

  • Now warning when columns are correctly named but not in the correct case. Thanks to Richard Borthwick for reporting this bug.
  • Now checks that object IDs are unique. Thanks to Ricardo Lima & Francisco Azevedo for highlighting this issue.

Distance version 0.9.1

  • Models with both covariates and adjustment terms can actually be specified -- this was not fully implemented in previous version.
  • ds() now tells the user the models which is returned (rather than previously fitted model)
  • links to mrds documentation on optimisation issues

Distance version 0.9

  • Flat file support example, see ?flatfile
  • New data set: simulated minke whale data, see ?minke and ?flatfile for an example analysis
  • Models with both covariates and adjustment terms can be specified.
  • Default left truncation is now 0, default right truncation is now the largest observed distance or furthest bin end.

Distance version 0.8.1

  • another fix to binning (redundant code/inconsistent definition between docs and code). (Thanks to Jason Roberts for finding this.)
  • binning would fail if there were NA distances, which might occur when using the simplified data tables
  • check implemented to ensure that samples have consistent (i.e. the same) effort (Eric Rexstad found this bug)
  • clarification that stratification only occurs at the abundance/density estimation stage (dht), rather than at the detection function modelling stage (thanks to Filipe Dias for this suggestion)
  • Setting order=0 is equivalent to adjustment=NULL to specify a detection function without adjustments. (Eric Rexstad brought this to my attention.)

Distance version 0.8.0

  • new simplified table data format (see ?ds)
  • bug in binning from cutpoints (thanks to Colin Beale for finding this)
  • removed percentage truncation for binned data, as it doesn't really make sense

Distance version 0.7.4

  • new initial values argument

Distance version 0.7.3

  • remove annoying crash when mrds failed to fit a model
  • NB the optimiser underlying mrds (optimx) has changed, update both of these packages to avoid issues.

Distance version 0.7.2

  • message tells the user the model that was selected

Distance version 0.7.1

  • debugging options
  • bug fixes (see github for further details)
    • automatic generation of adjustments did not generate any for poly/herm.

Distance version 0.7

  • "width" is now default for scaling

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("Distance")

0.9.8 by Laura Marshall, 2 months ago


http://github.com/DistanceDevelopment/Distance/


Report a bug at https://github.com/DistanceDevelopment/Distance/issues


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


Authors: David Lawrence Miller


Documentation:   PDF Manual  


Task views: Analysis of Ecological and Environmental Data


GPL (>= 2) license


Depends on mrds

Suggests testthat


Suggested by dsm.


See at CRAN