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dsm - Density surface modelling

What is dsm?

dsm provides a Generalized Additive Model (GAM)-based approach 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.

Open Access paper describing the methods: Miller, DL, ML Burt, EA Rexstad and L Thomas (2013). Spatial models for distance sampling data: recent developments and future directions. Methods in Ecology and Evolution.

Using dsm

Examples of how to use dsm and other distance sampling R packages are available at examples.distancesampling.org.

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Version

Install

install.packages('dsm')

Monthly Downloads

1,037

Version

2.3.1

License

GPL (>= 2)

Issues

15

Pull Requests

2

Stars

8

Forks

9

Maintainer

Laura Marshall

Last Published

March 27th, 2021

Functions in dsm (2.3.1)

dsm.var.movblk

Variance estimation via parametric moving block bootstrap
dsm_varprop

Variance propagation for density surface models
dsm.cor

Check for autocorrelation in residuals
check.cols

Check column names exist
dsm

Fit a density surface model to segment-specific estimates of abundance or density.
dsm-data

Data format for DSM
dsm.var.gam

Prediction variance estimation assuming independence
dsm.var.prop

Prediction variance propagation for DSMs
block.info.per.su

Find the block information
dsm-package

Density surface modelling
plot_pred_by_term

Spatially plot predictions per model term
dummy_ddf

Detection function objects when detection is certain
vis.concurvity

Visualise concurvity between terms in a GAM
matrixnotposdef.handler

Handler to suppress the "matrix not positive definite" warning
print.dsm_varprop

Print a description of a density surface model variance object
make.soapgrid

Create a knot grid for the internal part of a soap film smoother.
trim.var

Trimmed variance
generate.ds.uncertainty

Generate data from a fitted detection function
print.dsm.var

Print a description of a density surface model variance object
print.summary.dsm.var

Print summary of density surface model variance object
summary.dsm.var

Summarize the variance of a density surface model
print.summary.dsm_varprop

Print summary of density surface model variance object
plot.dsm

Plot a density surface model.
obs_exp

Observed versus expected diagnostics for fitted DSMs
print.dsm

Print a description of a density surface model object
predict.fake_ddf

Prediction for fake detection functions
mexdolphins

Pan-tropical spotted dolphins in the Gulf of Mexico
summary.dsm_varprop

Summarize the variance of a density surface model
latlong2km

Convert latitude and longitude to Northings and Eastings
summary.dsm

Summarize a fitted density surface model
generate.mb.sample

Moving block bootstrap sampler
rqgam.check

Randomised quantile residuals check plot for GAMs/DSMs
predict.dsm

Predict from a fitted density surface model
plot.dsm.var

Create plots of abundance uncertainty