R scripts and data files used to process, analyse and visualise eReefs catchment counter-factual scenario model data for the paper, "Kroon, Frederieke J., Joseph R. Crosswell, and Barbara J. Robson. The effect of catchment load reductions on water quality in the crown-of-thorn starfish outbreak initiation zone. Marine Pollution Bulletin 195 (2023): 115255." Four R scripts are included: cots1.R extracts all data from the eReefs model scenario outputs and produces an R data file for each scenario. These intermediate data files are not provided but can be re-created using this script and the original eReefs model data. cots_reprocess.R puts all six scenarios into one combined dataframe and produces daily_values_all_scenarios3.rda or daily_values_all_scenarios3_large.rda, depending on settings. These intermediate data files are not provided. ccip_salinity.R extracts salinity from the baseline scenario and adds it to the dataframe for all scenarios, producing daily_values_all_scenarios4.rda or daily_values_all_scenarios4_large.rda, depending on settings. These final data files are provided. cots_analysis.R produces the figures and tables used in the manuscript. Data used come from eReefs model counter-factual scenarios produced by CSIRO and available from https://dapds00.nci.org.au/thredds/catalogs/fx3/catalog.html

The activity of aminoacyl-tRNA synthetase (AARS), an index of growth rate, and of the electron transport system (ETS), an index of respiration, was measured in three size fractions (73-150 µm, >150 µm and >350 µm) of zooplankton during five cruises to tropical coastal waters of the Kimberley coast (North West Australia) and four cruises to waters of the Great Barrier Reef (GBR, North East Australia). Temperature, salinity and chlorophyll a data was also recorded. Data enables comparison of growth and secondary production of tropical zooplankton from waters of NW and NE Australia based on both AARS and ETS measurements, and also facilitates comparison of zooplankton respiration derived from ETS measurements. These estimates of growth and respiration enable calculation of grazing rates to better understand the fate of primary production in Australian tropical waters and the nature of pelagic food chains in these regions.