Salamander Capture-mark-recapture Data

Description

This is a capture-mark-recapture data set on male and female Spotted Salamanders (Ambystoma maculatum) recorded by Husting (1965). A total of 1244 unique individuals were captured in pitfall traps at a breeding site between 1959 and 1963.

Usage

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data(salamander)

Format

A data frame with 36 observations on the following 7 variables.

T1959

a binary variable, either 1 (captured) or 0 (not captured) during the 1959 breeding season.

T1960

a binary variable, either 1 (captured) or 0 (not captured) during the 1960 breeding season.

T1961

a binary variable, either 1 (captured) or 0 (not captured) during the 1961 breeding season.

T1962

a binary variable, either 1 (captured) or 0 (not captured) during the 1962 breeding season.

T1963

a binary variable, either 1 (captured) or 0 (not captured) during the 1963 breeding season.

Males

a numeric variable indicating the total number of males with a given capture history. Negative values indicate losses on capture (animals not released on last capture).

Females

a numeric variable indicating the total number of females with a given capture history. Negative values indicate losses on capture (animals not released on last capture).

Details

This data set is used to illustrate classic Cormack-Jolly-Seber and related models (Cormack 1964, Jolly 1965, Seber 1965, Lebreton et al. 1992).

Source

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

Husting, E. L. (1965) Survival and breeding structure in a population of Ambystoma maculatum. Copeia 1965, 352–362.

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.

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

Examples

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data(salamander)
str(salamander)

##convert raw capture data to capture histories
captures <- salamander[, c("T1959", "T1960", "T1961", "T1962", "T1963")]
salam.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
salam.full <- data.frame(ch = rep(salam.ch, 2),
                         freq = c(salamander$Males, salamander$Females),
                         Sex = c(rep("male", length(salam.ch)),
                           rep("female", length(salam.ch))))
str(salam.full)
salam.full$ch <- as.character(salam.full$ch)

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

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