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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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Version

Install

install.packages('mads')

Monthly Downloads

31

Version

0.1.5

License

GPL (>= 2)

Maintainer

Laura Marshall

Last Published

January 23rd, 2017

Functions in mads (0.1.5)

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