Caching as part of SpaDES | At the spades level | Module-level caching | Event-level caching | Function-level caching | Working with the Cache manually | Reproducible Workflow | Nested Caching | Cache the spades call | Cache a whole module | Cache individual functions | Data-to-decisions

Reproducible workflow | Differences with other approaches | Function-level caching | Caching examples | Basic use | Example 1: Basic cache use with tags | Example 2: using the "accessed" tag | Example 3: using keepCache | Example 4: searching for multiple objects in the cache | Example 5: using caching to speed up rerunning expensive computations | Nested Caching | cacheId | Working with the Cache manually | Alternative database backends

Introduction to SpaDES | Package description | Requirements | Objectives and motivations | Is R fast enough? | Discrete event simulation and SpaDES | SpaDES modules | SpaDES demos and sample modules | Simulation and data | Using SpaDES | Initializing a simulation: the simInit function | Running a simulation: the spades function | Types of models | Modelling spread processes | A simple fire model | Agent based models | Point agents | Polygon agents | Simulation experiments | Additional resources | SpaDES documentation and vignettes | Help files | Vignettes | Website | Wiki | Q&A Forum | SpaDES module repository | Reporting bugs | References

Introduction | Module overview | Simulation event list | Module events | Module event dependencies | Module structure | Module directory structure (moduleName/) | Module code file (moduleName.R) | Metadata | Defining module metadata: defineModule() | Defining module parameters: defineParameter() | Event types | Event functions | Event diagram | Module documentation (moduleName.Rmd) | Citation, LICENSE, and README files | Data | Versioned zip archives (moduleName_x.y.z.zip) | Passing data between modules | Data types | Global objects and the simulation environment | Module object dependencies | Core modules | .checkpoint module | .progress module | .load and .save modules | inputs argument to simInit | outputs argument to simInit | Plotting | Using existing SpaDES modules | Included sample modules | SpaDES module repository | Creating new modules | Module design considerations | Using the module template | Module groups | Debugging | Contributing modules | Minimum requirements | Module submission

Principles used in Require | How it works -- Version priority | Apparent package conflicts | New default as of version 2.0.0 | Key features (when usePak = TRUE) | Rerun-tolerance | Why these features help teams | All working on same project | Diverse projects | Differences between pak and Require | How Require differs from pak in philosophy | Stability vs. Most-recent | GitHub branches: exact pin vs. version minimum | Installs and loads in one line | Version constraints in the package name | Conflicts: resolved vs. raised as errors | Archived packages: automatic vs. manual | Installing from a snapshot | Why snapshot install needs Require's plumbing on top of pak | Working offline | Summary of differences | Set it and forget it speed | Why is it fast? | Extra from Require | renv and Require | Managing projects during development

Advanced SpaDES use | Memory monitoring | Static code checking | References

Overview | Setting up module tests | Using testing with new modules | Using testing with existing modules | Customizing the test configuration | Adding system dependencies

Basic landscape generation | Merging landscapes | Classifying categories | References

Setting Up Prerequisites: Installing System Dependencies, R, and RStudio | Installing SpaDES.project | Understanding SpaDES.project's Main Function: setupProject() | Function objectives | Function Tasks | What Makes this Function so Special | 1. Versatile Argument Types | 2. Sequential Argument Processing | 3. Handling Missing Values | Relationship between setupProject() and SpaDES.core::simInit Call | See Also | Examples of usage of setupProject() | Get modules from GitHub | Paths | Default values | Arguments sourced sequentially | Arguments not sourced to .GlobalEnv | With options and params set | Arguments as values or urls | Setting arbitrary arguments, using defaultDots | Pass args from GlobalEnv | Mixing argument: a named list, a github file and local file | studyArea argument | Alberta and British Columbia, Canada | Specify an epsg | require and objects arguments | Passing named arguments as part of the ... | Make project-level change to .libPaths() that is persistent

NetLogoR features | World and agents | Procedures | Variables | Agentsets | World topology | Tick counter | Lists and strings | Math and random numbers | Input/output | View, plot, screen output | How to build a model using NetLogoR

NetLogo constants | NetLogo primitives | A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W | X | Y | ?

Plotting in quickPlot | The Plot function | Spatial layer types | Other object types | ggplot2 objects | base plotting | Other classes | Colours | Plot arguments | grid graphical parameters: gp, gpText, gpAxis, size | visualSqueeze | legend and legendRange | zoomExtent | length | Modularity | The new argument | Calling Plot again and again | If there is a blank spot for a new plot | If there is not a blank spot for a new plot | A pre-existing name to a device | Plotting Speed | speedup | Overplotting: addTo | Clearing Plot | Plotting in RStudio | Interacting with plots | clickValues | clickExtent | Replotting or redrawing the entire plot window | Assigning Plot() to object

scfm | References

Find other's modules | A small selection of SpaDES modules | Some Biomass_ modules* | FireSense modules | LandR modules | A larger selection of "known" SpaDES modules | All SpaDES modules in a set of known accounts

Traditional installation | Windows | macOS | Linux | Alternate installation | Launching Rstudio using a specific version of R | Installing Rstudio

Usage examples | Example 1

Usage examples | Example 1

What is git? | Installation | Commandline tools | Desktop clients | Getting started with GitHub | Additonal commandline setup | Development workflow | Git submodules | Cloning a project with submodules | Adding submodules to a project | Updating submodules | Additional resources

Introduction | The SpaDES.core package: | The SpaDES.tools package: | The SpaDES.addins package: | The SpaDES.shiny package: | The quickPlot package: | The reproducible package:

Using RStudio addins | SpaDES module directory | SpaDES module development | Copy an existing module | Create a new SpaDES module from a template | SpaDES package development (advanced)