AICcmodavg (version 2.1-1)

salamander: 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

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).

Examples

# NOT RUN {
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), ]
# }