Dataset Catalogue

Every dataset is simulated for teaching and reproduced exactly by its seeded script in scripts/. All use the three farms: Aysén Salmon Co., Lago Verde Tilapia, Camarones del Golfo.

File (`data/`)	Rows	Used in	What it holds	Generator (`scripts/`)
`aquafarms_register.csv`	24	Ch 2–3	one-month health snapshot per unit (temp, stocking, mortality, PCR)	`make_aquafarms_register.R`
`weekly_monitoring.csv`	36	Ch 4, 13	12-week cohort per farm with an outbreak	`make_weekly_monitoring.R`
`bkd_watersource.csv`	16	Ch 5, 7	BKD by water source (river vs RAS)	`make_bkd_watersource.R`
`srs_diagnostics.csv`	400	Ch 6	qPCR, Ct, culture vs reference status	`make_srs_diagnostics.R`
`srs_confounding.csv`	1000	Ch 9	lice, SRS, season (confounding)	`make_srs_confounding.R`
`srs_vaccine.csv`	60	Ch 10	vaccinated vs not: mortality + time to outbreak	`make_srs_vaccine.R`
`amr_isolates.csv`	427	Ch 11	florfenicol MIC / S-I-R by year & genogroup	`make_amr_isolates.R`
`regional_srs_weekly.csv`	104	Ch 12, 13	2-year regional weekly case counts	`make_regional_srs_weekly.R`
`farms_spatial.csv`	40	Ch 14	farm coordinates + SRS mortality	`make_spatial_network.R`
`movements.csv`	~113	Ch 14	site-to-site movement edge list	`make_spatial_network.R`
`lice_srs_studies.csv`	6	Ch 15	study-level effect sizes for meta-analysis	`make_meta_studies.R`
`srs_challenge_families.csv`	2000	Ch 16	family challenge-test survival (heritability)	`make_srs_challenge_families.R`

Regenerating a dataset

# from the project root, in R:
source("scripts/make_aquafarms_register.R")

Each script sets a fixed seed, so re-running it reproduces the identical file.

Exercise solutions

Worked solutions to the end-of-chapter exercises are maintained separately and released alongside the teaching edition. Each exercise is designed to be solved with the code shown in its chapter; the datasets above are all that is required.