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AHMbook (version 0.2.5)

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 Kry 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

463

Version

0.2.5

License

GPL (>= 3)

Maintainer

Mike Meredith

Last Published

May 2nd, 2022

Functions in AHMbook (0.2.5)

BerneseOberland

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

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

Cross correlations for MCMC output

Warbler point count data from the Hubbard Brook Experimental Forest

Data for UK Marbled White butterflies

Data from the Swiss Breeding Bird Survey MHB 2014

AHMbook-package

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

SwissMarbledWhite

Data for Swiss Marbled White butterflies

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

Data for Dutch wagtails

Data for the Mighty Water Voles of Scotland, UK.

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

greenWoodpecker

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

spottedWoodpecker

Data for observations of Middle Spotted Woodpecker in Switzerland

Data for 1ha quadrats from the Swiss Breeding Bird Atlas

Converts capture-histories to an m-array

Constant effort site (CES) data for British Willow Warblers

Coordinates for a wiggly line transect

duskySalamanders

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

Function to play Royle-Nichols (RN) model

Fictional data for dragonflies

Model selection results from a list of 'unmarkedFitOccuFP' models

Compute multinomial cell probabilities

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

Helper function to draw scale for image

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

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

Mapping of residuals

Compute results of a Joint Species Distribution Model (JSDM)

Simulate community occupancy or community abundance data

Plot the results for a Gaussian state-space model

Produce some residual plots

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

FrenchPeregrines

Data for observations of peregrines from the French Jura mountains

Data from surveys of birds in Finnmark in NE Norway

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

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

Simulate detection data for diseased frogs

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

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

Simulate data for static occupancy models under wide range of conditions

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

Simulate data under a demographic dynamic occupancy model

Plot results from posterior predictive check

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

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

Simulate open distance sampling data for the Island Scrub Jays

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

Simulate data for replicate line transect surveys with temporary emigration

Simulate static occupancy data

Create a Gaussian random field with negative exponential correlation

Simulate open hierarchical distance sampling data

Simulate data under HDS protocol with groups

American Tree Sparrow data from Alaska

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

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

Simulate a Poisson point process

Simulate the multinomial-mixture model

Simulation of distance sampling data.

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

Simulates data for a hierarchical spatial distance sampling model

Simulates data for a basic spatial distance sampling model

Simulate a spatial point pattern in a heterogeneous landscape

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

simSpatialDSline

Simulate data for a standardized line transect

Validates simulated observational data against data-generating values.

Starting values for survival analysis in JAGS/BUGS

Calculates the pair-wise distances between two sets of points

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

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

Scaling and centering of vectors, matrices and arrays

Functions to return fit statistics

Simulate data under hierarchical distance sampling point transect protocol

Simulate HDS time-removal or double-observer data

Simulate count data under a binomial N-mixture model

Simulate line transect data for density surface modeling

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

Simulate data for binomial and multinomial mixture models

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

Generate counts under a variant of a 'phenomenological model'

Simulate data for a demographic state-space model