secr (version 2.3.2)

RMarkInput: Convert Data to RMark Input Format

Description

A single-session capthist object is formed by RMarkInput into a dataframe that may be passed directly to RMark.

Usage

RMarkInput(object, grouped = TRUE)
unRMarkInput(df)

Arguments

object

secr capthist object

grouped

logical for whether to replace each group of identical capture histories with a single line

df

dataframe with fields `ch' and `freq'

Value

• For RMarkInput -- Dataframe with fields ch and freq. `ch' is a character string of 0's and 1's. If grouped = FALSE the rownames are retained and the value of `freq' is 1 or -1. Negative values of `freq' indicate removal. The attribute `interval' is copied from `object', if present; otherwise it is set to a vector of zeros (indicating a closed-population sample). For unRMarkInput -- A single-session capthist object with no traps attribute and hence no detector type (i.e. non-spatial capture histories). Covariates are copied.

Details

To convert a multi-session object first collapse the sessions with join.

References

Laake, J. and Rexstad E. (2008) Appendix C. RMark - an alternative approach to building linear models in MARK. In: Cooch, E. and White, G. (eds) Program MARK: A Gentle Introduction. 6th edition. Available at http://www.phidot.org/software/mark/docs/book/.

See Also

join

Examples

## ovenCH is a 5-year mist-netting dataset
ovenRD <- RMarkInput (join(ovenCH))
ovenRD

unRMarkInput(ovenRD)

## fit robust-design model in RMark (MARK must be  installed)
library(RMark)
ovenRD.data <- process.data(ovenRD, model = 'Robust',
    time.interval = attr(ovenRD, 'interval'))
ovenRD.model <- mark(data = ovenRD.data, model = 'Robust',
    model.parameters = list(p = list(formula = ~1, share = TRUE),
    GammaDoublePrime = list(formula = ~1),
    GammaPrime = list(formula = ~1),
    N = list(formula = ~1)))
cleanup(ask = FALSE)