IPMbook-package | R Documentation |

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

The functions are listed by chapter below.

`demoMCMC`

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

`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)

`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)

`marrayDead`

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

`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.

`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.

Michael Schaub, Marc Kéry, Mike Meredith

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