mads: Multi-Analysis Distance Sampling

Performs distance sampling analyses on a number of species accounting for unidentified sightings, model uncertainty and covariate uncertainty.

AuthorLaura Marshall
Date of publication2016-08-10 20:43:31
MaintainerLaura Marshall <lhm@st-and.ac.uk>
LicenseGPL (>= 2)
Version0.1.4

View on CRAN

Man pages

accumulate.results: Enters the prorated results into the bootstrap.results array

calculate.dht: Calculates the abundance for each species code including the...

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...

check.species.presence: Checks the list of species presence definitions supplied by...

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,...

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...

renumber.duplicates: Renumbers the object IDs for the duplicate observations...

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...

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...

summary.ma.unid: Summary of multi-analysis object

Files in this package

mads
mads/inst
mads/inst/testData
mads/inst/testData/input_checks
mads/inst/testData/input_checks/region_table.robj
mads/inst/testData/input_checks/obs_table.robj
mads/inst/testData/input_checks/sample_table.robj
mads/inst/testData/input_checks/ddf_dat.robj
mads/tests
mads/tests/test-that.R
mads/tests/testthat
mads/tests/testthat/test_DataInputChecks.R
mads/tests/testthat/test_singleObserver.R
mads/tests/testthat/test_resampling.R
mads/NAMESPACE
mads/NEWS
mads/R
mads/R/get.datasets.R mads/R/create.result.arrays.R mads/R/summary.ma.species.R mads/R/summary.ma.unid.R mads/R/calculate.dht.R mads/R/fit.ddf.models.R mads/R/rtpois.R mads/R/accumulate.results.R mads/R/process.warnings.R mads/R/check.species.code.definitions.R mads/R/execute.multi.analysis.R mads/R/summary.ma.allunid.R mads/R/mae.warning.R mads/R/check.ddf.models.R mads/R/format.dht.results.R
mads/R/check.species.presence.r
mads/R/resample.data.R mads/R/renumber.duplicates.R mads/R/check.convergence.R mads/R/summary.ma.analysis.R mads/R/store.param.ests.R mads/R/check.fitted.R
mads/R/check.bootstrap.options.r
mads/R/resample.covariates.R mads/R/glossary.R mads/R/process.bootstrap.results.R mads/R/prorate.unidentified.R mads/R/summary.ma.R mads/R/check.covar.uncertainty.R mads/R/object.description.R mads/R/create.obs.table.R mads/R/model.description.R
mads/R/create.param.arrays.r
mads/R/summary.ma.allspecies.R
mads/MD5
mads/DESCRIPTION
mads/man
mads/man/format.dht.results.Rd mads/man/resample.data.Rd mads/man/execute.multi.analysis.Rd mads/man/check.species.code.definitions.Rd mads/man/check.ddf.models.Rd mads/man/mae.warning.Rd mads/man/accumulate.results.Rd mads/man/summary.ma.unid.Rd mads/man/check.convergence.Rd mads/man/calculate.dht.Rd mads/man/summary.ma.allspecies.Rd mads/man/create.param.arrays.Rd mads/man/rtpois.Rd mads/man/create.result.arrays.Rd mads/man/process.warnings.Rd mads/man/model.description.Rd mads/man/get.datasets.Rd mads/man/summary.ma.analysis.Rd mads/man/create.obs.table.Rd mads/man/check.fitted.Rd mads/man/store.param.ests.Rd mads/man/renumber.duplicates.Rd mads/man/prorate.unidentified.Rd mads/man/process.bootstrap.results.Rd mads/man/resample.covariates.Rd mads/man/summary.ma.Rd mads/man/check.covar.uncertainty.Rd mads/man/summary.ma.allunid.Rd mads/man/summary.ma.species.Rd mads/man/check.species.presence.Rd mads/man/fit.ddf.models.Rd

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