Package: AHMbook 0.2.12

Ken Kellner

AHMbook: Functions and Data for the Book 'Applied Hierarchical Modeling in Ecology' Vols 1 and 2

Provides functions to simulate data sets from hierarchical ecological models, including all the simulations described in the two volume publication 'Applied Hierarchical Modeling in Ecology: Analysis of distribution, abundance and species richness in R and BUGS' by Marc Kéry and Andy Royle: volume 1 (2016, ISBN: 978-0-12-801378-6) and volume 2 (2021, ISBN: 978-0-12-809585-0), <https://www.mbr-pwrc.usgs.gov/pubanalysis/keryroylebook/>. It also has all the utility functions and data sets needed to replicate the analyses shown in the books.

Authors:Marc Kéry [aut], Andy Royle [aut], Mike Meredith [aut], Ken Kellner [ctb, cre], Urs Breitenmoser [dtc], Richard Chandler [ctb], Bob Dorazio [ctb], Evan Grant [dtc], John-Andren Henden [dtc], Roland Kays [dtc], David King [dtc], Xavier Lambin [dtc], Jeremy Mizel [ctb, dtc], Anja Molinari-Jobin [dtc], René-Jean Monneret [dtc], Arielle Parsons [dtc], René Ruffinoni [dtc], Michael Schaub [ctb], Rahel Solmann [ctb], Nicolas Strebel [dtc], Chris Sutherland [ctb, dtc], Mathias Tobler [ctb], Gesa von Hirschheydt [ctb], Fridolin Zimmermann [dtc], Aargau Biodiversity Monitoring Program [dtc], British Ornithological Trust [dtc], Butterfly Conservation [dtc, cph], Centre for Ecology & Hydrology [dtc, cph], Dutch Centre for Field Ornithology [dtc], eMammal [dtc], Groupe Pèlerin Jura [dtc], Hubbard Brook Ecosystem Study [dtc], Joint Nature Conservation Committee [dtc, cph], North Carolina Museum of Natural Sciences [dtc], North Carolina State University [dtc], Progetto Lince Italia [dtc], Swiss Federal Statistical Office [dtc, cph], Swiss Foundation KORA Carnivore Ecology and Wildlife Management [dtc], Swiss Ornithological Institute [dtc], UK Butterfly Monitoring Scheme [dtc, cph]

AHMbook_0.2.12.tar.gz
AHMbook_0.2.12.zip(r-4.7)AHMbook_0.2.12.zip(r-4.6)AHMbook_0.2.12.zip(r-4.5)
AHMbook_0.2.12.tgz(r-4.6-any)AHMbook_0.2.12.tgz(r-4.5-any)
AHMbook_0.2.12.tar.gz(r-4.7-any)AHMbook_0.2.12.tar.gz(r-4.6-any)
AHMbook_0.2.12.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AHMbook/json (API)

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

Bug tracker:https://github.com/ecoverser/ahmbook/issues

Datasets:
  • BerneseOberland - Landscape data for the Bernese Oberland around Interlaken, in the Alps of central Switzerland
  • body - Fictional data for dragonflies
  • color - Fictional data for dragonflies
  • crestedTit - Count data from the Swiss Breeding Bird Survey MHB for crested tits from 1999 to 2015
  • crossbillAHM - Data from the Swiss Breeding Bird Survey MHB for European Crossbill from 2001 to 2012
  • cswa - Point count and spot-mapping data for Chestnut-sided Warbler
  • damage - Fictional data for dragonflies
  • duskySalamanders - Age-classified counts of dusky salamanders from two mid-Atlantic states in the USA
  • EurasianLynx - Data for Eurasian lynx from Switzerland and Italy (only Alps).
  • Finnmark - Data from surveys of birds in Finnmark in NE Norway
  • FrenchPeregrines - Data for observations of peregrines from the French Jura mountains
  • greenWoodpecker - Count data from the Swiss Breeding Bird Survey for Green Woodpeckers from 2004 to 2017
  • HubbardBrook - Warbler point count data from the Hubbard Brook Experimental Forest
  • MesoCarnivores - Camera trap data for Bobcat, Coyote and Red Fox
  • MHB2014 - Data from the Swiss Breeding Bird Survey MHB 2014
  • mites - Fictional data for dragonflies
  • pop - Fictional data for dragonflies
  • sex - Fictional data for dragonflies
  • simDynoccSpatialData - Simulated data from 'simDynoccSpatial' for AHM2 section 9.6.1.2
  • spottedWoodpecker - Data for observations of Middle Spotted Woodpecker in Switzerland
  • SwissAtlasHa - Data for 1ha quadrats from the Swiss Breeding Bird Atlas
  • SwissEagleOwls - Territory-level, multi-state detection/nondetection data for Eagle Owls in Switzerland
  • SwissMarbledWhite - Data for Swiss Marbled White butterflies
  • SwissTits - Data from the Swiss Breeding Bird Survey for 6 species of tits
  • treeSparrow - American Tree Sparrow data from Alaska
  • ttdPeregrine - Time-to-detection data for peregrines from the French Jura mountains
  • UKmarbledWhite - Data for UK Marbled White butterflies
  • wagtail - Data for Dutch wagtails
  • waterVoles - Data for the Mighty Water Voles of Scotland, UK.
  • wigglyLine - Coordinates for a wiggly line transect
  • willowWarbler - Constant effort site (CES) data for British Willow Warblers
  • wing - Fictional data for dragonflies

On CRAN:

Conda:

4.59 score 1 stars 389 scripts 755 downloads 1 mentions 70 exports 12 dependencies

Last updated from:cfa2e9ae7e. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK172
source / vignettesOK180
linux-release-x86_64OK156
macos-release-arm64OK134
macos-oldrel-arm64OK108
windows-develOK172
windows-releaseOK148
windows-oldrelOK152
wasm-releaseOK109

Exports:bigCrossCorrch2marraycrPiFuncrPiFun.Mbdata.fne2distfitstatsfitstats2getEcorrMatgetLVcorrMatgraphSSMimage_scaleinstRemPiFunissj.simmap.Nmix.resiMhPiFunmodSelFPplayRNplot_Nmix_resippc.plotrampBYRrampGBrrampGreensrampGreysrampYORsim.fnsim.ldatasim.pdatasim.spatialDSsim.spatialHDSsim3OccsimCJSsimCommsimDataDKsimDataDK1simDCMsimDemoDynoccsimDMsimDM0simDSMsimDynoccsimDynoccSpatialsimExpCorrRFsimFrogDiseasesimHDSsimHDSgsimHDSopensimHDSpointsimHDStrsimIDSsimMultMixsimNmixsimNmixSpatialsimNpCsimOccsimOccCatsimOccSpatialsimOccttdsimPHsimpleNmixsimPOPsimPPesimSpatialDSlinesimSpatialDStespline.prepstandardizestandardize2matchvalid_datawigglyOcczinit

Dependencies:latticeMASSMatrixmvtnormrbibutilsRcppRcppArmadilloRcppEigenRdpackreformulasTMBunmarked

Readme and manuals

Help Manual

Help pageTopics
Functions and data for the Book "Applied Hierarchical Modeling in Ecology" Volumes 1 and 2AHMbook-package AHMbook
Landscape data for the Bernese Oberland around Interlaken, in the Alps of central SwitzerlandBerneseOberland
Cross correlations for MCMC outputbigCrossCorr
Converts capture-histories to an m-arraych2marray
Color RampsColor_Ramps rampBYR rampGBr rampGreens rampGreys rampYOR
Count data from the Swiss Breeding Bird Survey MHB for crested tits from 1999 to 2015crestedTit
Data from the Swiss Breeding Bird Survey MHB for European Crossbill from 2001 to 2012crossbillAHM
Point count and spot-mapping data for Chestnut-sided Warblercswa
Simulate count data under a binomial N-mixture modeldata.fn
Fictional data for dragonfliesbody color damage dragonflies mites pop sex wing
Age-classified counts of dusky salamanders from two mid-Atlantic states in the USAduskySalamanders
Calculates the pair-wise distances between two sets of pointse2dist
Data for Eurasian lynx from Switzerland and Italy (only Alps).EurasianLynx
Data from surveys of birds in Finnmark in NE NorwayFinnmark
Functions to return fit statisticsfitstats fitstats2
Data for observations of peregrines from the French Jura mountainsFrenchPeregrines
Compute results of a Joint Species Distribution Model (JSDM)getEcorrMat getLVcorrMat
Plot the results for a Gaussian state-space modelgraphSSM
Count data from the Swiss Breeding Bird Survey for Green Woodpeckers from 2004 to 2017greenWoodpecker
Warbler point count data from the Hubbard Brook Experimental ForestHubbardBrook
Helper function to draw scale for imageimage.scale image_scale
Simulate open distance sampling data for the Island Scrub Jaysissj.sim
Mapping of residualsmap.Nmix.resi
Camera trap data for Bobcat, Coyote and Red FoxMesoCarnivores
Data from the Swiss Breeding Bird Survey MHB 2014MHB2014
Model selection results from a list of 'unmarkedFitOccuFP' modelsmodSelFP
Compute multinomial cell probabilitiescrPiFun crPiFun.Mb instRemPiFun MhPiFun piFuns
Function to play Royle-Nichols (RN) modelplayRN
Produce some residual plotsplot.Nmix.resi plot_Nmix_resi
Plot results from posterior predictive checkppc.plot
Simulate a Poisson point processsim.fn
Simulation of distance sampling data.sim.ldata
Simulate non-hierarchical point transect (= point count) datasim.pdata
Simulates data for a basic spatial distance sampling modelsim.spatialDS
Simulates data for a hierarchical spatial distance sampling modelsim.spatialHDS
Simulate detection/nondetection data for static 3-level occupancy modelssim3Occ
Simulate individual capture-histories under a Cormack-Jolly-Seber (CJS) survival modelsimCJS
Simulate community occupancy or community abundance datasimComm
Simulate data for an integrated species distribution model (SDM) of Dorazio-KoshkinasimDataDK simDataDK1
Simulate detection/nondetection data under a general dynamic community (site-occupancy) modelsimDCM
Simulate data under a demographic dynamic occupancy modelsimDemoDynocc
Simulate count data under the dynamic N-mixture model of Dail-MadsensimDM simDM0
Simulate line transect data for density surface modelingsimDSM
Simulate detection/nondetection data under a wide variety of non-spatial dynamic occupancy modelssimDynocc
Simulate data under a dynamic occupancy model with spatial autocorrelationsimDynoccSpatial
Simulated data from 'simDynoccSpatial' for AHM2 section 9.6.1.2 (page 564)simDynoccSpatialData
Create a Gaussian random field with negative exponential correlationsimExpCorrRF
Simulate detection data for diseased frogssimFrogDisease
Simulate data under hierarchical distance sampling protocol (line or point)simHDS
Simulate data under HDS protocol with groupssimHDSg
Simulate open hierarchical distance sampling datasimHDSopen
Simulate data under hierarchical distance sampling point transect protocolsimHDSpoint
Simulate HDS time-removal or double-observer datasimHDStr
Simulate data for an integrated distance sampling, point count and occupancy studysimIDS
Simulate the multinomial-mixture modelsimMultMix
Simulate data for binomial and multinomial mixture modelssimNmix
Simulate replicated counts under a spatial, static binomial N-mixture modelsimNmixSpatial
Generate counts from a single population observed over T years under a binomial observation processsimNpC
Simulate data for static occupancy models under wide range of conditionssimOcc simOccCat
Simulate replicated detection/nondetection data under a spatial, static occupancy modelsimOccSpatial
Simulate time-to-detection occupancy data (single visits)simOccttd
Generate counts under a variant of a 'phenomenological model'simPH
Simulate N-mixture data under a time-for-space substitution designsimpleNmix
Simulate data for a demographic state-space modelsimPOP
Simulate a spatial point pattern in a heterogeneous landscapesimPPe
Simulate data for a standardized line transectsimSpatialDSline
Simulate data for replicate line transect surveys with temporary emigrationsimSpatialDSte
Prepare input for BUGS model when fitting a spline for a covariatespline.prep
Data for observations of Middle Spotted Woodpecker in SwitzerlandspottedWoodpecker
Scaling and centering of vectors, matrices and arraysstandardize standardize2match
Data for 1ha quadrats from the Swiss Breeding Bird AtlasSwissAtlasHa
Territory-level, multi-state detection/nondetection data for Eagle Owls in SwitzerlandSwissEagleOwls
Data for Swiss Marbled White butterfliesSwissMarbledWhite
Data for Red Squirrels in Switzerland from the Swiss breeding bird survey MHBSwissSquirrels
Data from the Swiss Breeding Bird Survey for 6 species of titsSwissTits
American Tree Sparrow data from AlaskatreeSparrow
Time-to-detection data for peregrines from the French Jura mountainsttdPeregrine
Data for UK Marbled White butterfliesUKmarbledWhite
Validates simulated observational data against data-generating values.valid_data
Data for Dutch wagtailswagtail
Data for the Mighty Water Voles of Scotland, UK.waterVoles
Coordinates for a wiggly line transectwigglyLine
Simulate static occupancy datawigglyOcc
Constant effort site (CES) data for British Willow WarblerswillowWarbler
Starting values for survival analysis in JAGS/BUGSzinit