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


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Documentation for package ‘AHMbook’ version 0.2.2

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A B C D E F G H I M P R S T U V W Z

AHMbook-package Functions and data for the Book "Applied Hierarchical Modeling in Ecology" Volumes 1 and 2

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AHMbook Functions and data for the Book "Applied Hierarchical Modeling in Ecology" Volumes 1 and 2

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BerneseOberland Landscape data for the Bernese Oberland around Interlaken, in the Alps of central Switzerland
bigCrossCorr Cross correlations for MCMC output
body Fictional data for dragonflies

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ch2marray Converts capture-histories to an m-array
color Fictional data for dragonflies
Color_Ramps Color Ramps
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
crPiFun Compute multinomial cell probabilities
crPiFun.Mb Compute multinomial cell probabilities
cswa Point count and spot-mapping data for Chestnut-sided Warbler

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damage Fictional data for dragonflies
data.fn Simulate count data under a binomial N-mixture model
dragonflies Fictional data for dragonflies
duskySalamanders Age-classified counts of dusky salamanders from two mid-Atlantic states in the USA

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e2dist Calculates the pair-wise distances between two sets of points
EurasianLynx Data for Eurasian lynx from Switzerland and Italy (only Alps).

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Finnmark Data from surveys of birds in Finnmark in NE Norway
fitstats Functions to return fit statistics
fitstats2 Functions to return fit statistics
FrenchPeregrines Data for observations of peregrines from the French Jura mountains

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getEcorrMat Compute results of a Joint Species Distribution Model (JSDM)
getLVcorrMat Compute results of a Joint Species Distribution Model (JSDM)
graphSSM Plot the results for a Gaussian state-space model
greenWoodpecker Count data from the Swiss Breeding Bird Survey for Green Woodpeckers from 2004 to 2017

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HubbardBrook Warbler point count data from the Hubbard Brook Experimental Forest

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image.scale Helper function to draw scale for image
image_scale Helper function to draw scale for image
instRemPiFun Compute multinomial cell probabilities
issj.sim Simulate open distance sampling data for the Island Scrub Jays

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map.Nmix.resi Mapping of residuals
MesoCarnivores Camera trap data for Bobcat, Coyote and Red Fox
MHB2014 Data from the Swiss Breeding Bird Survey MHB 2014
MhPiFun Compute multinomial cell probabilities
mites Fictional data for dragonflies
modSelFP Model selection results from a list of 'unmarkedFitOccuFP' models

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piFuns Compute multinomial cell probabilities
playRN Function to play Royle-Nichols (RN) model
plot.Nmix.resi Produce some residual plots
plot_Nmix_resi Produce some residual plots
pop Fictional data for dragonflies
ppc.plot Plot results from posterior predictive check

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rampBYR Color Ramps
rampGBr Color Ramps
rampGreens Color Ramps
rampGreys Color Ramps
rampYOR Color Ramps

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sex Fictional data for dragonflies
sim.fn Simulate a Poisson point process
sim.ldata Simulation of distance sampling data.
sim.pdata Simulate non-hierarchical point transect (= point count) data
sim.spatialDS Simulates data for a basic spatial distance sampling model
sim.spatialHDS Simulates data for a hierarchical spatial distance sampling model
sim3Occ Simulate detection/nondetection data for static 3-level occupancy models
simCJS Simulate individual capture-histories under a Cormack-Jolly-Seber (CJS) survival model
simComm Simulate community occupancy or community abundance data
simDataDK Simulate data for an integrated species distribution model (SDM) of Dorazio-Koshkina
simDataDK1 Simulate data for an integrated species distribution model (SDM) of Dorazio-Koshkina
simDCM Simulate detection/nondetection data under a general dynamic community (site-occupancy) model
simDemoDynocc Simulate data under a demographic dynamic occupancy model
simDM Simulate count data under the dynamic N-mixture model of Dail-Madsen
simDM0 Simulate count data under the dynamic N-mixture model of Dail-Madsen
simDSM Simulate line transect data for density surface modeling
simDynocc Simulate detection/nondetection data under a wide variety of non-spatial dynamic occupancy models
simDynoccSpatial Simulate data under a dynamic occupancy model with spatial autocorrelation
simExpCorrRF Create a Gaussian random field with negative exponential correlation
simFrogDisease Simulate detection data for diseased frogs
simHDS Simulate data under hierarchical distance sampling protocol (line or point)
simHDSg Simulate data under HDS protocol with groups
simHDSopen Simulate open hierarchical distance sampling data
simHDStr Simulate HDS time-removal or double-observer data
simMultMix Simulate the multinomial-mixture model
simNmix Simulate data for binomial and multinomial mixture models
simNmixSpatial Simulate replicated counts under a spatial, static binomial N-mixture model
simNpC Generate counts from a single population observed over T years under a binomial observation process
simOcc Simulate data for static occupancy models under wide range of conditions
simOccSpatial Simulate replicated detection/nondetection data under a spatial, static occupancy model
simOccttd Simulate time-to-detection occupancy data (single visits)
simPH Generate counts under a variant of a 'phenomenological model'
simpleNmix Simulate N-mixture data under a time-for-space substitution design
simPOP Simulate data for a demographic state-space model
simPPe Simulate a spatial point pattern in a heterogeneous landscape
simSpatialDSline Simulate data for a standardized line transect
simSpatialDSte Simulate data for replicate line transect surveys with temporary emigration
spline.prep Prepare input for BUGS model when fitting a spline for a covariate
spottedWoodpecker Data for observations of Middle Spotted Woodpecker in Switzerland
standardize Scaling and centering of vectors, matrices and arrays
standardize2match Scaling and centering of vectors, matrices and arrays
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
SwissSquirrels Data for Red Squirrels in Switzerland from the Swiss breeding bird survey MHB
SwissTits Data from the Swiss Breeding Bird Survey for 6 species of tits

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treeSparrow American Tree Sparrow data from Alaska
ttdPeregrine Time-to-detection data for peregrines from the French Jura mountains

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UKmarbledWhite Data for UK Marbled White butterflies

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valid_data Validates simulated observational data against data-generating values.

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wagtail Data for Dutch wagtails
waterVoles Data for the Mighty Water Voles of Scotland, UK.
wigglyLine Coordinates for a wiggly line transect
wigglyOcc Simulate static occupancy data
willowWarbler Constant effort site (CES) data for British Willow Warblers
wing Fictional data for dragonflies

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zinit Starting values for survival analysis in JAGS/BUGS