mads: Multi-Analysis Distance Sampling

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

Author
Laura Marshall
Date of publication
2016-08-10 20:43:31
Maintainer
Laura Marshall <lhm@st-and.ac.uk>
License
GPL (>= 2)
Version
0.1.4

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