IPMbook-package {IPMbook}

Functions and data for the book 'Integrated Population Models'

Description

Provides functions and data sets to accompany the book Integrated Population Models by Michael Schaub and Marc Kéry (ISBN: 9780128205648).

Details

The functions are listed by chapter below.

Chapter 2

demoMCMC

Demonstration of a random-walk sampler for MCMC (section 2.5)

Chapter 4

simMHB

Simulates detection and count data with spatial and temporal replication (section 4.3.3)

createAge

Creates an age matrix (section 4.5.1.1)

marray

Converts single- or multistate capture histories to an m-array for one age class (section 4.5.1.2)

marrayAge

Converts single-state capture histories to age-dependent m-arrays (section 4.5.1.2)

Chapter 5

simPop

Simulates a population based on demographic parameters (section 5.5.1)

simCapHist

Simulates capture histories from a population (section 5.5.1)

simProd

Simulates productivity data for a population (section 5.5.1)

simCount

Simulates population survey data for a population (section 5.5.1)

Chapter 12

marrayDead

Converts dead-recovery capture histories to an m-array (section 12.4.2)

DATA SETS

bats

Data for greater horseshoe bats from Switzerland, 1989-2017, chapter 13.

bear

Data for black bears from USA, 2007-2012, chapter 21.

catbird

Data for catbirds from USA, 1992-2008, chapter 19.

cormorant

Data for cormorants from Denmark, 1991-2004, chapter 18.

elk

Data for elk cows from USA, 1988-1993, chapter 17.

grouse

Data for black grouse from Italy, 1997-2016, chapter 15.

hoopoe

Data for hoopoe from Switzerland, 2001-2017, chapter 14.

kestrel

Data for kestrels from Switzerland, 2002-2016, chapter 20.

peregrine

Data for peregrine falcons from France and Switzerland, 1965-2007, chapter 12.

redbacked

Data for red-backed shrike from Germany, 1971-2006, section 8.2.

stork

Data for white storks from Germany, 1986-2001, section 4.5.4.

swallow

Data for barn swallow from Switzerland, 1997-2003, chapter 16.

woodchat5

Simulated data for woodchat shrike for use in chapter 5.

woodchat6

Simulated data for woodchat shrike for use in chapter 6.

woodchat64

Simulated data for woodchat shrike for use in section 6.4.

woodchat66

Simulated data for woodchat shrike for use in section 6.6.

woodchat7

Simulated data for woodchat shrike for use in chapter 7.

woodchat10

Simulated data for woodchat shrike for use in chapter 10.

woodchat11

Data for woodchat shrike from Germany, 1964-1992, chapter 11.

wryneck

Nest survival data for wryneck from Switzerland, 2002-2006, section 4.4.6.

UTILITY FUNCTIONS

ch2matrix

Convert capture histories in text format to a matrix.

cleanCH

Removes all-zero rows from a capture history matrix.

dbeta2

Beta distribution with mean and sd.

dbeta3

Beta distribution with mode and concentration.

dgamma2

Gamma distribution with mean and sd.

getFirst

Calculates the occasion of first capture from a capture history matrix.

rmFirst

Removes the records of first capture from a capture history matrix.

zInit

Converts a capture history matrix to one with 1 after the occasion of first capture, NA elsewhere.

zInitDR

Converts a dead-recovery capture history matrix to one with 1 after the occasion of first capture until the occasion of dead recovery, then 0; NA elsewhere.

zKnown

Converts a capture history matrix to one with 1 where the animal is know to be alive, NA elsewhere.

Author(s)

Michael Schaub, Marc Kéry, Mike Meredith