Encounter Histories Format
Each data type of Program MARK requires a primary form of data entry provided by the encounter histories. Encounter histories can be either information on only live encounters (LLLL) or information on both live and dead encounters (LDLDLDLD). In addition, some data types allow a summary format that reduces the amount of input. The following table summaries the input for each data type as specified in the encounter histories file.
Data TypeEncounter History Format Additional Input Format, Notes
Recaptures only (CJS) LLLL allows . in enc. hist.
Recoveries only LDLDLDLD Recovery matrix
Both (Burnham) LDLDLDLD
Known Fate LDLDLDLD Known fate
Closed Captures LLLL
BTO Ring Recoveries LDLDLDLD Recovery matrix
Robust Design LLLL
Both (Barker) LDLDLDLD
Multi-strata Recaptures LLLL
Brownie et al. Recoveries LDLDLDLD Recovery matrix
Huggins' Closed Captures LLLL
Robust Design (Huggins Est.) LLLL
Pradel Recruitment only LLLL
Pradel Survival and Seniority LLLL
Pradel Survival and Lambda LLLL
Pradel Survival and RecruitmentLLLL
Barker Robust Design LDLDLDLD
VPA -- Virtual Population Analysis LDLDLDLD
Multi-strata -- Live and Dead Enc.LDLDLDLD
Closed Captures with Het. LLLL
Full Closed Captures with Het. LLLL
Nest Survival LDLDLDLD Nest survival
Occupancy Estimation LLLL allows . in enc. hist.
Robust Design Occupancy EstimationLLLL allows . in enc. hist.
Open Robust Design Multi-strataLLLL
Closed Robust Design Multi-strataLLLL
Density using radio-tracking LLLL grid total allows . in enc. hist.
Following each encounter encounter history is the number of animals with this encounter history for each group (known as frequencies). One or more spaces are used to separate the encounter history from the frequencies. Note that frequencies are counts, and are not limited to just the values of 0 and 1. In other words, the frequencies are not indicator or dummy variables to specify the group identification. The frequencies are used in the log likelihood to provide the observed number of animals with this cell probability in the form observed*log(probability).
If individual covariates are included, these values follow the frequencies for each group. Typically with individual covariates, only one frequency will be non-zero, usually with a value of 1 because only one animal would have the specific set of individual covariate values. One or more speces are used to separate the individual covariates.
A semicolon terminates the input for each encounter history.