Multi-Analysis Distance Sampling


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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