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AHMbook (version 0.2.2)

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

Description

Provides functions and data sets to accompany 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), .

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Version

Install

install.packages('AHMbook')

Monthly Downloads

446

Version

0.2.2

License

GPL (>= 3)

Maintainer

Mike Meredith

Last Published

October 26th, 2020

Functions in AHMbook (0.2.2)

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

Converts capture-histories to an m-array

Data from the Swiss Breeding Bird Survey MHB 2014

BerneseOberland

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

Data from surveys of birds in Finnmark in NE Norway

FrenchPeregrines

Data for observations of peregrines from the French Jura mountains

Warbler point count data from the Hubbard Brook Experimental Forest

Cross correlations for MCMC output

AHMbook-package

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

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

Camera trap data for Bobcat, Coyote and Red Fox

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

SwissMarbledWhite

Data for Swiss Marbled White butterflies

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

Data for Dutch wagtails

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

Data for 1ha quadrats from the Swiss Breeding Bird Atlas

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

Calculates the pair-wise distances between two sets of points

Function to play Royle-Nichols (RN) model

Data for the Mighty Water Voles of Scotland, UK.

American Tree Sparrow data from Alaska

Produce some residual plots

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

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

spottedWoodpecker

Data for observations of Middle Spotted Woodpecker in Switzerland

greenWoodpecker

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

Data for UK Marbled White butterflies

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

Functions to return fit statistics

Helper function to draw scale for image

Coordinates for a wiggly line transect

Constant effort site (CES) data for British Willow Warblers

Fictional data for dragonflies

Simulate count data under a binomial N-mixture model

Simulate line transect data for density surface modeling

Simulate data under HDS protocol with groups

Simulate open hierarchical distance sampling data

Simulate a spatial point pattern in a heterogeneous landscape

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

Simulate data for binomial and multinomial mixture models

Model selection results from a list of 'unmarkedFitOccuFP' models

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

Mapping of residuals

Simulate detection data for diseased frogs

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

Compute multinomial cell probabilities

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

Create a Gaussian random field with negative exponential correlation

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

duskySalamanders

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

Simulate a Poisson point process

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

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

Simulates data for a hierarchical spatial distance sampling model

Simulate data for replicate line transect surveys with temporary emigration

Simulate community occupancy or community abundance data

Plot results from posterior predictive check

Simulation of distance sampling data.

Simulate the multinomial-mixture model

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

Simulate open distance sampling data for the Island Scrub Jays

Simulate HDS time-removal or double-observer data

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

Simulates data for a basic spatial distance sampling model

simSpatialDSline

Simulate data for a standardized line transect

Simulate data for static occupancy models under wide range of conditions

Validates simulated observational data against data-generating values.

Starting values for survival analysis in JAGS/BUGS

Simulate static occupancy data

Compute results of a Joint Species Distribution Model (JSDM)

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

Plot the results for a Gaussian state-space model

Simulate data under a demographic dynamic occupancy model

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

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

Generate counts under a variant of a 'phenomenological model'

simDynoccSpatial

Simulate data under a dynamic occupancy model with spatial autocorrelation

Simulate data for a demographic state-space model

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

Scaling and centering of vectors, matrices and arrays