Man pages for SpaDES.core
Core Utilities for Developing and Running Spatially Explicit Discrete Event Models
| addChangedAttr | '.addChangedAttr' for 'simList' objects |
| addDepends | Add simulation dependencies |
| addTagsToOutput | '.addTagsToOutput' for 'simList' objects |
| all.equal.simList | All equal method for 'simList' objects |
| anyPlotting | Test whether there should be any plotting from '.plots'... |
| append_attr | Append attributes |
| bindrows | Simple wrapper around 'data.table::rbindlist' |
| cacheMessage | '.cacheMessage' for 'simList' objects |
| checkCacheRepo | '.checkCacheRepo' for 'simList' objects |
| checkModule | Check for the existence of a remote module |
| checkModuleLocal | Check for the existence of a module locally |
| checkObject | Check for existence of object(s) referenced by a 'objects'... |
| checkParams | Check use and existence of parameters passed to simulation. |
| checkpoint | Simulation checkpoints |
| checksums | Calculate checksum for a module's data files |
| citation | A citation method for 'SpaDES' modules |
| classFilter | Filter objects by class |
| clearCache | 'clearCache' for 'simList' objects |
| convertToPackage | Convert standard module code into an R package |
| Copy | Copy for 'simList' class objects |
| copyModule | Create a copy of an existing module |
| coreModules | Named list of core 'SpaDES' modules |
| createsOutput | Define an output object of a module |
| dealWithClass | Methods for '.wrap' and '.unwrap' |
| defineEvent | Alternative way to define events in SpaDES.core |
| defineModule | Define a new module. |
| defineParameter | Define a parameter used in a module |
| deprecated | Zip a 'simList' and various files |
| depsEdgeList | Build edge list for module dependency graph |
| depsGraph | Build a module dependency graph |
| depsLoadOrder | Determine module load order |
| depsPruneEdges | Prune edges to remove cycles in module dependencies |
| doEvent | Process a simulation event |
| dot-cleanPkgs | strip GitHub repo info from vector of packages |
| dot-findObjects | Find objects if passed as character strings |
| dot-guessPkgFun | Guess package of a function |
| dot-params | Reserved module parameter names |
| downloadData | Download module data |
| downloadModule | Download a module from a SpaDES module GitHub repository |
| emptyEventList | Blank (template) event list |
| emptyMetadata | Default (empty) metadata |
| eventDiagram | Simulation event diagram |
| expectsInput | Define an input object that the module expects. |
| extractURL | Extract a url from module metadata |
| fileEdit | Open a file for editing |
| fileName | Extract filename (without extension) of a file |
| fileTable | Create empty 'fileTable' for inputs and outputs |
| fillInputRows | An internal function for coercing a data.frame to 'inputs()' |
| fillOutputRows | An internal function for coercing a data.frame to 'outputs()' |
| findElements | Find all references to sim$ |
| findModuleName | Identify module names up to a given recursive level |
| findSimList | Find 'simList' in a nested list |
| ganttStatus | 'ganttStatus' |
| getModuleInputObjects | Extract the user-defined '.inputObjects' function from a... |
| getModuleVersion | Find the latest module version from a SpaDES module... |
| getOption | A slightly modified version of 'getOption()' |
| getSampleFiles | Get copies of sample files for examples and tests |
| globals | Get and set global simulation parameters |
| identifyChildModules | Identify child modules from a recursive list |
| initialize-method | Generate a 'simList' object |
| inputObjectsDF | Create an empty 'data.frame' object for use with... |
| isNamespaced | Check is module uses module namespacing |
| keepAttrs | Attach missing attributes from 'x' to 'y' |
| loadFiles | File extensions map |
| loadSimList | Load a saved 'simList' and ancillary files |
| makeMemoisable | Make 'simList' correctly work with 'memoise' |
| maxTimeunit | Determine the largest timestep unit in a simulation |
| memoryUse | Estimate memory used with 'system("ps")' |
| minTimeunit | Determine the smallest timeunit in a simulation |
| modifySearchPath | Modify package order in search path |
| moduleCodeFiles | Extract the full file paths for R source code |
| moduleCoverage | Calculate module coverage of unit tests |
| moduleDefaults | Defaults values used in 'defineModule' |
| moduleDeps-class | The '.moduleDeps' class |
| moduleDiagram | Simulation module dependency diagram |
| moduleGraph | Build a module dependency graph |
| moduleMetadata | Parse and extract module metadata |
| moduleParamsInputsOuputs | Extract a module's parameters, inputs, or outputs |
| moduleVersion | Parse and extract a module's version |
| namespacing | Namespacing within 'SpaDES' |
| newModule | Create new module from template |
| newModuleCode | Create new module code file |
| newModuleDocumentation | Create new module documentation |
| newModuleTests | Create template testing structures for new modules |
| newProject | Create new SpaDES project |
| newProjectCode | Create new module code file |
| noEventWarning | Text for no event with that name |
| objectDiagram | Simulation object dependency diagram |
| objects | Extract or replace an object from the simulation environment |
| objectSynonyms | Identify synonyms in a 'simList' |
| objSize.simList | Object size for 'simList' |
| openModules | Open all modules nested within a base directory |
| packages | Get module or simulation package dependencies |
| paramCheckOtherMods | Test and update a parameter against same parameter in other... |
| params | Get and set simulation parameters |
| parseElems | '.parseElems' for 'simList' class objects |
| parseMessage | Prepend module name to a message |
| parseModule | Parse and initialize a module |
| pkgEnv | The 'SpaDES.core' package environment |
| Plot | Plot method for 'simList' objects |
| Plots | 'Plot' wrapper intended for use in a SpaDES module |
| preDigestByClass | Pre-digesting method for 'simList' |
| prepareOutput | '.prepareOutput' for 'simList' objects |
| priority | Event priority |
| progress | Get and set simulation progress bar details |
| progressBar | Progress bar |
| quickCheck | The 'SpaDES.core' variable to switch between quick and robust... |
| rasterCreate | Simple wrapper to load any Raster* object |
| rasterToMemory | Read raster to memory |
| reexports | Objects exported from other packages |
| remoteFileSize | Determine the size of a remotely hosted file |
| restartR | Restart R programmatically |
| restartSpades | Restart an interrupted simulation |
| rndstr | Generate random strings |
| robustDigest | '.robustDigest' for 'simList' objects |
| runCodeChecks | Runs a series of code checks during 'simInit()' |
| runModuleInputsObjects | Run module's '.inputObjects' |
| savedSimEnv | Retrieve environment for saving interrupted simulations |
| saveFiles | Save objects using '.saveObjects' in 'params' slot of... |
| saveSimList | Save a whole 'simList' object to disk |
| scheduleConditionalEvent | Schedule a conditional simulation event |
| scheduleEvent | Schedule a simulation event |
| setPaths | Get and set default working directories |
| show-method | Show an Object |
| sim2gantt | sim2gantt |
| simDeps-class | The '.simDeps' class |
| simFile | Generate simulation file name |
| simInit | Initialize a new simulation |
| simInitAndSpades | Call 'simInit' and 'spades' together |
| simList-accessors-envir | Simulation environment |
| simList-accessors-events | Simulation event lists |
| simList-accessors-inputs | Simulation inputs |
| simList-accessors-metadata | Metadata accessors |
| simList-accessors-modules | Simulation modules and dependencies |
| simList-accessors-objects | Show which objects were first created in a 'simInit' or... |
| simList-accessors-outputs | Simulation outputs |
| simList-accessors-paths | Specify paths for modules, inputs, outputs, and temporary... |
| simList-accessors-times | Time usage in 'SpaDES' |
| simList-class | The 'simList' class |
| spades | Run a spatial discrete event simulation |
| spades-classes | Classes defined in SpaDES |
| SpaDES.core-package | Categorized overview of the 'SpaDES.core' package |
| spadesOptions | 'SpaDES.core' options |
| spadesTime | SpaDES time units |
| sub-simList-character-ANY-method | Extract an intact 'simList' but with subset of objects |
| suppliedElsewhere | Assess whether an object has or will be supplied from... |
| tagsByClass | '.tagsByClass' for 'simList' objects |
| timeConversion | Convert time units |
| tryCatch | 'tryCatch' that keeps warnings, errors and value (result) |
| unparsed | Determine which modules in a list are unparsed |
| updateList | Update elements of a named list with elements of a second... |
| use_gha | Use GitHub actions for automated module checking |
| verb | Chose verb conjugation for "to be" |
| writeEventInfo | Write simulation event info to file |
| writeRNGInfo | Write RNG state info to file |
| zipModule | Create a zip archive of a module subdirectory |
