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

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

## Documentation for package ‘AHMbook’ version 0.2.12

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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