marray: Converts capture-histories to an m-array for one age class

Description Usage Arguments Details Value Author(s) References Examples

View source: R/marray.R

Description

Creates an m-array for a single- or multistate capture-recapture data with one age class and optionally more than one group.

Usage

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marray(ch, unobs = 0, freq = 1, groups = NULL)

Arguments

ch

an individuals x time matrix with single- or multistate capture histories (0: not captured; 1...X: captured in the 1...X states). See Details.

unobs

number of unobserved states (default is 0, needs to be given only in specific cases).

freq

a vector with the number of animals with each capture history, or a matrix with a column for each group. If a single value is supplied, it will be used for all rows in the capture history; the default is to assume each row corresponds to a single animal.

groups

a factor (or a vector that can be coerced to a factor) which identifies the group that each row of ch refers to. Ignored if freq is a matrix with > 1 column.

Details

The argument ch can be a matrix of unique capture histories accompanied by a vector or matrix, freq, specifying the number of animals with each capture history. Trap losses can be indicated either by negative values for freq, or by filling the row with NA after the last capture. For other formats, see ch2matrix.

Value

For single-state capture recapture data, an m-array which is a (years-1) x years x groups array, where element [i, j, g] contains the number of individuals in group g released in year i and recaptured in year j+1 (by definition no recaptures can occur in year 1). If no groups are specified, this will be a (years-1) x years matrix. The last column contains the number of individuals released in year i and never recaptured.

For multi-state capture-recapture data with s states (including potential unobservable states), an m-array which is a (years-1)*s x (years-1)*2 + 1 x groups array. An element [i, j, g] contains the number of individuals in group g released in year t and state n (i = (t-1)*s + n) and recaptured in year k+1 in state m (j = (k-1)*s + m). If no groups are specified, this will be a matrix. The last column contains the number of individuals released in year t and state s and never recaptured. The labeling of unobserved states starts with the number of observed states + 1.

Author(s)

Michael Schaub

References

Schaub, M., Kéry, M. (2022) Integrated Population Models, Academic Press, section 4.5.1.2.

Examples

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# Convert a single state capture history matrix into an m-array
data(woodchat5)
dim(woodchat5$ch)  # 1902 animals x 20 years
ch1 <- cleanCH(woodchat5$ch[, 11:20])  # Use last 10 years only
marray(ch1)

# Convert a multistate capture history into an m-array
data(cormorant)
dim(cormorant$ms.ch) # 12,659 animals x 14 years
ch2 <- cleanCH(cormorant$ms.ch[, 11:14])  # Use last 4 years only
table(ch2) # 6 states
marray(ch2)

IPMbook documentation built on Dec. 11, 2021, 9:59 a.m.