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

Documentation for package ‘AHMbook’ version 0.2.9

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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

-- A --

AHMbook

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

-- B --

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

-- C --

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

-- D --

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

-- E --

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

-- F --

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

-- G --

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

-- H --

HubbardBrook

Warbler point count data from the Hubbard Brook Experimental Forest

-- I --

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

-- M --

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

-- P --

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

-- R --

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

-- S --

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
simDynoccSpatialData	Simulated data from 'simDynoccSpatial' for AHM2 section 9.6.1.2 (page 564)
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
simHDSpoint	Simulate data under hierarchical distance sampling point transect protocol
simHDStr	Simulate HDS time-removal or double-observer data
simIDS	Simulate data for an integrated distance sampling, point count and occupancy study
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
simOccCat	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

-- T --

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

-- U --

UKmarbledWhite

Data for UK Marbled White butterflies

-- V --

valid_data

Validates simulated observational data against data-generating values.

-- W --

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

-- Z --

zinit

Starting values for survival analysis in JAGS/BUGS