DOI: 10.5061/dryad.3hd6sb6/1
title: Rabbit capture-mark-recapture and serology (disease) state data

description: Rabbit capture-mark-recapture and serology (disease) state data of 2,200 selected rabbit individuals with unequivocal serology data for all capture events live-captured at Turretfield Agricultural Research Centre (34°33′S, 138°50′E, South Australia) between January 2000 and August 2016 at 8-12 week intervals. All live captures were uniquely marked with serially numbered ear tags, weighed to the nearest 10 g and sexed. Blood was collected from an ear vein for serological tests of rabbit haemorrhagic disease virus (RHDV) and myxoma virus (MYXV) antibodies. Additionally, the study area and warrens were regularly surveyed for dead rabbits at intervals ≤ four weeks, increasing to weekly searches during spring (Sept-Nov) when epizootics were most likely to occur, and at 1-7 day intervals following any evidence of disease-related mortality.
Capture events are assigned to capture session (n = 83) The date of the capture session was calculated as the median date of all captures made during a capture session and given as the number of days elapsed after the first date of capture (i.e. 19/01/2000 corresponds to day count ‘1’). Capture sessions were also assigned to one of the following (southern hemispheric) seasons according to local climate: 1 = Autumn: Mar – May, 2 = Winter: Jun – Aug, 3 = Spring: Sept-Nov, 4 = Summer: Dec-Feb.
The full data set with further details is hold by Biosecurity SA, Adelaide, Australia.

Data are arranged in 7 spreadsheets with the content described below.
1) ‘y’
Table of capture events/ individual encounter histories y, denoting the capture of individuals in the different capture session as “1” if an individual has been captured and “0” otherwise. Individuals are identified in the column “indNo”, the columns entitled “trip_1” to “trip_83” refer to the different capture session.
2) ‘z’
Table of the (partially known) state variable z, denoting of whether an individual is known to be 1= alive, 0 = dea or NA = in an unknown state. Individuals are identified in the column “indNo”, the columns entitled “trip_1” to “trip_83” refer to the different capture session.
3) ‘d_RHDV'
Table of RHDV disease state, classifying rabbits as 1 = seronegative (“susceptible”) 2 = seropositive kittens with maternal antibodies (“protected young”) and 3 = seropositive due to previous infection (“immune”). Individuals are identified in the column “indNo”, the columns entitled “trip_1” to “trip_83” refer to the different capture session.
4) ‘d_MYXV'
Table of MYXV disease state, classifying rabbits as 1 = seronegative with no detectable antibodies and therefore susceptible to infection/disease (“susceptible”) or 2 = seropositive with antibodies against disease. Individuals are identified in the column “indNo”, the columns entitled “trip_1” to “trip_83” refer to the different capture session.
5) ‘individuals’
Table of individual attributes used in the capture-mark-recapture analysis, namely "sex": individual gender; "birthmin": minimum day count of possible birth date; "birthmax": maximum day count of possible birth date; "trip_LowerLimit": earliest capture session for which individual data are modelled according to unknown states variables z;  "trip_UpperLimit": latest capture session for which individual data are modelled according to unknown state variables z.
6) ‘capture session’
Table of capture session classifications, with "trip_No":  identification number of capture session	“daycount”: day count of capture session; “season” season classification (see above); “year”: year of capture session (‘1’ corresponds to the year 2000); “deltaT”: scaling factor to account for unequal time intervals between capture sessions.
7) ‘individuals’
Table of body mass measures of rabbit individuals during various individual capture events with “indNo”: individual number;	weight” body mass measure (in gram); “daycount”” day count of individual capture events.