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 publication2017-01-23 15:00:12
MaintainerLaura Marshall <lhm@st-and.ac.uk>
LicenseGPL (>= 2)
Version0.1.5

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

Functions

accumulate.results Man page
calculate.dht Man page
check.convergence Man page
check.covar.uncertainty Man page
check.ddf.models Man page
check.fitted Man page
check.species.code.definitions Man page
check.species.presence Man page
create.obs.table Man page
create.param.arrays Man page
create.result.arrays Man page
execute.multi.analysis Man page
fit.ddf.models Man page
format.dht.results Man page
get.datasets Man page
mae.warning Man page
model.description Man page
process.bootstrap.results Man page
process.warnings Man page
prorate.unidentified Man page
renumber.duplicates Man page
resample.covariates Man page
resample.data Man page
rtpois Man page
store.param.ests Man page
summary.ma Man page
summary.ma.allspecies Man page
summary.ma.allunid Man page
summary.ma.analysis Man page
summary.ma.species Man page
summary.ma.unid Man page

Files

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/tests/testthat/test_mrdsOptions.R
mads/tests/testthat/test_doubleObserver.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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.