`SpaDES.tools`

package`R/spades-tools-package.R`

`SpaDES.tools-package.Rd`

Spatial contagion is a key phenomenon for spatially explicit simulation models. Contagion can be modelled using discrete approaches or continuous approaches. Several functions assist with these:

`adj` | |

An optimized (i.e., faster) version of | |

`adjacent` | |

`cir` | |

Identify pixels in a circle around a | |

`SpatialPoints*` | object |

`directionFromEachPoint` | |

Fast calculation of direction and | distance surfaces |

`distanceFromEachPoint` | |

Fast calculation of distance surfaces | |

`rings` | |

Identify rings around focal cells (e.g., buffers and donuts) | |

`spokes` | |

TO DO: need description | |

`spread` | |

Contagious cellular automata | |

`wrap` | |

Create a torus from a grid |

Agents have several methods and functions specific to them:

`crw` | |

Simple correlated random walk function | |

`heading` | |

Determines the heading between SpatialPoints* | |

`makeLines` | |

Makes | `SpatialLines` |

object for, | e.g., drawing arrows |

`move` | |

A meta function that can currently only take "crw" | |

`specificNumPerPatch` | |

Initiate a specific number of agents per patch | |

In addition to the vast amount of GIS operations available in R (mostly from
contributed packages such as `sp`

, `raster`

, `maps`

, `maptools`

and many others), we provide the following GIS-related functions:

`equalExtent` | |

Assess whether a list of extents are all equal |

These functions convert between reduced and mapped representations of the same data. This allows compact representation of, e.g., rasters that have many individual pixels that share identical information.

`rasterizeReduced` | |

Convert reduced representation to full raster |

It is often useful to build dummy maps with which to build simulation models before all data are available. These dummy maps can later be replaced with actual data maps.

`gaussMap` | |

Creates a random map using Gaussian random fields | |

`randomPolygons` | |

Creates a random polygon with specified number of classes | |

These functions are essentially skeletons and are not fully implemented. They are intended to make translations from SELES. You must know how to use SELES for these to be useful:

`agentLocation` | |

Agent location | |

`initiateAgents` | |

Initiate agents into a | |

`SpatialPointsDataFrame` | |

`numAgents` | |

Number of agents | |

`probInit` | |

Probability of initiating an agent or event | |

`transitions` | |

Transition probability |

`SpaDES`

packages use the following `options`

to configure behaviour:

`spades.lowMemory`

: If true, some functions will use more memory efficient (but slower) algorithms. Default`FALSE`

.