R code and data from: Preserving identity in capture-mark-recapture studies: Increasing the accuracy of minimum number alive (MNA) estimates by incorporating inter-census trapping efficiency variation

Each file is summarized below: Abundance estimation script.R: an R code file with detailed workflow for computing and testing a number of abundance enumeration metrics according to the text laid out in "Preserving identity in capture-mark-recapture studies: Increasing the accuracy of minimum number alive (MNA) estimates by incorporating inter-census trapping efficiency variation". Prepared badger data.RData: R objects prepared from badger data, used in the analysis from the paper. Comprises the following objects: - trueAlive, a matrix with rows for individuals and columns for years. 1s indicate an individual was alive in a given year; 0s indicate it was not. - trueAge, a matrix with the same structure as trueAlive, but where each position indicates the individual's age in that year. - trueTeeth, a matrix with the same structure as trueAlive and trueAge, but where each position indicates the toothwear of the individual on a scale of 1 to 5. - toothAgeMod, a model that contains the relationship between tooth-wear and age. - trueSex, a vector with the sex of each individual corresponding to the row in the life-history and context matrices.