Multi-Analysis Distance Sampling

Documentation for package ‘mads’ version 0.1.5

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accumulate.results	Enters the prorated results into the bootstrap.results array
calculate.dht	Calculates the abundance for each species code including the unidentified codes if supplied.
check.convergence	Checks whether the model has converged
check.covar.uncertainty	Performs checks on the covariate.uncertainty dataframe
check.ddf.models	Checks the list of model names supplied by the user
check.fitted	Checks whether the model's fitted values make sense
check.species.code.definitions	Checks the list of species code deifinitions supplied by the user
check.species.presence	Checks the list of species presence definitions supplied by the user
create.obs.table	Creates a subsetted observation table
create.param.arrays	Creates a list of arrays for storing the ddf results
create.result.arrays	Creates a list of arrays for storing the dht results
execute.multi.analysis	Performs Multiple Analyses on Distance Data
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.
get.datasets	Extracts the data and models from the ddf objects
mae.warning	Warning function
model.description	Extracts the model description
process.bootstrap.results	Summarises the bootstrap results.
process.warnings	Summarises warnings
prorate.unidentified	Prorate the estimated abundances of the unidentified sightings to the other identified species categories.
renumber.duplicates	Renumbers the object IDs for the duplicate observations generated when bootstrapping
resample.covariates	Parametrcally resamples selected variables in the dataset.
resample.data	Resamples the data for the bootstrap
rtpois	Ramdonly generates values from a zero-truncated Poisson distribution
store.param.ests	Updates bootstrap.ddf.statistics
summary.ma	Summary of multi-analysis object
summary.ma.allspecies	Summary of multi-analysis object
summary.ma.allunid	Summary of multi-analysis object
summary.ma.analysis	Summary of multi-analysis object
summary.ma.species	Print a summary of an element of a multi-analysis result correcponding to a single species included in the analyses.
summary.ma.unid	Summary of multi-analysis object