Newt Capture-mark-recapture Data

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Description

This is a capture-mark-recapture data set on adult male and female Red-spotted Newts (Notophthalmus viridescens) recorded by Gill (1985). A total of 1079 unique individuals were captured in pitfall traps at a breeding site (White Oak Flat pond, Virginia) between 1975 and 1983.

Usage

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data(newt)

Format

A data frame with 78 observations on the following 11 variables.

T1975

a binary variable, either 1 (captured) or 0 (not captured) during the 1975 breeding season.

T1976

a binary variable, either 1 (captured) or 0 (not captured) during the 1976 breeding season.

T1977

a binary variable, either 1 (captured) or 0 (not captured) during the 1977 breeding season.

T1978

a binary variable, either 1 (captured) or 0 (not captured) during the 1978 breeding season.

T1979

a binary variable, either 1 (captured) or 0 (not captured) during the 1979 breeding season.

T1980

a binary variable, either 1 (captured) or 0 (not captured) during the 1980 breeding season.

T1981

a binary variable, either 1 (captured) or 0 (not captured) during the 1981 breeding season.

T1982

a binary variable, either 1 (captured) or 0 (not captured) during the 1982 breeding season.

T1983

a binary variable, either 1 (captured) or 0 (not captured) during the 1983 breeding season.

Males

a numeric variable indicating the total number of males with a given capture history.

Females

a numeric variable indicating the total number of females with a given capture history.

Details

A single cohort of individuals was followed throughout the study, as all individuals were marked in 1975 and no new individuals were added during the subsequent years. This data set is used to illustrate classic Cormack-Jolly-Seber and related models (Cormack 1964, Jolly 1965, Seber 1965, Lebreton et al. 1992, Mazerolle 2015).

Source

Cormack, R. M. (1964) Estimates of survival from the sighting of marked animals. Biometrika 51, 429–438.

Gill, D. E. (1985) Interpreting breeding patterns from census data: a solution to the Husting dilemma. Ecology 66, 344–354.

Jolly, G. M. (1965) Explicit estimates from capture-recapture data with both death and immigration: stochastic model. Biometrika 52, 225–247.

Laake, J. L. (2013) RMark: an R interface for analysis of capture-recapture data with MARK. Alaska Fisheries Science Center (AFSC), National Oceanic and Atmospheric Administration, National Marine Fisheries Service, AFSC Report 2013-01.

Lebreton, J.-D., Burnham, K. P., Clobert, J., Anderson, D. R. (1992) Modeling survival and testing biological hypotheses using marked animals: a unified approach with case-studies. Ecological Monographs 62, 67-118.

Mazerolle, M. J. (2015) Estimating detectability and biological parameters of interest with the use of the R environment. Journal of Herpetology 49, 541–559.

Seber, G. A. F. (1965) A note on the multiple-recapture census. Biometrika 52, 249–259.

Examples

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data(newt)
str(newt)

##convert raw capture data to capture histories
captures <- newt[, c("T1975", "T1976", "T1977", "T1978", "T1979",
                      "T1980", "T1981", "T1982", "T1983")]
newt.ch <- apply(captures, MARGIN = 1, FUN = function(i)
                  paste(i, collapse = ""))

##organize as a data frame readable by RMark package (Laake 2013)
##RMark requires at least one column called "ch" 
##and another "freq" if summarized captures are provided
newt.full <- data.frame(ch = rep(newt.ch, 2),
                        freq = c(newt$Males, newt$Females),
                        Sex = c(rep("male", length(newt.ch)),
                        rep("female", length(newt.ch))))
str(newt.full)
newt.full$ch <- as.character(newt.full$ch)

##delete rows with 0 freqs
newt.full.orig <- newt.full[which(newt.full$freq != 0), ]

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