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AHMbook (version 0.2.10)

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

Description

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), . It also has all the utility functions and data sets needed to replicate the analyses shown in the books.

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Version

Install

install.packages('AHMbook')

Monthly Downloads

464

Version

0.2.10

License

GPL (>= 3)

Maintainer

Ken Kellner

Last Published

September 11th, 2024

Functions in AHMbook (0.2.10)

Fictional data for dragonflies

duskySalamanders

Age-classified counts of dusky salamanders from two mid-Atlantic states in the USA

Data for the Mighty Water Voles of Scotland, UK.

American Tree Sparrow data from Alaska

spottedWoodpecker

Data for observations of Middle Spotted Woodpecker in Switzerland

Point count and spot-mapping data for Chestnut-sided Warbler

Coordinates for a wiggly line transect

Compute multinomial cell probabilities

Model selection results from a list of 'unmarkedFitOccuFP' models

Plot the results for a Gaussian state-space model

Function to play Royle-Nichols (RN) model

Data for Dutch wagtails

greenWoodpecker

Count data from the Swiss Breeding Bird Survey for Green Woodpeckers from 2004 to 2017

Mapping of residuals

Helper function to draw scale for image

Compute results of a Joint Species Distribution Model (JSDM)

Functions to return fit statistics

Time-to-detection data for peregrines from the French Jura mountains

simDynoccSpatialData

Simulated data from simDynoccSpatial for AHM2 section 9.6.1.2 (page 564)

Produce some residual plots

Simulate count data under a binomial N-mixture model

Calculates the pair-wise distances between two sets of points

Simulate data for an integrated species distribution model (SDM) of Dorazio-Koshkina

Constant effort site (CES) data for British Willow Warblers

Simulate count data under the dynamic N-mixture model of Dail-Madsen

Simulate line transect data for density surface modeling

Simulate community occupancy or community abundance data

Simulate detection/nondetection data under a general dynamic community (site-occupancy) model

Plot results from posterior predictive check

Simulate individual capture-histories under a Cormack-Jolly-Seber (CJS) survival model

Simulate detection/nondetection data for static 3-level occupancy models

Simulate data under hierarchical distance sampling point transect protocol

Simulate open hierarchical distance sampling data

Simulate data under HDS protocol with groups

Simulate data under hierarchical distance sampling protocol (line or point)

Simulate detection data for diseased frogs

Create a Gaussian random field with negative exponential correlation

Simulate a Poisson point process

simDynoccSpatial

Simulate data under a dynamic occupancy model with spatial autocorrelation

Simulate data for static occupancy models under wide range of conditions

Simulate detection/nondetection data under a wide variety of non-spatial dynamic occupancy models

Simulate replicated detection/nondetection data under a spatial, static occupancy model

Simulate the multinomial-mixture model

Simulate replicated counts under a spatial, static binomial N-mixture model

Starting values for survival analysis in JAGS/BUGS

Generate counts from a single population observed over T years under a binomial observation process

Simulate data for a demographic state-space model

Simulate data under a demographic dynamic occupancy model

Simulate non-hierarchical point transect (= point count) data

Simulates data for a basic spatial distance sampling model

Simulate static occupancy data

simSpatialDSline

Simulate data for a standardized line transect

Simulate data for binomial and multinomial mixture models

Simulate N-mixture data under a time-for-space substitution design

Simulates data for a hierarchical spatial distance sampling model

Scaling and centering of vectors, matrices and arrays

Simulate data for replicate line transect surveys with temporary emigration

Validates simulated observational data against data-generating values.

Simulate data for an integrated distance sampling, point count and occupancy study

Simulate HDS time-removal or double-observer data

Simulation of distance sampling data.

Simulate a spatial point pattern in a heterogeneous landscape

Simulate open distance sampling data for the Island Scrub Jays

Prepare input for BUGS model when fitting a spline for a covariate

Simulate time-to-detection occupancy data (single visits)

Generate counts under a variant of a 'phenomenological model'

Warbler point count data from the Hubbard Brook Experimental Forest

Data from the Swiss Breeding Bird Survey MHB 2014

Converts capture-histories to an m-array

Cross correlations for MCMC output

AHMbook-package

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

Data for UK Marbled White butterflies

Data from surveys of birds in Finnmark in NE Norway

FrenchPeregrines

Data for observations of peregrines from the French Jura mountains

Count data from the Swiss Breeding Bird Survey MHB for crested tits from 1999 to 2015

Camera trap data for Bobcat, Coyote and Red Fox

Data for 1ha quadrats from the Swiss Breeding Bird Atlas

Data from the Swiss Breeding Bird Survey for 6 species of tits

Data for Red Squirrels in Switzerland from the Swiss breeding bird survey MHB

BerneseOberland

Landscape data for the Bernese Oberland around Interlaken, in the Alps of central Switzerland

Territory-level, multi-state detection/nondetection data for Eagle Owls in Switzerland

SwissMarbledWhite

Data for Swiss Marbled White butterflies

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

Data from the Swiss Breeding Bird Survey MHB for European Crossbill from 2001 to 2012