dsm: Density Surface Modelling of Distance Sampling Data

Density surface modelling of line transect data. A Generalized Additive Model-based approach is used to calculate spatially-explicit estimates of animal abundance from distance sampling (also presence/absence and strip transect) data. Several utility functions are provided for model checking, plotting and variance estimation.

Author
David L. Miller, Eric Rexstad, Louise Burt, Mark V. Bravington, Sharon Hedley.
Date of publication
2016-10-03 22:59:34
Maintainer
Laura Marshall <lhm@st-andrews.ac.uk>
License
GPL (>= 2)
Version
2.2.13
URLs

View on CRAN

Man pages

block.info.per.su
Find the block information
check.cols
Check column names exist
dsm
Fit a density surface model to segment-specific estimates of...
dsm.cor
Check for autocorrelation in residuals
dsm-data
Data format for DSM
dsm-package
Density surface modelling
dsm.var.gam
Variance estimation via Bayesian results
dsm.var.movblk
Variance estimation via parametric moving block bootstrap
dsm.var.prop
Variance propogation for DSM models
generate.ds.uncertainty
Generate data from a fitted detection function
generate.mb.sample
Moving block bootstrap sampler
latlong2km
Convert latitude and longitude to Northings and Eastings
make.soapgrid
Create a knot grid for the internal part of a soap film...
matrixnotposdef.handler
Handler to suppress the "matrix not positive definite"...
mexdolphins
Pan-tropical spotted dolphins in the Gulf of Mexico
offsets
Offsets
plot.dsm
Plot a density surface model.
plot.dsm.var
Create plots of abundance uncertainty
predict.dsm
Predict from a fitted density surface model
print.dsm
Print a description of a density surface model object
print.dsm.var
Print a description of a density surface model variance...
print.summary.dsm.var
Print summary of density surface model variance object
rqgam.check
Randomised quantile residuals check plots for GAMs/DSMs
summary.dsm
Summarize a fitted density surface model
summary.dsm.var
Summarize the variance of a density surface model
trim.var
Trimmed variance

Files in this package

dsm
dsm/tests
dsm/tests/testthat.R
dsm/tests/testthat
dsm/tests/testthat/test_vargam.R
dsm/tests/testthat/test_movblk.R
dsm/tests/testthat/test_mex.R
dsm/tests/testthat/test_input.R
dsm/NAMESPACE
dsm/NEWS
dsm/data
dsm/data/mexdolphins.rda
dsm/R
dsm/R/rqgam.check.R
dsm/R/block.info.per.su.R
dsm/R/print.dsm.var.R
dsm/R/check.cols.R
dsm/R/trim.var.R
dsm/R/plot.dsm.var.R
dsm/R/matrixnotposdef.handler.R
dsm/R/plot.dsm.R
dsm/R/summary.dsm.R
dsm/R/ddf.model.description.R
dsm/R/print.dsm.R
dsm/R/make.soapgrid.R
dsm/R/dsm.var.movblk.R
dsm/R/latlong2km.R
dsm/R/make.data.R
dsm/R/dsm-package.R
dsm/R/summary.dsm.var.R
dsm/R/dsm.var.gam.R
dsm/R/dsm.cor.R
dsm/R/print.summary.dsm.var.R
dsm/R/dsm.var.prop.R
dsm/R/dsm.R
dsm/R/zzz.R
dsm/R/generate.mb.sample.R
dsm/R/predict.dsm.R
dsm/R/generate.ds.uncertainty.R
dsm/README.md
dsm/MD5
dsm/DESCRIPTION
dsm/man
dsm/man/print.dsm.Rd
dsm/man/print.summary.dsm.var.Rd
dsm/man/latlong2km.Rd
dsm/man/dsm.var.movblk.Rd
dsm/man/plot.dsm.var.Rd
dsm/man/make.soapgrid.Rd
dsm/man/block.info.per.su.Rd
dsm/man/dsm-package.Rd
dsm/man/offsets.Rd
dsm/man/generate.ds.uncertainty.Rd
dsm/man/summary.dsm.Rd
dsm/man/check.cols.Rd
dsm/man/dsm-data.Rd
dsm/man/dsm.Rd
dsm/man/mexdolphins.Rd
dsm/man/rqgam.check.Rd
dsm/man/dsm.var.gam.Rd
dsm/man/predict.dsm.Rd
dsm/man/matrixnotposdef.handler.Rd
dsm/man/plot.dsm.Rd
dsm/man/dsm.var.prop.Rd
dsm/man/dsm.cor.Rd
dsm/man/generate.mb.sample.Rd
dsm/man/trim.var.Rd
dsm/man/summary.dsm.var.Rd
dsm/man/print.dsm.var.Rd