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 Ecolo...
Cross correlations for MCMC output
Converts capture-histories to an m-array
Color Ramps
Landscape data for the Bernese Oberland around Interlaken, in the Alps...
Count data from the Swiss Breeding Bird Survey MHB for crested tits fr...
Data from the Swiss Breeding Bird Survey MHB for European Crossbill fr...
Point count and spot-mapping data for Chestnut-sided Warbler
Fictional data for dragonflies
Age-classified counts of dusky salamanders from two mid-Atlantic state...
Data for Eurasian lynx from Switzerland and Italy (only Alps).
Data from surveys of birds in Finnmark in NE Norway
Data for observations of peregrines from the French Jura mountains
Count data from the Swiss Breeding Bird Survey for Green Woodpeckers f...
Warbler point count data from the Hubbard Brook Experimental Forest
Camera trap data for Bobcat, Coyote and Red Fox
Data from the Swiss Breeding Bird Survey MHB 2014
Simulated data from simDynoccSpatial for AHM2 section 9.6.1.2 (page ...
Data for observations of Middle Spotted Woodpecker in Switzerland
Data for 1ha quadrats from the Swiss Breeding Bird Atlas
Territory-level, multi-state detection/nondetection data for Eagle Owl...
Data for Swiss Marbled White butterflies
Data for Red Squirrels in Switzerland from the Swiss breeding bird sur...
Data from the Swiss Breeding Bird Survey for 6 species of tits
American Tree Sparrow data from Alaska
Time-to-detection data for peregrines from the French Jura mountains
Data for UK Marbled White butterflies
Data for Dutch wagtails
Data for the Mighty Water Voles of Scotland, UK.
Coordinates for a wiggly line transect
Constant effort site (CES) data for British Willow Warblers
Calculates the pair-wise distances between two sets of points
Functions to return fit statistics
Compute results of a Joint Species Distribution Model (JSDM)
Plot the results for a Gaussian state-space model
Helper function to draw scale for image
Mapping of residuals
Model selection results from a list of 'unmarkedFitOccuFP' models
Compute multinomial cell probabilities
Function to play Royle-Nichols (RN) model
Produce some residual plots
Plot results from posterior predictive check
Simulate detection/nondetection data for static 3-level occupancy mode...
Simulate individual capture-histories under a Cormack-Jolly-Seber (CJS...
Simulate community occupancy or community abundance data
Simulate count data under a binomial N-mixture model
Simulate data for an integrated species distribution model (SDM) of Do...
Simulate detection/nondetection data under a general dynamic community...
Simulate data under a demographic dynamic occupancy model
Simulate count data under the dynamic N-mixture model of Dail-Madsen
Simulate line transect data for density surface modeling
Simulate detection/nondetection data under a wide variety of non-spati...
Simulate data under a dynamic occupancy model with spatial autocorrela...
Create a Gaussian random field with negative exponential correlation
Simulate a Poisson point process
Simulate detection data for diseased frogs
Simulate data under hierarchical distance sampling protocol (line or p...
Simulate data under HDS protocol with groups
Simulate open hierarchical distance sampling data
Simulate data under hierarchical distance sampling point transect prot...
Simulate HDS time-removal or double-observer data
Simulate data for an integrated distance sampling, point count and occ...
Simulate open distance sampling data for the Island Scrub Jays
Simulation of distance sampling data.
Simulate the multinomial-mixture model
Simulate data for binomial and multinomial mixture models
Simulate replicated counts under a spatial, static binomial N-mixture ...
Generate counts from a single population observed over T years under a...
Simulate data for static occupancy models under wide range of conditio...
Simulate replicated detection/nondetection data under a spatial, stati...
Simulate time-to-detection occupancy data (single visits)
Simulate non-hierarchical point transect (= point count) data
Generate counts under a variant of a 'phenomenological model'
Simulate N-mixture data under a time-for-space substitution design
Simulate data for a demographic state-space model
Simulate a spatial point pattern in a heterogeneous landscape
Simulates data for a basic spatial distance sampling model
Simulate data for a standardized line transect
Simulate data for replicate line transect surveys with temporary emigr...
Simulates data for a hierarchical spatial distance sampling model
Simulate static occupancy data
Prepare input for BUGS model when fitting a spline for a covariate
Scaling and centering of vectors, matrices and arrays
Validates simulated observational data against data-generating values.
Starting values for survival analysis in JAGS/BUGS
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.
Useful links