IPMbook-package: Functions and data for the book 'Integrated Population...
In IPMbook: Functions and Data for the Book 'Integrated Population Models'

IPMbook-package

R Documentation

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.