Study 2 datasets from: Harfoot, M. B. J., Newbold T., Tittensor, D. P., Emmott, S., Hutton, J., Lyutsarev, V., Smith, M. J., Scharlemann, J. P. W., Purves, D. W. (2014), Emergent global patterns of ecosystem structure and function from a mechanistic General Ecosystem Model, PLoS Biology. Email: mike.harfoot@unep-wcmc.org This study is comprised of a single simulation for each of the 4 focal grid cells listed in Table 4 of the manuscript. The folder contains a set of files which contain information about how the model was set up and parameterised for this set of studies: these are briefly described below - refer to the ReadMe-ModelSetup.txt file for a more detailed description of these files. CohortFunctionalGroupDefinitions.csv - contains the list of heterotrophic functional groups defined for these simulations and the values of traits for each. EcosystemModelInitialisation.csv - lists the model setup parameters for these simulations EnvironmentalDataLayers.csv - details the environmental data files to be used in this simulation Parameters.txt - lists the parameters used in the model for these simulations Scenarios.csv - contains the scenario types and number of simulations within this ensemble SpecificLocations.csv - details the locations of the grid cells used in this set of simulations StockFunctionalGroupDefinitions.csv - contains the autotrophic functional groups defined for these simulations In addition to these files there are a set of output files for a set of cells, indexed by [cell index] that are described below: _______________________________________________________ BasicOutputs_no_0_Cell[cell index].nc _______________________________________________________ File of type NetCDF. Contains outputs for a set of variables for a specific grid cell and simulation. Variables are of the type: biomass density [kg km-2]: The wet matter biomass density of the set of organisms in . Dimension = timestep density [Individuals km-2]: The count of number of individuals per km2 of the set of organisms in . Dimension = timestep Where includes: Autotroph: Above ground non-structural plant matter (terrestrial cells) or phytoplankton (marine cells). Carnivore: Organisms belonging to functional groups whose nutrition source is carnivory ("DEFINITION_Nutrition source" is Carnivore in CohortFunctionalGroupDefinitions.csv) Deciduous: Deciduous above ground non-structural plant matter (terrestrial cells only) Ectotherm: Organisms belonging to functional groups whose metabolic pathway is ectothermy ("DEFINITION_Endo/Ectotherm" is Ectotherm in CohortFunctionalGroupDefinitions.csv) Endotherm: Organisms belonging to functional groups whose metabolic pathway is endothermy ("DEFINITION_Endo/Ectotherm" is Endotherm in CohortFunctionalGroupDefinitions.csv) Evergreen: Eergreen above ground non-structural plant matter (terrestrial cells only) Herbivore: Organisms belonging to functional groups whose nutrition source is herbivory ("DEFINITION_Nutrition source" is Herbivore in CohortFunctionalGroupDefinitions.csv) Omnivore: Organisms belonging to functional groups whose nutrition source is omnivory ("DEFINITION_Nutrition source" is Omnivore in CohortFunctionalGroupDefinitions.csv) na: Not used And the following s that are specific to marine cells only: Baleen whales: Organisms belonging to a functional group corresponding to baleen whales. Obligate zooplankton: Organisms belonging to a functional group corresponding to oligate zooplankton. Zooplankton: Organisms that have a current body mass lower than the plankton threshold (set by "Plankton Size Threshold" in EcosystemModelInitialisation.csv). Incoming NPP [gC m-2 day-1]: Marine net primary production used in the model. Dimension = timestep _______________________________________________________ Extinction_no_0_Cell[cell index].txt _______________________________________________________ A tab-delimited text file containing information on when cohorts were made extinct: Latitude [decimal degrees]: the latitude of the grid cell Longitude [decimal degrees]: the longitude of the grid cell time_step: the timestep in which the extinction event occurred merged [boolean]: whether the cohorts had been previously merged during its lifetime cohortID: the ID number of the cohort being removed from the model _______________________________________________________ Growth_no_0_Cell[cell index].txt _______________________________________________________ A tab-delimited text file containing information on the growth rate of cohorts through time: Latitude [decimal degrees]: the latitude of the grid cell Longitude [decimal degrees]: the longitude of the grid cell time_step: the timestep in which the extinction event occurred Current_body_mass_g [g]: the current body mass of the cohort functional_group: the functional group to which the cohort belongs (a zero based index that links to the functional groups defined in CohortFunctionalGroupDefinitions.csv) growth_g [g]: the biomass accumulated for growth metabolism_g [g]: the biomass metabolised predation_g [g]: the biomass assimilated from predation herbivory_g [g]: the biomass assimilated from herbivory _________________________________________________________ MassBinOutputs_no_0_Cell[cell index].nc _________________________________________________________ A NetCDF file containing abundances and biomass densities of organisms within current body mass or juvenile and adult mass bins. Variables are of the format: Log abundance in juvenile vs adult mass bins [log(individuals)]: the number of individuals in each juvenile and adult mass bin in each time step. Dimensions = Time step, Juvenile Mass bin, Adult Mass bin Log abundance in mass bins [log(individuals)]: the number of individuals in each current body mass bin in each time step. Dimensions = Time step, Mass bin Log biomass in juvenile vs adult mass bins [log(g)]: the biomass of organisms in each juvenile and adult mass bin in each time step. Dimensions = Time step, Juvenile Mass bin, Adult Mass bin Log biomass in mass bins [log(g)]: the biomass of organisms in each current body mass bin in each time step. Dimensions = Time step, Mass bin Where is: carnivore carnivore ectotherm carnivore endotherm ectotherm endotherm herbivore herbivore ectotherm herbivore endotherm omnivore omnivore ectotherm omnivore endotherm _________________________________________________________ Maturity_no_0_Cell[cell index].txt _________________________________________________________ A tab-delimited text file listing the timestep in which cohorts reach reproductive maturity (when their current body mass reaches their adult body mass): Latitude [decimal degrees]: the latitude of the grid cell Longitude [decimal degrees]: the longitude of the grid cell time_step: the timestep in which the extinction event occurred birth_step: the timestep in which the cohort was born into the model juvenile Mass [g]: the juvenile mass of the cohort adult mass [g]: the adult mass of the cohort functional_group: the functional group to which the cohort belongs (a zero based index that links to the functional groups defined in CohortFunctionalGroupDefinitions.csv) _________________________________________________________ Metabolism_no_0_Cell[cell index].txt _________________________________________________________ A tab-delimited text file listing the metabolic losses of cohorts in each timestep: Latitude [decimal degrees]: the latitude of the grid cell Longitude [decimal degrees]: the longitude of the grid cell time_step: the timestep in which the extinction event occurred Current_body_mass [g]: the current body mass of the cohort functional_group: the functional group to which the cohort belongs (a zero based index that links to the functional groups defined in CohortFunctionalGroupDefinitions.csv) Ambient_temp [degrees C]: the ambient temperature experienced by the cohort Metabolic_mass_loss [g]: the change in body mass as a result of metabolism (negative values indicate mass loss) _________________________________________________________ Mortality_no_0_Cell[cell index].txt _________________________________________________________ A tab-delimited text file listing the numbers of individuals per cohort being lost to mortality in each timestep: Latitude [decimal degrees]: the latitude of the grid cell Longitude [decimal degrees]: the longitude of the grid cell birth_step: the timestep in which the cohort was born into the model time_step: the timestep in which the extinction event occurred current mass [g]: the current body mass of the cohort adult mass [g]: the adult mass of the cohort functional_group: the functional group to which the cohort belongs (a zero based index that links to the functional groups defined in CohortFunctionalGroupDefinitions.csv) cohortID: the ID number of the cohort being removed from the model number died [individuals]: the number of individuals died mortality source: the process leading to that mortality ("predation" or "sen/bg/starv") _________________________________________________________ NewCohorts_no_0_Cell[cell index].txt _________________________________________________________ A tab-delimited text file listing the metabolic losses of cohorts in each timestep: Latitude [decimal degrees]: the latitude of the grid cell Longitude [decimal degrees]: the longitude of the grid cell time_step: the timestep in which the extinction event occurred abundance [individuals]: the number of individuals in the offspring cohort functional group: the functional group to which the cohort belongs (a zero based index that links to the functional groups defined in CohortFunctionalGroupDefinitions.csv) adult mass [g]: the adult mass of the parent cohort parent cohort IDs: the ID number of the parent cohort offspring cohort ID: the ID number of the offspring cohort __________________________________________________________ PredationFlows_no_0_Cell[cell index].txt __________________________________________________________ A NetCDF file containing the log-transformed biomasses eaten from prey mass bins for each predator mass bin: Log mass (g) [log(g)]: the biomass being eaten by a predator mass bin from a prey mass bin. Dimensions = Time steps, Predator mass bin, Prey mass bin ____________________________________________________________________ TrackedCohortsProperties_no_0_Cell[cell index].txt ____________________________________________________________________ A tab-delimited text file containing the properties of specific cohorts tracked in the model Output ID: an output index Cohort ID: the ID number of each cohort Functional group index: the functional group to which the cohort belongs (a zero based index that links to the functional groups defined in CohortFunctionalGroupDefinitions.csv) Nutrition source: the feeding mode of the cohort (as defined by the trait value of "DEFINITION_Nutrition source" in CohortFunctionalGroupDefinitions.csv for the cohort's functional group) Diet: the diet value of the cohort (as defined by the trait value of "DEFINITION_Diet" in CohortFunctionalGroupDefinitions.csv for the cohort's functional group) Realm: The realm to which the cohort belongs (as defined by the trait value of "DEFINITION_Realm" in CohortFunctionalGroupDefinitions.csv for the cohort's functional group) Mobility: The mobility trait for the cohort (as defined by the trait value of "DEFINITION_Mobility" in CohortFunctionalGroupDefinitions.csv for the cohort's functional group) Juvenile mass [g]: the juvenile mass of the cohort Adult mass [g]: the adult mass of the cohort ___________________________________________________________________ TrackedCohortsOutputs_no_0_Cell[cell index].nc ___________________________________________________________________ A NetCDF file containing the individual body masses and number of individuals for tracked cohorts: CohortID: the ID number of each cohort Individual body mass [g]: the body mass of individuals in each tracked cohort. Dimensions = CohortID, Time step Number of individuals [individuals]: the number of individuals in each tracked cohort. Dimensions = CohortID, Time step ___________________________________________________________________ TrophicFlows_no_0_Cell[cell index].txt ___________________________________________________________________ A tab-delimited text file listing the flow of biomass between trophic levels: Latitude [decimal degrees]: the latitude of the grid cell Longitude [decimal degrees]: the longitude of the grid cell time_step: the timestep in which the extinction event occurred fromIndex: the trophic level index of the prey item [0 = autotrophs, 1 = non-planktonic herbivores, 2 = non-planktonic omnivores, 3 = non-planktonic carnivores, 4 = obligate zooplankton, 5 = non-obligate zooplankton, 6 = baleen whales] toIndex: the trophic level index of the predator cohort [0 = autotrophs, 1 = non-planktonic herbivores, 2 = non-planktonic omnivores, 3 = non-planktonic carnivores, 4 = obligate zooplankton, 5 = non-obligate zooplankton, 6 = baleen whales] Note that a trophic flow from index 0 to index 0 indicates the net primary productivity of autotrophs