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mads (version 0.1.5)
Multi-Analysis Distance Sampling
Description
Performs distance sampling analyses on a number of species accounting for unidentified sightings, model uncertainty and covariate uncertainty.
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Install
install.packages('mads')
Monthly Downloads
73
Version
0.1.5
License
GPL (>= 2)
Maintainer
Laura Marshall
Last Published
January 23rd, 2017
Functions in mads (0.1.5)
Search functions
check.ddf.models
Checks the list of model names supplied by the user
model.description
Extracts the model description
summary.ma
Summary of multi-analysis object
fit.ddf.models
Refits the detection functions to the resampled data
format.dht.results
Formats the estimated abundances of all species categories, to be consistent with the prorated results.
rtpois
Ramdonly generates values from a zero-truncated Poisson distribution
resample.data
Resamples the data for the bootstrap
process.bootstrap.results
Summarises the bootstrap results.
mae.warning
Warning function
get.datasets
Extracts the data and models from the ddf objects
summary.ma.species
Print a summary of an element of a multi-analysis result correcponding to a single species included in the analyses.
process.warnings
Summarises warnings
prorate.unidentified
Prorate the estimated abundances of the unidentified sightings to the other identified species categories.
create.result.arrays
Creates a list of arrays for storing the dht results
summary.ma.analysis
Summary of multi-analysis object
summary.ma.allunid
Summary of multi-analysis object
execute.multi.analysis
Performs Multiple Analyses on Distance Data
summary.ma.allspecies
Summary of multi-analysis object
store.param.ests
Updates bootstrap.ddf.statistics
renumber.duplicates
Renumbers the object IDs for the duplicate observations generated when bootstrapping
resample.covariates
Parametrcally resamples selected variables in the dataset.
summary.ma.unid
Summary of multi-analysis object
check.covar.uncertainty
Performs checks on the covariate.uncertainty dataframe
check.fitted
Checks whether the model's fitted values make sense
accumulate.results
Enters the prorated results into the bootstrap.results array
check.convergence
Checks whether the model has converged
check.species.code.definitions
Checks the list of species code deifinitions supplied by the user
create.param.arrays
Creates a list of arrays for storing the ddf results
calculate.dht
Calculates the abundance for each species code including the unidentified codes if supplied.
check.species.presence
Checks the list of species presence definitions supplied by the user
create.obs.table
Creates a subsetted observation table