search_index.js

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[{"location":"nature.html#Nature","page":"Nature","title":"Nature","text":"","category":"section"},{"location":"nature.html#nature.jl","page":"Nature","title":"nature.jl","text":"","category":"section"},{"location":"nature.html","page":"Nature","title":"Nature","text":"This file is responsible for managing the animal modules.","category":"page"},{"location":"nature.html","page":"Nature","title":"Nature","text":"Modules = [Persefone]\nPages = [\"nature/nature.jl\"]","category":"page"},{"location":"nature.html#Persefone.Animal","page":"Nature","title":"Persefone.Animal","text":"Animal\n\nThis is the generic agent type for all animals. Species are differentiated by trait dictionaries passed by them during initialisation. (Note that each trait variable can still be accessed as if it were a normal field name, i.e. the trait phase can be accessed and modified with animal.phase.)\n\n\n\n\n\n","category":"type"},{"location":"nature.html#Persefone.animalid-Tuple{Animal}","page":"Nature","title":"Persefone.animalid","text":"animalid(animal)\n\nA small utility function to return a string with the species name and ID of an animal.\n\n\n\n\n\n","category":"method"},{"location":"nature.html#Persefone.initnature!-Tuple{Agents.AgentBasedModel}","page":"Nature","title":"Persefone.initnature!","text":"initnature!(model)\n\nInitialise the model with all simulated animal populations.\n\n\n\n\n\n","category":"method"},{"location":"nature.html#Persefone.stepagent!-Tuple{Animal, Agents.AgentBasedModel}","page":"Nature","title":"Persefone.stepagent!","text":"stepagent!(animal, model)\n\nUpdate an animal by one day, executing it's currently active phase function.\n\n\n\n\n\n","category":"method"},{"location":"nature.html#Persefone.@countanimals-Tuple","page":"Nature","title":"Persefone.@countanimals","text":"@countanimals(species=\"\", radius=0)\n\nCount the number of animals of the given species in this location. This is a utility wrapper that can only be used nested within @phase or @habitat.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@cropheight-Tuple{}","page":"Nature","title":"Persefone.@cropheight","text":"@cropheight\n\nReturn the height of the crop at this position, or 0 if there is no crop here. This is a utility wrapper that can only be used nested within @phase or @habitat.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@croptype-Tuple{}","page":"Nature","title":"Persefone.@croptype","text":"@croptype\n\nReturn the local croptype, or nothing if there is no crop here. This is a utility wrapper that can only be used nested within @phase or @habitat.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@distanceto-Tuple{Any}","page":"Nature","title":"Persefone.@distanceto","text":"@distanceto(habitat)\n\nCalculate the distance to the closest habitat of the specified type or descriptor. This is a utility wrapper that can only be used nested within @phase or @habitat.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@distancetoedge-Tuple{}","page":"Nature","title":"Persefone.@distancetoedge","text":"@distancetoedge\n\nCalculate the distance to the closest neighbouring habitat. This is a utility wrapper that can only be used nested within @phase or @habitat.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@habitat-Tuple{Any}","page":"Nature","title":"Persefone.@habitat","text":"@habitat\n\nSpecify habitat suitability for spatial ecological processes.\n\nThis macro works by creating an anonymous function that takes in a model object and a position, and returns true or false depending on the conditions specified in the macro body.\n\nSeveral utility macros can be used within the body of @habitat as a short-hand for common expressions: @landcover, @croptype, @cropheight, @distanceto, @distancetoedge, @countanimals. The variables model and pos can be used for checks that don't have a macro available.\n\nTwo example uses of @habitat might look like this:\n\nmovementhabitat = @habitat(@landcover() in (grass agriculture soil))\n\nnestinghabitat = @habitat((@landcover() == grass || \n                           (@landcover() == agriculture && @croptype() != maize &&\n                            @cropheight() < 10)) &&\n                          @distanceto(forest) > 20)\n\nFor more complex habitat suitability checks, the use of this macro can be circumvented by directly creating an equivalent function.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@initialise-Tuple{Any, Vararg{Any}}","page":"Nature","title":"Persefone.@initialise","text":"@initialise(habitatdescriptor; kwargs...)\n\nCall this macro within the body of @species. It passes the given habitat descriptor function and keyword arguments on to initpopulation when setting up the simulation.\n\nNote: if this macro is not used, the variable initialise! must be set manually in the species definition.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@kill-Tuple","page":"Nature","title":"Persefone.@kill","text":"@kill\n\nKill this animal (and immediately abort its current update). This is a thin wrapper around kill!, and passes on any arguments. This can only be used nested within @phase.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@landcover-Tuple{}","page":"Nature","title":"Persefone.@landcover","text":"@landcover\n\nReturns the local landcover. This is a utility wrapper that can only be used nested within @phase or @habitat.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@neighbours-Tuple{Any}","page":"Nature","title":"Persefone.@neighbours","text":"@neighbours(radius)\n\nReturn an iterator over all animals in the given radius around this animal, excluding itself. This can only be used nested within @phase.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@phase-Tuple{Any, Any}","page":"Nature","title":"Persefone.@phase","text":"@phase(name, body)\n\nThis macro is designed to be used within a species definition block (i.e. within the body of a call to @species).\n\nThe idea behind this is that species show very different behaviour during different phases of their lives. Therefore, @phase can be used define the behaviour for one such phase, and the conditions under which the animal transitions to another phase.\n\n@phase works by creating a function that will be called by the model if the animal is in the relevant phase. When it is called, it has access to the following variables:\n\nanimal a reference to the animal itself. This provides access to animal.age,   animal.sex, and animal.<trait> (where <trait> is a variable that was defined   in the top part of the species definition body).\npos gives the animal's current position as a coordinate tuple.\nmodel a reference to the model world (an object of type AgentBasedModel).   This allows access to model.date (the current simulation date) and   model.landscape (a two-dimensional array of pixels containing geographic   information).\n\nSeveral utility macros can be used within the body of @phase as a short-hand for common expressions: @trait, @setphase, @respond, @kill, @reproduce, @neighbours, @rand, @shuffle!.\n\nNote that the first phase that is defined in a species definition block will be the phase that animals are assigned at birth, unless the variable phase is explicitly defined by the user in the species definition block.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@reproduce-Tuple","page":"Nature","title":"Persefone.@reproduce","text":"@reproduce\n\nLet this animal reproduce. This is a thin wrapper around reproduce!, and passes on any arguments. This can only be used nested within @phase.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@respond-Tuple{Any, Any}","page":"Nature","title":"Persefone.@respond","text":"@respond(eventname, body)\n\nDefine how an animal responds to a landscape event that affects its current position. This can only be used nested within @phase.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@setphase-Tuple{Any}","page":"Nature","title":"Persefone.@setphase","text":"@setphase(newphase)\n\nSwitch this animal over to a different phase. This can only be used nested within @phase.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@species-Tuple{Any, Any}","page":"Nature","title":"Persefone.@species","text":"@species(name, body)\n\nA macro used to create new species definitions for the nature model. This is effectively a simple domain-specific language, establishing a custom syntax to describe species' biology:\n\n@species name begin\n\n    @initialise(@habitat(...))\n    speciesvar1 = 3.14\n    ...\n\n    @phase phase1 begin\n        ...\n    end\nend\n\nThe definition body (enclosed in the begin/end block) has two sections. First comes a call to @initialise, and optionally a list of species-specific parameters, which are assigned just like normal variables. Second come one or more phase definitions, that describe the behaviour of the species during various parts of its life cycle. (See the documentation to @initialise and @phase for details).\n\nCode in a species definition block can access the rest of the model using the model variable (an object of type AgentBasedModel).\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#Persefone.@trait-Tuple{Any}","page":"Nature","title":"Persefone.@trait","text":"@trait(traitname)\n\nA utility macro to quickly access an animal's trait value. This can only be used nested within @phase.\n\n\n\n\n\n","category":"macro"},{"location":"nature.html#populations.jl","page":"Nature","title":"populations.jl","text":"","category":"section"},{"location":"nature.html","page":"Nature","title":"Nature","text":"This file contains a set of utility functions for species, including initialisation, reproduction, and mortality.","category":"page"},{"location":"nature.html","page":"Nature","title":"Nature","text":"Modules = [Persefone]\nPages = [\"nature/populations.jl\"]","category":"page"},{"location":"nature.html#Persefone.countanimals-Tuple{Tuple{Int64, Int64}, Agents.AgentBasedModel}","page":"Nature","title":"Persefone.countanimals","text":"countanimals(pos, model; species=\"\", radius=0)\n\nCount the number of animals in this location (optionally supplying a species name and radius).\n\n\n\n\n\n","category":"method"},{"location":"nature.html#Persefone.initpopulation-Tuple{Function}","page":"Nature","title":"Persefone.initpopulation","text":"initpopulation(habitatdescriptor; popsize=-1, pairs=false, asexual=false)\n\nCreates a function that initialises individuals at random locations across the landscape. This can be used to create the initialise! variable in a species definition block.\n\nhabitatdescriptor is a function that determines whether a given location is suitable   or not (create this using @habitat).\nphase determines which life phase individuals will be assigned to. If this is nothing,   the species' default post-natal life stage will be used (although note that this is   probably not what you want).\npopsize determines the number of individuals that will be created. If this is zero or   negative, one individual will be created in every suitable location in the landscape.   If popsize is greater than the number of suitable locations, multiple individuals   will be created in one place. (Maximum population density can be set in the habitat   descriptor using the @countanimals macro.)\nIf pairs is true, a male and a female individual will be created in each selected   location, otherwise, only one individual will be created at a time.\nIf asexual is true, all created individuals are assigned the sex hermaphrodite,   otherwise, they are randomly assigned male of female. (If pairs is true, asexual   is ignored.)\n\n\n\n\n\n","category":"method"},{"location":"nature.html#Persefone.initrandompopulation-Tuple{Int64}","page":"Nature","title":"Persefone.initrandompopulation","text":"initrandompopulation(popsize; kwargs...)\n\nA simplified version of initpopulation. Creates a function that initialises popsize individuals, spread at random across the landscape.\n\n\n\n\n\n","category":"method"},{"location":"nature.html#Persefone.kill!","page":"Nature","title":"Persefone.kill!","text":"kill(animal, model, probability=1.0, cause=\"\")\n\nKill this animal, optionally with a given percentage probability. Returns true if the animal dies, false if not.\n\n\n\n\n\n","category":"function"},{"location":"nature.html#Persefone.nearby_animals-Tuple{Animal, Agents.AgentBasedModel, Int64}","page":"Nature","title":"Persefone.nearby_animals","text":"nearby_animals(animal, model, radius)\n\nReturn an iterator over all animals in the given radius around this animal, excluding itself.\n\n\n\n\n\n","category":"method"},{"location":"nature.html#Persefone.nearby_animals-Tuple{Tuple{Int64, Int64}, Agents.AgentBasedModel, Int64}","page":"Nature","title":"Persefone.nearby_animals","text":"nearby_animals(pos, model, radius)\n\nReturn an iterator over all animals in the given radius around this position.\n\n\n\n\n\n","category":"method"},{"location":"nature.html#Persefone.reproduce!","page":"Nature","title":"Persefone.reproduce!","text":"reproduce!(animal, model, n=1)\n\nProduce one or more offspring for the given animal at its current location.\n\n\n\n\n\n","category":"function"},{"location":"nature.html#ecologicaldata.jl","page":"Nature","title":"ecologicaldata.jl","text":"","category":"section"},{"location":"nature.html","page":"Nature","title":"Nature","text":"This file contains a set of life-history related utility functions needed by species.","category":"page"},{"location":"nature.html","page":"Nature","title":"Nature","text":"Modules = [Persefone]\nPages = [\"nature/ecologicaldata.jl\"]","category":"page"},{"location":"nature.html#Persefone.initecologicaldata-Tuple{Agents.AgentBasedModel}","page":"Nature","title":"Persefone.initecologicaldata","text":"initecologicaldata()\n\nCreate output files for each data group collected by the nature model.\n\n\n\n\n\n","category":"method"},{"location":"nature.html#Persefone.saveindividualdata-Tuple{Agents.AgentBasedModel}","page":"Nature","title":"Persefone.saveindividualdata","text":"saveindividualdata(model)\n\nReturn a comma-separated set of lines (to be printed to individuals.csv), listing all properties of all animal individuals in the model. May be called never, daily, monthly, yearly, or at the end of a simulation, depending on the parameter nature.indoutfreq. WARNING: Produces very big files!\n\n\n\n\n\n","category":"method"},{"location":"nature.html#Persefone.savepopulationdata-Tuple{Agents.AgentBasedModel}","page":"Nature","title":"Persefone.savepopulationdata","text":"savepopulationdata(model)\n\nReturn a comma-separated set of lines (to be printed to populations.csv), giving the current date and population size for each animal species. May be called never, daily, monthly, yearly, or at the end of a simulation, depending on the parameter nature.popoutfreq.\n\n\n\n\n\n","category":"method"},{"location":"io.html#Input,-Output,-and-Settings","page":"Input, Output, and Settings","title":"Input, Output, and Settings","text":"","category":"section"},{"location":"io.html","page":"Input, Output, and Settings","title":"Input, Output, and Settings","text":"These functions are responsible for reading in all model configurations (passed by config file or commandline), administrating them during a run, and printing any output.","category":"page"},{"location":"io.html#parameters.toml","page":"Input, Output, and Settings","title":"parameters.toml","text":"","category":"section"},{"location":"io.html","page":"Input, Output, and Settings","title":"Input, Output, and Settings","text":"This is the default configuration file for Persefone, containing all model parameters. The syntax is described here: https://toml.io/en/","category":"page"},{"location":"io.html","page":"Input, Output, and Settings","title":"Input, Output, and Settings","text":"DO NOT MODIFY THIS FILE FOR SIMULATION EXPERIMENTS! Instead, copy it to another directory, modify the copy, and then pass it to the model using the --config parameter.","category":"page"},{"location":"io.html#input.jl","page":"Input, Output, and Settings","title":"input.jl","text":"","category":"section"},{"location":"io.html","page":"Input, Output, and Settings","title":"Input, Output, and Settings","text":"Modules = [Persefone]\nPages = [\"core/input.jl\"]","category":"page"},{"location":"io.html#Persefone.PARAMFILE","page":"Input, Output, and Settings","title":"Persefone.PARAMFILE","text":"The file that stores all default parameters: src/parameters.toml\n\n\n\n\n\n","category":"constant"},{"location":"io.html#Persefone.flattenTOML-Tuple{Any}","page":"Input, Output, and Settings","title":"Persefone.flattenTOML","text":"flattenTOML(dict)\n\nAn internal utility function to convert the two-dimensional dict returned by TOML.parsefile() into a one-dimensional dict, so that instead of writing settings[\"domain\"][\"param\"] one can use settings[\"domain.param\"]. Can be reversed with prepareTOML.\n\n\n\n\n\n","category":"method"},{"location":"io.html#Persefone.getsettings","page":"Input, Output, and Settings","title":"Persefone.getsettings","text":"getsettings(configfile, seed=nothing)\n\nCombines all configuration options to produce a single settings dict. Precedence: commandline parameters - user config file - default values\n\n\n\n\n\n","category":"function"},{"location":"io.html#Persefone.parsecommandline-Tuple{}","page":"Input, Output, and Settings","title":"Persefone.parsecommandline","text":"parsecommandline()\n\nCertain software parameters can be set via the commandline.\n\n\n\n\n\n","category":"method"},{"location":"io.html#Persefone.preprocessparameters-Tuple{Dict{String, Any}, String}","page":"Input, Output, and Settings","title":"Persefone.preprocessparameters","text":"preprocessparameters(settings)\n\nTake the raw input parameters and process them (convert types, perform checks, etc.). This is a helper function for getsettings.\n\n\n\n\n\n","category":"method"},{"location":"io.html#Persefone.@param-Tuple{Any}","page":"Input, Output, and Settings","title":"Persefone.@param","text":"@param(domainparam)\n\nReturn a configuration parameter from the global settings. The argument should be in the form <domain>.<parameter>, for example @param(core.outdir). Possible values for <domain> are core, nature, farm, or crop. For a full list of parameters, see src/parameters.toml.\n\nNote: this macro only works in a context where the model object is available!\n\n\n\n\n\n","category":"macro"},{"location":"io.html#Persefone.@rand-Tuple","page":"Input, Output, and Settings","title":"Persefone.@rand","text":"@rand(args...)\n\nReturn a random number or element from the sample, using the model RNG. This is a utility wrapper that can only be used a context where the model object is available.\n\n\n\n\n\n","category":"macro"},{"location":"io.html#Persefone.@shuffle!-Tuple{Any}","page":"Input, Output, and Settings","title":"Persefone.@shuffle!","text":"@shuffle!(collection)\n\nShuffle the given collection in place, using the model RNG. This is a utility wrapper that can only be used a context where the model object is available.\n\n\n\n\n\n","category":"macro"},{"location":"io.html#output.jl","page":"Input, Output, and Settings","title":"output.jl","text":"","category":"section"},{"location":"io.html","page":"Input, Output, and Settings","title":"Input, Output, and Settings","text":"Modules = [Persefone]\nPages = [\"core/output.jl\"]","category":"page"},{"location":"io.html#Persefone.DataOutput","page":"Input, Output, and Settings","title":"Persefone.DataOutput","text":"DataOutput\n\nA struct for organising model output. This is designed for text-based data output that is updated more or less regularly (e.g. population data in csv files). Submodels can register their own output functions using newdataoutput!.\n\nStruct fields:     - filename: the name of the file to be created in the user-specified output directory     - header: a string to be written to the start of the file as it is initialised     - outputfunction: a function that takes a model object and returns a string to write to file     - frequency: how often to call the output function (daily/monthly/yearly/end/never)\n\n\n\n\n\n","category":"type"},{"location":"io.html#Persefone.createdatadir-Tuple{String, Union{Bool, String}}","page":"Input, Output, and Settings","title":"Persefone.createdatadir","text":"createdatadir(outdir, overwrite)\n\nCreates the output directory, dealing with possible conflicts.\n\n\n\n\n\n","category":"method"},{"location":"io.html#Persefone.modellogger-Tuple{String, String}","page":"Input, Output, and Settings","title":"Persefone.modellogger","text":"modellogger(loglevel, outdir)\n\nCreate a logger object that writes output both to screen and to a logfile. This object is stored as model.logger and can then be used with with_logger(). Note: requires createdatadir to be run first.\n\n\n\n\n\n","category":"method"},{"location":"io.html#Persefone.newdataoutput!-Tuple{Agents.AgentBasedModel, String, String, Function, String}","page":"Input, Output, and Settings","title":"Persefone.newdataoutput!","text":"newdataoutput!(model, filename, header, outputfunction, frequency)\n\nCreate and register a new data output. This function must be called by all submodels that want to have their output functions called regularly.\n\n\n\n\n\n","category":"method"},{"location":"io.html#Persefone.outputdata-Tuple{Agents.AgentBasedModel}","page":"Input, Output, and Settings","title":"Persefone.outputdata","text":"outputdata(model)\n\nCycle through all registered data outputs and activate them according to their configured frequency.\n\n\n\n\n\n","category":"method"},{"location":"io.html#Persefone.prepareTOML-Tuple{Any}","page":"Input, Output, and Settings","title":"Persefone.prepareTOML","text":"prepareTOML(dict)\n\nAn internal utility function to re-convert the one-dimensional dict created by flattenTOML into the two-dimensional dict needed by TOML.print, and convert any data types into TOML-compatible types where necessary.\n\n\n\n\n\n","category":"method"},{"location":"io.html#Persefone.saveinputfiles-Tuple{Agents.AgentBasedModel}","page":"Input, Output, and Settings","title":"Persefone.saveinputfiles","text":"saveinputfiles(model)\n\nCopy all input files into the output directory, including the actual parameter settings used. This allows replicating a run in future.\n\n\n\n\n\n","category":"method"},{"location":"io.html#Persefone.withtestlogger-Tuple{Agents.AgentBasedModel}","page":"Input, Output, and Settings","title":"Persefone.withtestlogger","text":"withtestlogger(model)\n\nReplace the model logger with the currently active logger. This is intended to be used in the testsuite to circumvent a Julia issue, where @test_logs doesn't work with local loggers.\n\n\n\n\n\n","category":"method"},{"location":"architecture.html#Source-code-architecture","page":"Source code architecture","title":"Source code architecture","text":"","category":"section"},{"location":"architecture.html#Model-components","page":"Source code architecture","title":"Model components","text":"","category":"section"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"(Image: \"model architecture\")","category":"page"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"Persefone is divided into four components, three of which are semi-independent submodels:","category":"page"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"core: This is the foundation of the model software, which sets up and executes simulation runs. It also reads in the configuration file and landscape maps, and provides data output functionality. (Eventually, it will also provide weather data.)\nnature: This is an individual-based model of species in agricultural landscapes. It defines the Animal agent type, and a set of macros that can be used to rapidly create new species. It also includes ecological process functions that are useful for all species.\nfarm: This is an agent-based model of farmer decision making. It is not yet implemented, but will provide the Farmer agent type.\ncrop: This is a mathematical growth model for various crops. It is not yet implemented, but already provides the agent type FarmPlot, representing one field and its associated extent and crop type.","category":"page"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"Conceptually, core provides functionality that is needed by all of the submodels. Decisions made by Farmers affect the FarmPlots they own, and (directly or indirectly) the Animals in the model landscape.","category":"page"},{"location":"architecture.html#Important-implementation-details","page":"Source code architecture","title":"Important implementation details","text":"","category":"section"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"(Image: \"the model object\")","category":"page"},{"location":"architecture.html#The-model-object","page":"Source code architecture","title":"The model object","text":"","category":"section"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"A cursory reading of the source code will quickly show that most functions take an  AgentBasedModel object as one of their arguments. This is the key data structure  of Agents.jl, and holds all state that is in any way relevant to a simulation run. (Persefone has a strict \"no global state\" policy to avoid state-dependent bugs and allow parallelisation.) The model object gives access to all agent instances (via model[id], where id is the unique identifier of this agent). It also stores the configuration (model.settings), the landscape (model.landscape, a matrix of Pixel objects that store the local land cover, amongst other things), and the current simulation date (model.date). (See initmodel for details.)","category":"page"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"For more information about working with agent objects, see the  Agents.jl API.","category":"page"},{"location":"architecture.html#Model-configuration/the-@param-macro","page":"Source code architecture","title":"Model configuration/the @param macro","text":"","category":"section"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"The model is configured via a TOML file, the default version of which is at  src/parameters.toml. An individual run can be configured using a user-defined configuration file, commandline arguments, or function calls (when Persefone is used as a package rather than an application). During a model run, the @param macro can be used to access parameter values.  Note that parameter names are prepended with the name of the component they are associated  with. For example, the outdir parameter belongs to the [core] section of the TOML file,  and must therefore be referenced as  @param(core.outdir). (See  src/core/input.jl  for details.)","category":"page"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"info: @param and other macros\nAs @param(parameter) expands to model.settings[\"parameter\"], it can obviously only be used in a context where the model object is actually available. (This is the case for most functions in Persefone, but not for all.) Similarly, many of the nature macros depend on specific variables being available where they are called, and can therefore only be used in specific contexts (this is indicated in their documentation).","category":"page"},{"location":"architecture.html#Output-data","page":"Source code architecture","title":"Output data","text":"","category":"section"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"Persefone can output model data into text files with a specified frequency (daily, monthly, yearly, or at the simulation end). Submodels can use newdataoutput! to plug into this system. For an example of how to use this, see src/nature/ecologicaldata.jl.  (See src/core/output.jl for details.)","category":"page"},{"location":"architecture.html#Farm-events","page":"Source code architecture","title":"Farm events","text":"","category":"section"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"The FarmEvent struct is used to communicate farming-related events between  submodels. An event can be triggered with createevent! and affects all pixels  within a FarmPlot. (See  src/core/landscape.jl  for details.)","category":"page"},{"location":"architecture.html#Random-numbers-and-logging","page":"Source code architecture","title":"Random numbers and logging","text":"","category":"section"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"By default in Julia, the random number generator (RNG) and the system logger are two globally accessible variables. As Persefone needs to avoid all global data (since this would interfere with reproducibility in parallel runs), the model object stores a  local logger and a local RNG. The local logger generally does not change the way the  model uses log statements, it is  only relevant for some functions in src/core/simulation.jl.","category":"page"},{"location":"architecture.html","page":"Source code architecture","title":"Source code architecture","text":"info: Using the model RNG\nWhenever you need to use a random number,  you must use the model.rng. The easiest way to do this is with the @rand  and @shuffle! macros. (Note that these, too, require access to the model object.)","category":"page"},{"location":"species.html#Species","page":"Species","title":"Species","text":"","category":"section"},{"location":"species.html","page":"Species","title":"Species","text":"The ecological submodel in Persefone simulates a range of species in agricultural landscapes.","category":"page"},{"location":"species.html#Skylark","page":"Species","title":"Skylark","text":"","category":"section"},{"location":"species.html","page":"Species","title":"Species","text":"Modules = [Persefone]\nPages = [\"nature/species/skylark.jl\"]","category":"page"},{"location":"species-dsl.html#Defining-new-species","page":"Defining new species","title":"Defining new species","text":"","category":"section"},{"location":"species-dsl.html#The-Persefone-species-DSL","page":"Defining new species","title":"The Persefone species DSL","text":"","category":"section"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"In order to make implementing new species as easy as possible, Persefone includes a domain-specific language (DSL) built from a collection of macros and functions.","category":"page"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"Here is an example of what this looks like, using a hypothetical mermaid species:","category":"page"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"@species Mermaid begin\n    ageofmaturity = 2\n    pesticidemortality = 1.0\n    @initialise(@habitat(@landcover() == water), pairs=true)\n\t\n    @phase life begin\n        @debug \"$(animalid(animal)) is swimming happily in its pond.\"\n        @respond pesticide @kill(@trait(pesticidemortality), \"poisoning\")\n        @respond harvest @setphase(drought)\n        @debug \"Animal: $animal\"\n        if @trait(sex) == female && @countanimals() < 3 &&\n            @trait(age) >= @trait(ageofmaturity) && @landcover() == water\n            @reproduce()\n        end\n    end\n\t\n    @phase drought begin\n        n = sum(1 for a in @neighbours(0))\n        @debug \"$(animalid(animal)) is experiencing drought with $n neighbour(s).\"\n        @respond sowing @setphase(life)\n    end\nend","category":"page"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"The two most important macros are @species and @phase,  followed by @initialise, @trait, @respond,  and @habitat. Other macros provide convenience wrappers for common  functions. (See src/nature/nature.jl for details.)","category":"page"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"The top-level macro is @species. This takes two arguments: a species  name and a definition block (enclosed in begin and end tags). At the start of the definition block, species-specific variables can be defined that should be available throughout a species' lifetime. Code in this section has access to the model object and can thus reference the current model state. In this section, the user also has to call the @initialise macro. This wraps the initpopulation function, and takes a habitat descriptor (see @habitat below) and several  options to specify how the species' population should be distributed in the landscape during model initialisation.","category":"page"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"Following this section, each species must define one or more @phase blocks. The concept behind this is that species show different behaviours at different phases of their lifecycle. Each @phase block defines the behaviour in one of these phases. (Technically, it defines a function that will be called daily, so long as the species' phase variable is set to the name of this phase.) Code in this section has access to the model object as well as an animal object, which is the currently active animal agent. Properties of the animal agent, regardless of whether they were defined by the user or by Persefone, can be accessed using the @trait macro. Within a phase block, @respond  can be used to define the species' response to a FarmEvent that affects  the species' current location, while a variety of other macros provide wrappers to  ecological process functions from src/nature/populations.jl.","category":"page"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"Another important macro is @habitat. This defines a \"habitat descriptor\", i.e. a predicate function that tests whether or not a given landscape pixel is  suitable for a specified purpose. Such habitat descriptors are used as arguments to various functions, for example for population initialisation or movement. The argument to @habitat consists of a logical expression, which has access to the animal's current position (the pos tuple variable) and the model. Various macros are available to easily reference information about the current location, such as @landcover or @distancetoedge.","category":"page"},{"location":"species-dsl.html#Implementation-details","page":"Defining new species","title":"Implementation details","text":"","category":"section"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"Due to a known performance problem  with multi-agent models, the underlying implementation of species is  rather complicated (see src/nature/nature.jl for details.)","category":"page"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"Rather than creating a new type/struct for each species, all Animal agents have the same type. Instead, they are differentiated by a traits dict, which stores both species-specific parameters and run-time variables. Note that due to a redefinition of the getproperty()/setproperty!() methods, variables from the trait dict can be accessed and modified just like normal struct fields (i.e. although phase is defined in the dict, not the struct, animal.phase = \"newphase\" works just fine - one does not have to use animal.traits[\"phase\"] = \"newphase\".)","category":"page"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"Under the hood, the @species macro generates a function (with the name of the species), which in turn creates the trait dict when called. Thus, adding a new animal agent to the model involves instantiating an Animal object, then calling the relevant species function and attaching the returned dict to the agent object.","category":"page"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"Similarly, the @phase macro too works by defining a new function, which is stored in the species' trait dict. These functions take an animal object and the model object as input, and define what the species does during its daily update.","category":"page"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"Once again, @habitat creates a function that takes model and pos as input and returns a boolean response. Functions that require a habitat descriptor thus take in this (anonymous) function and call it internally.","category":"page"},{"location":"species-dsl.html","page":"Defining new species","title":"Defining new species","text":"Finally, the @initialise macro is a wrapper around initpopulation, which (yet again) creates a function that specifies how a species' population is to be initialised at the beginning of a simulation run. This function is stored in the species trait dict and accessed during model setup.","category":"page"},{"location":"developing.html#Developing-Persefone","page":"Developing Persefone","title":"Developing Persefone","text":"","category":"section"},{"location":"developing.html#Workflow","page":"Developing Persefone","title":"Workflow","text":"","category":"section"},{"location":"developing.html","page":"Developing Persefone","title":"Developing Persefone","text":"Pull the current version from the master branch on Gitlab:  https://git.idiv.de/xo30xoqa/persephone.\nIf you are working on a new feature, create a new branch to avoid breaking the master branch. (The master branch on Github should always be in a runnable and error-free state.)\nImplement your changes.\nRun an example simulation and the test suite to make sure everything works without crashing (make run and make test on Linux, or execute run.jl and test/runtests.jl manually.)\nCommit your work frequently, and try to keep each commit small. Don't forget to add relevant tests to the test suite.\nOnce your satisfied with your work, do another pull/merge from the master branch in case somebody else changed the branch in the meantime. Then merge your work into master and push to the Gitlab server.\nRepeat :-)","category":"page"},{"location":"developing.html","page":"Developing Persefone","title":"Developing Persefone","text":"The Gitlab issue tracker can be used  to create, discuss, and assign tasks, as well as to monitor progress towards milestones/releases.  Once we have a first release, we will start using semantic versioning.","category":"page"},{"location":"developing.html#Libraries","page":"Developing Persefone","title":"Libraries","text":"","category":"section"},{"location":"developing.html#Agents.jl","page":"Developing Persefone","title":"Agents.jl","text":"","category":"section"},{"location":"developing.html","page":"Developing Persefone","title":"Developing Persefone","text":"Our model uses Agents.jl as a framework. Their repository can be used to inspect the source code or submit bug reports (the authors are quick to respond). Questions can be asked at the  Julia Discourse forum.","category":"page"},{"location":"developing.html","page":"Developing Persefone","title":"Developing Persefone","text":"Tutorial on collaborating on Julia packages:  https://www.matecdev.com/posts/julia-package-collaboration.html.","category":"page"},{"location":"developing.html#Revise.jl","page":"Developing Persefone","title":"Revise.jl","text":"","category":"section"},{"location":"developing.html","page":"Developing Persefone","title":"Developing Persefone","text":"Revise.jl allows one to reload code without restarting the Julia interpreter. Get it with Pkg.add(\"Revise\"), then  add using Revise to .julia/config/startup.jl to have it automatically available.","category":"page"},{"location":"developing.html#Test","page":"Developing Persefone","title":"Test","text":"","category":"section"},{"location":"developing.html","page":"Developing Persefone","title":"Developing Persefone","text":"Persefone uses the inbuilt Julia testing framework. All new functions should have appropriate tests written for them in the appropriate file in the test directory. (See test/runtests.jl for details.) There are three ways to run the test suite: in the terminal, executing make test or cd test; julia runtests.jl; or in the Julia REPL,  Pkg.activate(\".\"); Pkg.test().","category":"page"},{"location":"developing.html#Documenter.jl","page":"Developing Persefone","title":"Documenter.jl","text":"","category":"section"},{"location":"developing.html","page":"Developing Persefone","title":"Developing Persefone","text":"The HTML documentation is generated using Documenter.jl. Therefore, all new functions should have docstrings attached. New files need to be integrated into the relevant documentation source files in docs/src, and if necessary into docs/builddocs.jl. To build the documentation, run make docs, or cd docs; julia builddocs.jl (if using the latter, don't forget to update the date and commit in docs/src/index.md).","category":"page"},{"location":"developing.html#Julia-editors","page":"Developing Persefone","title":"Julia editors","text":"","category":"section"},{"location":"developing.html#Emacs","page":"Developing Persefone","title":"Emacs","text":"","category":"section"},{"location":"developing.html","page":"Developing Persefone","title":"Developing Persefone","text":"There are a couple of addons that make working with Julia much nicer in Emacs:","category":"page"},{"location":"developing.html","page":"Developing Persefone","title":"Developing Persefone","text":"julia-mode gives syntax highlighting. Install with M-x package-install julia-mode.\njulia-snail provides IDE-like features,  especially a fully-functional REPL and the ability to evaluate code straight from inside a buffer. Note that the installation can be somewhat tricky. You first need to manually install all the dependencies of its dependency vterm, then install vterm itself with M-x package-install vterm, before you can do M-x package-install julia-snail. Then add it to your init.el with (require 'julia-snail) and (add-hook 'julia-mode-hook #'julia-snail-mode).\ncompany-mode integrates with Snail to give code  completion. Install with M-x package-install company, then add  (add-hook 'julia-mode-hook #'company-mode) and  (global-set-key (kbd \"C-<tab>\") 'company-complete) to your init.el.\nmagit is a great git interface for Emacs. Install with M-x package-install magit and add (global-set-key (kbd \"C-x g\") 'magit-status) to your init.el.","category":"page"},{"location":"developing.html#VSCode","page":"Developing Persefone","title":"VSCode","text":"","category":"section"},{"location":"developing.html","page":"Developing Persefone","title":"Developing Persefone","text":"See here.","category":"page"},{"location":"developing.html","page":"Developing Persefone","title":"Developing Persefone","text":"TODO: add more detail.","category":"page"},{"location":"simulation.html#Simulation","page":"Simulation","title":"Simulation","text":"","category":"section"},{"location":"simulation.html","page":"Simulation","title":"Simulation","text":"The core directory holds source files that are important for all submodels, including scheduling, landscape, and input/output functions.","category":"page"},{"location":"simulation.html#simulation.jl","page":"Simulation","title":"simulation.jl","text":"","category":"section"},{"location":"simulation.html","page":"Simulation","title":"Simulation","text":"This file includes the basal functions for initialising and running simulations.","category":"page"},{"location":"simulation.html","page":"Simulation","title":"Simulation","text":"Modules = [Persefone]\nPages = [\"core/simulation.jl\"]","category":"page"},{"location":"simulation.html#Persefone.finalise!-Tuple{Agents.AgentBasedModel}","page":"Simulation","title":"Persefone.finalise!","text":"finalise!(model)\n\nWrap up the simulation. Currently doesn't do anything except print some information.\n\n\n\n\n\n","category":"method"},{"location":"simulation.html#Persefone.initialise","page":"Simulation","title":"Persefone.initialise","text":"initialise(config=PARAMFILE, seed=nothing)\n\nInitialise the model: read in parameters, create the output data directory, and instantiate the AgentBasedModel object(s). Optionally allows specifying the configuration file and overriding the seed parameter. This returns a single model object, unless the config file contains multiple values for one or more parameters, in which case it creates a full-factorial simulation experiment and returns a vector of model objects.\n\n\n\n\n\n","category":"function"},{"location":"simulation.html#Persefone.initmodel-Tuple{Dict{String, Any}}","page":"Simulation","title":"Persefone.initmodel","text":"initmodel(settings)\n\nInitialise a model object using a ready-made settings dict. This is a helper function for initialise().\n\n\n\n\n\n","category":"method"},{"location":"simulation.html#Persefone.paramscan-Tuple{Dict{String, Any}, Vector{String}}","page":"Simulation","title":"Persefone.paramscan","text":"paramscan(settings)\n\nCreate a list of settings dicts, covering all possible parameter combinations given by the input settings (i.e. a full-factorial experiment). This is a helper function for initialise().\n\n\n\n\n\n","category":"method"},{"location":"simulation.html#Persefone.simulate","page":"Simulation","title":"Persefone.simulate","text":"simulate(config=PARAMFILE, seed=nothing)\n\nInitialise one or more model objects and carry out a full simulation experiment, optionally specifying a configuration file and a seed for the RNG.\n\nThis is the default way to run a Persefone simulation.\n\n\n\n\n\n","category":"function"},{"location":"simulation.html#Persefone.simulate!-Tuple{Agents.AgentBasedModel}","page":"Simulation","title":"Persefone.simulate!","text":"simulate!(model)\n\nCarry out a complete simulation run using a pre-initialised model object.\n\n\n\n\n\n","category":"method"},{"location":"simulation.html#Persefone.stepsimulation!-Tuple{Agents.AgentBasedModel}","page":"Simulation","title":"Persefone.stepsimulation!","text":"stepsimulation!(model)\n\nExecute one update of the model.\n\n\n\n\n\n","category":"method"},{"location":"simulation.html#landscape.jl","page":"Simulation","title":"landscape.jl","text":"","category":"section"},{"location":"simulation.html","page":"Simulation","title":"Simulation","text":"This file manages the landscape maps that underlie the model.","category":"page"},{"location":"simulation.html","page":"Simulation","title":"Simulation","text":"Modules = [Persefone]\nPages = [\"core/landscape.jl\"]","category":"page"},{"location":"simulation.html#Persefone.EventType","page":"Simulation","title":"Persefone.EventType","text":"The types of landscape event that can be simulated\n\n\n\n\n\n","category":"type"},{"location":"simulation.html#Persefone.FarmEvent","page":"Simulation","title":"Persefone.FarmEvent","text":"FarmEvent\n\nA data structure to define a landscape event, giving its type, spatial extent, and duration.\n\n\n\n\n\n","category":"type"},{"location":"simulation.html#Persefone.LandCover","page":"Simulation","title":"Persefone.LandCover","text":"The land cover classes encoded in the Mundialis Sentinel data.\n\n\n\n\n\n","category":"type"},{"location":"simulation.html#Persefone.Pixel","page":"Simulation","title":"Persefone.Pixel","text":"Pixel\n\nA pixel is a simple data structure to combine land use and ownership information in a single object. The model landscape consists of a matrix of pixels. (Note: further landscape information may be added here in future.)\n\n\n\n\n\n","category":"type"},{"location":"simulation.html#Persefone.createevent!","page":"Simulation","title":"Persefone.createevent!","text":"createevent!(model, pixels, name, duration=1)\n\nAdd a farm event to the specified pixels (a vector of position tuples) for a given duration.\n\n\n\n\n\n","category":"function"},{"location":"simulation.html#Persefone.distanceto-Tuple{Tuple{Int64, Int64}, Agents.AgentBasedModel, Function}","page":"Simulation","title":"Persefone.distanceto","text":"distanceto(pos, model, habitatdescriptor)\n\nCalculate the distance from the given location to the closest location matching the habitat descriptor function. Caution: can be computationally expensive!\n\n\n\n\n\n","category":"method"},{"location":"simulation.html#Persefone.distanceto-Tuple{Tuple{Int64, Int64}, Agents.AgentBasedModel, Persefone.LandCover}","page":"Simulation","title":"Persefone.distanceto","text":"distanceto(pos, model, habitattype)\n\nCalculate the distance from the given location to the closest habitat of the specified type. Caution: can be computationally expensive!\n\n\n\n\n\n","category":"method"},{"location":"simulation.html#Persefone.distancetoedge-Tuple{Tuple{Int64, Int64}, Agents.AgentBasedModel}","page":"Simulation","title":"Persefone.distancetoedge","text":"distancetoedge(pos, model)\n\nCalculate the distance from the given location to the closest neighbouring habitat. Caution: can be computationally expensive!\n\n\n\n\n\n","category":"method"},{"location":"simulation.html#Persefone.farmplot-Tuple{Tuple{Int64, Int64}, Agents.AgentBasedModel}","page":"Simulation","title":"Persefone.farmplot","text":"farmplot(position, model)\n\nReturn the farm plot at this position, or nothing if there is none (utility wrapper).\n\n\n\n\n\n","category":"method"},{"location":"simulation.html#Persefone.initlandscape-Tuple{String, String}","page":"Simulation","title":"Persefone.initlandscape","text":"initlandscape(landcovermap, farmfieldsmap)\n\nInitialise the model landscape based on the map files specified in the configuration. Returns a matrix of pixels.\n\n\n\n\n\n","category":"method"},{"location":"simulation.html#Persefone.landcover-Tuple{Tuple{Int64, Int64}, Agents.AgentBasedModel}","page":"Simulation","title":"Persefone.landcover","text":"landcover(position, model)\n\nReturn the land cover class at this position (utility wrapper).\n\n\n\n\n\n","category":"method"},{"location":"simulation.html#Persefone.updateevents!-Tuple{Agents.AgentBasedModel}","page":"Simulation","title":"Persefone.updateevents!","text":"updateevents!(model)\n\nCycle through the list of events, removing those that have expired.\n\n\n\n\n\n","category":"method"},{"location":"farm.html#Farm-submodel","page":"Farm submodel","title":"Farm submodel","text":"","category":"section"},{"location":"farm.html","page":"Farm submodel","title":"Farm submodel","text":"Eventually, Persefone will include multiple farm-decision submodels. At the moment,  we are only working with a very basic mock-up.","category":"page"},{"location":"farm.html#farm.jl","page":"Farm submodel","title":"farm.jl","text":"","category":"section"},{"location":"farm.html","page":"Farm submodel","title":"Farm submodel","text":"This file is responsible for managing the farm module(s).","category":"page"},{"location":"farm.html","page":"Farm submodel","title":"Farm submodel","text":"Modules = [Persefone]\nPages = [\"farm/farm.jl\"]","category":"page"},{"location":"farm.html#Persefone.Farmer","page":"Farm submodel","title":"Persefone.Farmer","text":"Farmer\n\nThis is the agent type for the farm ABM. (Not yet implemented.)\n\n\n\n\n\n","category":"type"},{"location":"farm.html#Persefone.initfarms!-Tuple{Agents.AgentBasedModel}","page":"Farm submodel","title":"Persefone.initfarms!","text":"initfarms!(model)\n\nInitialise the model with a set of farm agents.\n\n\n\n\n\n","category":"method"},{"location":"farm.html#Persefone.stepagent!-Tuple{Farmer, Agents.AgentBasedModel}","page":"Farm submodel","title":"Persefone.stepagent!","text":"stepagent!(farmer, model)\n\nUpdate a farmer by one day.\n\n\n\n\n\n","category":"method"},{"location":"adapting.html#Adapting-Persefone","page":"Adapting Persefone","title":"Adapting Persefone","text":"","category":"section"},{"location":"adapting.html","page":"Adapting Persefone","title":"Adapting Persefone","text":"A key development goal of Persefone is to be FAIR: findable, accessible, interoperable, and reusable. We aim to build a model that is both easy  to use and easy to adapt to new situations.","category":"page"},{"location":"adapting.html","page":"Adapting Persefone","title":"Adapting Persefone","text":"There are multiple ways to adapt Persefone for a new modelling study:","category":"page"},{"location":"adapting.html#Changing-the-parameters","page":"Adapting Persefone","title":"Changing the parameters","text":"","category":"section"},{"location":"adapting.html","page":"Adapting Persefone","title":"Adapting Persefone","text":"The simplest way to adapt Persefone is simply by changing the parameters. Copy src/parameters.toml to a new location, adjust it to your needs, and run the model using julia run.jl -c <configfile>.","category":"page"},{"location":"adapting.html#Changing-the-region","page":"Adapting Persefone","title":"Changing the region","text":"","category":"section"},{"location":"adapting.html","page":"Adapting Persefone","title":"Adapting Persefone","text":"To apply Persefone to a new region, you need to create new input maps of land cover and farmplots. How to do so is described here.","category":"page"},{"location":"adapting.html","page":"Adapting Persefone","title":"Adapting Persefone","text":"You may also need to change aspects of the farm submodel. This is not yet implemented.","category":"page"},{"location":"adapting.html#Adding-new-animal-species","page":"Adapting Persefone","title":"Adding new animal species","text":"","category":"section"},{"location":"adapting.html","page":"Adapting Persefone","title":"Adapting Persefone","text":"To implement a new species to the nature submodel, add a new file to the  src/nature/species directory and include it in src/Persefone.jl, as well as adding the name of the species to the nature.targetspecies parameter. In the new file, implement the species using the @species syntax as described here.","category":"page"},{"location":"adapting.html#Adding-new-crop-species","page":"Adapting Persefone","title":"Adding new crop species","text":"","category":"section"},{"location":"adapting.html","page":"Adapting Persefone","title":"Adapting Persefone","text":"Crop growth is not yet implemented.","category":"page"},{"location":"adapting.html#Adding-new-farmer-behaviour","page":"Adapting Persefone","title":"Adding new farmer behaviour","text":"","category":"section"},{"location":"adapting.html","page":"Adapting Persefone","title":"Adapting Persefone","text":"Farmer behaviour is not yet implemented.","category":"page"},{"location":"adapting.html#Adding-a-new-submodel","page":"Adapting Persefone","title":"Adding a new submodel","text":"","category":"section"},{"location":"adapting.html","page":"Adapting Persefone","title":"Adapting Persefone","text":"To add a new submodel in addition to the existing ones (nature, crop, and farm), you need to familiarise yourself with the software architecture. In particular, you need to understand how initialisation and scheduling works in src/core/simulation.jl, and what information is stored in the model object.","category":"page"},{"location":"adapting.html","page":"Adapting Persefone","title":"Adapting Persefone","text":"If you want to add a new agent type, use Agents.jl's  @agent macro. (But be aware that Persefone already has three agent types and you may encounter performance problems.) Having implemented the new agent type, add it to the model objects type definition and scheduler, and write an initialisation function and a stepagent! function. (See initmodel and stepsimulation! for details.)","category":"page"},{"location":"adapting.html#Linking-to-another-model","page":"Adapting Persefone","title":"Linking to another model","text":"","category":"section"},{"location":"adapting.html","page":"Adapting Persefone","title":"Adapting Persefone","text":"Persefone can also be used as a software library and be called from another application. For this purpose, it is set up as a Julia package, with a module exporting various model functions, types, and macros (see  src/Persefone.jl). Of particular interest are the functions simulate (set up and run a complete simulation based on a config file), initialise (create one or more model objects from a config file), simulate! (do a simulation run with an existing model object), and stepsimulation! (update a model object by one time step).","category":"page"},{"location":"adapting.html","page":"Adapting Persefone","title":"Adapting Persefone","text":"To interface with Julia from another language, see the Julia docs here and here.","category":"page"},{"location":"odd.html#Overview,-Design,-Details-(ODD)","page":"Overview, Design, Details (ODD)","title":"Overview, Design, Details (ODD)","text":"","category":"section"},{"location":"odd.html","page":"Overview, Design, Details (ODD)","title":"Overview, Design, Details (ODD)","text":"TODO","category":"page"},{"location":"gis.html#GIS-data","page":"GIS data","title":"GIS data","text":"","category":"section"},{"location":"gis.html","page":"GIS data","title":"GIS data","text":"Persefone currently requires two separate map input files: one for land cover, the other for field geometry. This documents describe how to obtain and process the data needed for each of these.","category":"page"},{"location":"gis.html#Land-cover-maps","page":"GIS data","title":"Land cover maps","text":"","category":"section"},{"location":"gis.html","page":"GIS data","title":"GIS data","text":"Land cover maps for Germany at 10m resolution can be obtained from  Mundialis. These are generated annually from Sentinel data and comprise the following  land cover classes:","category":"page"},{"location":"gis.html","page":"GIS data","title":"GIS data","text":"10: forest\n20: low vegetation\n30: water\n40: built-up\n50: bare soil\n60: agriculture","category":"page"},{"location":"gis.html","page":"GIS data","title":"GIS data","text":"To create a Persefone map input file, you need to crop the national Mundialis map to the extent that you want to simulate (suggestion: approx. 10x10km is a  reasonable size).","category":"page"},{"location":"gis.html","page":"GIS data","title":"GIS data","text":"To do so, download the Mundialis map and import it into QGIS. Then create a new vector layer and create a rectangle feature to delimit the extent of your region. Then go to Raster -> Extraction -> Clip Raster by Extent. Select the Mundialis map as the input layer, set the clipping extent by choosing your region vector layer under Calculate from Layer and specify the output file name before clicking Run. This will generate a TIF file that you can pass to Persefone as the landcovermap parameter.","category":"page"},{"location":"gis.html#Field-ID-maps","page":"GIS data","title":"Field ID maps","text":"","category":"section"},{"location":"gis.html","page":"GIS data","title":"GIS data","text":"In addition to the land cover data explained above, Persefone also needs information about agricultural field boundaries in order to assign these to the farming agents. Unfortunately, getting this is rather more complicated.","category":"page"},{"location":"gis.html","page":"GIS data","title":"GIS data","text":"In the EU, every country runs a Land Parcel Information System (LPIS) to administer CAP payments. In Germany, this is called InVeKoS and is run by the Länder. For example, you can view and download the InVeKoS data for Thüringen here. This gives you a vector layer which can be loaded into QGIS. However, it needs to be converted to a raster layer and cropped to your region extent before it can be used in Persefone.","category":"page"},{"location":"gis.html","page":"GIS data","title":"GIS data","text":"The first thing to do is to make sure that the vector layer has a numeric (!) field with a unique identifier for each field block (check the attribute table).  The Thüringen data has the FBI (\"Feldblockident\") field, but this is a string value and therefore not usable by the rasteriser. So, we set the vector layer to edit mode, open the field calculator, enter the information for a new field  (call it \"FID\" and set it to a 32-bit integer), and enter @row_number in the  expression field. Then save the layer and close the calculator.","category":"page"},{"location":"gis.html","page":"GIS data","title":"GIS data","text":"Secondly, you need to filter out all non-field/non-grassland plot types. (LPIS also has data on forests and various landscape elements that are not relevant to our use case.) Assuming you're working with the Thüringen InVeKoS data (other data sets may have a different structure), right-click on the layer name in QGIS' layer overview and click on \"Filter...\". Then, enter this expression in the query builder: \"BNK\" = 'AL' OR \"BNK\" = 'GL' and click \"OK\". This will select only field and grassland plots.","category":"page"},{"location":"gis.html","page":"GIS data","title":"GIS data","text":"Next, open the rasteriser (Raster -> Conversion -> Rasterize). Select your FID field as the \"Field to use for a burn-in value\", and your land cover map (as created above - this ensures the two layers match) as the output extent. Make sure  the \"fixed value to burn\" is \"Not set\". Then choose \"Georeferenced units\" as the  \"Out raster size units\" and set horizontal and vertical resolution to 10.0. In  the advanced parameters, set the output data type to UInt32. Finally, enter an  output file name and run. The resulting TIF file can be passed to Persefone as the farmfieldmap parameter.","category":"page"},{"location":"crops.html#Crop-submodel","page":"Crop submodel","title":"Crop submodel","text":"","category":"section"},{"location":"crops.html","page":"Crop submodel","title":"Crop submodel","text":"Eventually, Persefone will include a full-blown crop-growth model (an adaptation of AquaCrop, created by the FAO). At the moment, we are only working with a very basic mock-up.","category":"page"},{"location":"crops.html#crops.jl","page":"Crop submodel","title":"crops.jl","text":"","category":"section"},{"location":"crops.html","page":"Crop submodel","title":"Crop submodel","text":"This includes the types and functions needed for all crop growth model, which are also referenced by the other submodels.","category":"page"},{"location":"crops.html","page":"Crop submodel","title":"Crop submodel","text":"Modules = [Persefone]\nPages = [\"crop/crops.jl\"]","category":"page"},{"location":"crops.html#Persefone.CropType","page":"Crop submodel","title":"Persefone.CropType","text":"The crop types simulated by the model\n\n\n\n\n\n","category":"type"},{"location":"crops.html#Persefone.FarmPlot","page":"Crop submodel","title":"Persefone.FarmPlot","text":"FarmPlot\n\nThis represents one field, i.e. a collection of pixels with the same management. This is the spatial unit with which the crop growth model and the farm model work.\n\n\n\n\n\n","category":"type"},{"location":"crops.html#Persefone.averagefieldsize-Tuple{Agents.AgentBasedModel}","page":"Crop submodel","title":"Persefone.averagefieldsize","text":"averagefieldsize(model)\n\nCalculate the average field size in hectares for the model landscape.\n\n\n\n\n\n","category":"method"},{"location":"crops.html#Persefone.cropheight-Tuple{Tuple{Int64, Int64}, Agents.AgentBasedModel}","page":"Crop submodel","title":"Persefone.cropheight","text":"cropheight(model, position)\n\nReturn the height of the crop at this position, or nothing if there is no crop here (utility wrapper).\n\n\n\n\n\n","category":"method"},{"location":"crops.html#Persefone.croptype-Tuple{Tuple{Int64, Int64}, Agents.AgentBasedModel}","page":"Crop submodel","title":"Persefone.croptype","text":"croptype(model, position)\n\nReturn the crop at this position, or nothing if there is no crop here (utility wrapper).\n\n\n\n\n\n","category":"method"},{"location":"crops.html#Persefone.initfields!-Tuple{Agents.AgentBasedModel}","page":"Crop submodel","title":"Persefone.initfields!","text":"initfields!(model)\n\nInitialise the model with its farm plots.\n\n\n\n\n\n","category":"method"},{"location":"crops.html#Persefone.stepagent!-Tuple{FarmPlot, Agents.AgentBasedModel}","page":"Crop submodel","title":"Persefone.stepagent!","text":"stepagent!(farmplot, model)\n\nUpdate a farm plot by one day.\n\n\n\n\n\n","category":"method"},{"location":"index.html","page":"Introduction","title":"Introduction","text":"CurrentModule = Persefone","category":"page"},{"location":"index.html#Introduction","page":"Introduction","title":"Introduction","text":"","category":"section"},{"location":"index.html","page":"Introduction","title":"Introduction","text":"Persefone is an agent-based, socio-economic-ecological model of agricultural landscapes in Europe under the Common Agricultural Policy (CAP).","category":"page"},{"location":"index.html","page":"Introduction","title":"Introduction","text":"It's aim is to investigate how policy affects farmer decision-making, and how this in turn affects various animal species. It includes a farm submodel, a crop-growth submodel, and an ecological submodels.","category":"page"},{"location":"index.html#Running-the-model","page":"Introduction","title":"Running the model","text":"","category":"section"},{"location":"index.html","page":"Introduction","title":"Introduction","text":"To run a single experiment, execute run.jl:","category":"page"},{"location":"index.html","page":"Introduction","title":"Introduction","text":"julia run.jl -c <CONFIG>","category":"page"},{"location":"index.html","page":"Introduction","title":"Introduction","text":"Other commandline arguments are:","category":"page"},{"location":"index.html","page":"Introduction","title":"Introduction","text":"usage: run.jl [-c CONFIGFILE] [-s SEED] [-o OUTDIR] [-l LOGLEVEL] \n              [--version] [-h]\n\noptional arguments:\n  -c, --configfile CONFIGFILE\n                        name of the configuration file\n  -s, --seed SEED       inital random seed (type: Int64)\n  -o, --outdir OUTDIR   location of the output directory\n  -l, --loglevel LOGLEVEL\n                        verbosity: \"debug\", \"info\", or \"quiet\"\n  --version             show version information and exit\n  -h, --help            show this help message and exit","category":"page"},{"location":"index.html#Model-input","page":"Introduction","title":"Model input","text":"","category":"section"},{"location":"index.html","page":"Introduction","title":"Introduction","text":"Persefone requires three input files: a configuration file and two map files. How to generate the map files is documented elsewhere. The configuration file defines parameter values and looks like this (see src/parameters.toml for a complete list  of parameters):","category":"page"},{"location":"index.html","page":"Introduction","title":"Introduction","text":"### Persefone - a socio-economic-ecological model of European agricultural landscapes.\n###\n### This is the default configuration file for Persefone, containing all model parameters.\n### The syntax is described here: https://toml.io/en/\n\n[core]\nconfigfile = \"src/parameters.toml\" # location of the configuration file\nlandcovermap = \"data/landcover_jena.tif\" # location of the landcover map\nfarmfieldsmap = \"data/fields_jena.tif\" # location of the field geometry map\noutdir = \"results\" # location and name of the output folder\noverwrite = \"ask\" # overwrite the output directory? (true/false/\"ask\")\nloglevel = \"debug\" # verbosity level: \"debug\", \"info\", \"warn\"\nprocessors = 2 # number of processors to use on parallel runs\nseed = 2 # seed value for the RNG (0 -> random value)\n# dates to start and end the simulation\nstartdate = 2022-01-01\nenddate = 2022-12-31\n\n[farm]\nfarmmodel = \"FieldManager\" # which version of the farm model to use (not yet implemented)\n\n[nature]\ntargetspecies = [\"Wolpertinger\", \"Wyvern\"] # list of target species to simulate\npopoutfreq = \"daily\" # output frequency population-level data, daily/monthly/yearly/end/never\nindoutfreq = \"end\" # output frequency individual-level data, daily/monthly/yearly/end/never\n\t\n[crop]\ncropmodel = \"linear\" # crop growth model to use, \"linear\" or \"aquacrop\" (not yet implemented)","category":"page"},{"location":"index.html","page":"Introduction","title":"Introduction","text":"info: Parameter scanning\nYou can set any parameter to a list of different values, e.g. seed = [1,2,3]. Persefone will then set up and run multiple simulations, one for every possible combination of parameters that you entered (i.e. do a full-factorial simulation experiment).","category":"page"},{"location":"index.html","page":"Introduction","title":"Introduction","text":"Last updated: 2023-05-28 (commit 60e9012)","category":"page"}]
}