Package: dsm 2.3.3.9001

Laura Marshall

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.

Authors:David L. Miller, Eric Rexstad, Louise Burt, Mark V. Bravington, Sharon Hedley, Megan Ferguson, Natalie Kelly.

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dsm.pdf |dsm.html✨
dsm/json (API)
NEWS

# Install 'dsm' in R:
install.packages('dsm', repos = c('https://distancedevelopment.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/distancedevelopment/dsm/issues

Datasets:
  • distdata - Pan-tropical spotted dolphins in the Gulf of Mexico
  • obsdata - Pan-tropical spotted dolphins in the Gulf of Mexico
  • preddata - Pan-tropical spotted dolphins in the Gulf of Mexico
  • segdata - Pan-tropical spotted dolphins in the Gulf of Mexico

On CRAN:

22 exports 8 stars 2.51 score 38 dependencies 7 mentions 132 scripts 518 downloads

Last updated 2 years agofrom:f882c7896b. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 22 2024
R-4.5-winNOTEAug 22 2024
R-4.5-linuxNOTEAug 22 2024
R-4.4-winNOTEAug 22 2024
R-4.4-macNOTEAug 22 2024
R-4.3-winOKAug 22 2024
R-4.3-macOKAug 22 2024

Exports:dsmdsm_cordsm_var_gamdsm_var_movblkdsm_var_propdsm_varpropdsm.cordsm.var.gamdsm.var.movblkdsm.var.propdummy_ddfgenerate.ds.uncertaintygenerate.mb.samplelatlong2kmmake.soapgridobs_expplot_pred_by_termrqgam_checkrqgam.checktrim.varvis_concurvityvis.concurvity

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmrdsmunsellnlmenloptrnumDerivoptimxpillarpkgconfigplyrpracmaR6RColorBrewerRcpprlangRsolnpscalesstatmodtibbletruncnormutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Density surface modellingdsm-package
Find the block informationblock.info.per.su
Check column names existcheck.cols
Fit a density surface model to segment-specific estimates of abundance or density.dsm
Check for autocorrelation in residualsdsm_cor
Prediction variance estimation assuming independencedsm_var_gam
Variance estimation via parametric moving block bootstrapdsm_var_movblk
Prediction variance propagation for DSMsdsm_var_prop
Variance propagation for density surface modelsdsm_varprop
Data format for DSMdsm-data
Check for autocorrelation in residualsdsm.cor
Prediction variance estimation assuming independencedsm.var.gam
Variance estimation via parametric moving block bootstrapdsm.var.movblk
Prediction variance propagation for DSMsdsm.var.prop
Detection function objects when detection is certaindummy_ddf
Generate data from a fitted detection functiongenerate.ds.uncertainty
Moving block bootstrap samplergenerate.mb.sample
Convert latitude and longitude to Northings and Eastingslatlong2km
Create a knot grid for the internal part of a soap film smoother.make.soapgrid
Pan-tropical spotted dolphins in the Gulf of Mexicodistdata mexdolphins obsdata pred.polys preddata segdata survey.area
Observed versus expected diagnostics for fitted DSMsobs_exp
Spatially plot predictions per model termplot_pred_by_term
Plot a density surface model.plot.dsm
Create plots of abundance uncertaintyplot.dsm.var
Predict from a fitted density surface modelpredict.dsm
Prediction for fake detection functionspredict.fake_ddf
Print a description of a density surface model objectprint.dsm
Print a description of a density surface model variance objectprint.dsm_varprop
Print a description of a density surface model variance objectprint.dsm.var
Print summary of density surface model variance objectprint.summary.dsm_varprop
Print summary of density surface model variance objectprint.summary.dsm.var
Randomised quantile residuals check plot for GAMs/DSMsrqgam_check
Randomised quantile residuals check plot for GAMs/DSMsrqgam.check
Summarize a fitted density surface modelsummary.dsm
Summarize the variance of a density surface modelsummary.dsm_varprop
Summarize the variance of a density surface modelsummary.dsm.var
Trimmed variancetrim.var
Visualise concurvity between terms in a GAMvis_concurvity
Visualise concurvity between terms in a GAMvis.concurvity