calcConnectivityMatrix: Calculate a connectivity matrix dataframe from a connectivity...
In wStockhausen/rDisMELS: Basic functions for dealing with DisMELS IBM model output

calcConnectivityMatrix

R Documentation

Calculate a connectivity matrix dataframe from a connectivity results sf dataframe

Description

Function to calculate a connectivity matrix datafarme from a connectivity results dataframe.

Usage

calcConnectivityMatrix(
  sfs_points,
  sf_zones,
  startStage = "Z1",
  endStage = "C1F",
  endStageFac = 2,
  startZones = c(1:8),
  endZones = c(1:18),
  plotStartLocs = FALSE,
  plotEndLocs = FALSE,
  bmls = NULL,
  crs = wtsGIS::get_crs(4326),
  nSZpG = 2,
  nPlotCols = 2,
  colours = c("red", "blue", "green", "cyan", "black")
)

Arguments

`sfs_points`	- list by life stage of sf dataframes with connectivity results and point locations from a single model run
`sf_zones`	- sf dataframe with connectivity zone information (polygons)
`startStage`	- name of start life stage for connectivity matrix
`endStage`	- name of end life stage for connectivity matrix
`endStageFac`	- multiplier on apparent number successful (e.g., 2 if sexes were split after starting life stage)
`startZones`	- vector of starting zone id's (integers) for sf_zones
`endZones`	- vector of ending zone id's (integers) for sf_zones
`plotStartLocs`	- flag to plot start locations
`plotEndLocs`	- flag to plot end locations
`bmls`	- list of ggplot2 basemap layers
`crs`	- sf coordinate reference system (crs) for maps
`nSZpG`	- number of start zones to include in a group for end location maps
`nPlotCols`	- number of columns for end location maps
`colours`	- vector of colours to use to distinguish start zones in an end location map

Details

Calculates the connectivity matrices by unique startTime for a model run based on the connectivity zones defined in sf_zones. Optionally, ggplot2-style maps of the starting and ending locations of individuals can be created. End zone locations are colored according to their start zone.

Value

list with elements

step3_StartEndZones - dataframe with start/end zones for each individual
step3_ConnectivityDataframe - connectivity matrices by unique startTime as a dataframe
pStartMap - ggplot2 map of start locations (or NULL)
pEndMap - ggplot2 map of end locations (or NULL)