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 |

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

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 |

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 |

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 |

e2dist | Calculates the pair-wise distances between two sets of points |

EurasianLynx | Data for Eurasian lynx from Switzerland and Italy (only Alps). |

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 |

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 |

HubbardBrook | Warbler point count data from the Hubbard Brook Experimental Forest |

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 |

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 |

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 |

rampBYR | Color Ramps |

rampGBr | Color Ramps |

rampGreens | Color Ramps |

rampGreys | Color Ramps |

rampYOR | Color Ramps |

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 |

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 |

valid_data | Validates simulated observational data against data-generating values. |

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 |

zinit | Starting values for survival analysis in JAGS/BUGS |