Supplemental material for:
"Hidden cost of disease in a free-ranging ungulate: brucellosis reduces mid-winter pregnancy in elk" Cotterill et al., 2018
Data files:
1) age-prev.csv
"Age" denotes the age of individual elk during mid-winter.
"prev" denotes a modeled estimate for age-specific seroprevalence of brucellosis across 20+ years of data collection at 23 feedgrounds. These are the point estimates from a generalized additive model.
2) calf-data.csv
"Capture_Year" corresponds to the year in which the feeding season ended.
"Capture_Location" corresponds to a specific feedground.
"Calf_Ratio" is an extrapolated number of calves per 100 female elk based on ground counts performed at feedgrounds during peak winter.
3) preg-data.csv
"UID" is a unique identifier which enables tracking individuals over time.
"FPA" is the fluorescent polarization assay score in millipolarization units.
"Capture_Date" is the day when an animal was processed for serology or pregnancy testing.
"Capture_Year", self-explanatory.
"pregnant": 1 = pregnant, 0 = not pregnant
"s": a categorical interpretation of serostatus where 1 = seropositive, 0 = seronegative.
"m": method used for determining pregnancy where 1 = PSPB, 0 = transrectal ultrasound.
"year_id" is an integer value corresponding to the capture year for use in STAN programming language.
"age_id" is an integer value where 1-19 correspond to actual ages, 20 corresponds to unknown age.
"age_class2" is an integer value where 1-4 correspond to age bins used in analyses (yearling, 2 years old, 3-9 years old, 10+ years old) and 5 corresponds to unknown age.
4) prev-data.csv
"Capture_Location", self-explanatory.
"Capture_Year", self-explanatory.
"prev": herd-level seroprevalence for a given feedground in a given year. These are point estimates from generalized additive models fit to each of the sites which had the most robust longitudinal data.
Annotated code files
1) main_models.R: Includes main pregnancy models, the creation of figures 1 and 2, Appendix C, figures C2 and D2.
2) fpa_tsi_and_jd.R: Includes FP, time-since-infection, and Julian day analyses, appendices A and B.
3) calf_cow.R: Includes calf:cow analysis and figure 1 in appendix D.