percolate: Percolation

In SCSchmidt/percopackage: Percolation Analysis functions

Description

This is a function built based on the scripts by Simon Maddison, who based it on code developed by Elsa Arcaute, which is published under: E.Arcaute, C.Molinero, E.Hatna, R.Murcio, C.Vargas-Ruiz, A.P.Masucci and M.Batty. Cities and Regions in Britain through hierarchical percolation. J. R. Soc. Open Science, 3 (4),150691. doi:10.1098/rsos.150691, 2016.

Usage

percolate(
  data,
  distance_table = NULL,
  upper_radius,
  lower_radius,
  step_value,
  limit,
  radius_unit
)

Arguments

data	needs input of data.frame as specified below
distance_table	to give a distance matrix instead of calculating one. Default is NULL, and Euclidean distance will be calculated from the given point data.
upper_radius	needs input of integer, is the upper value of the radius range to be used
lower_radius	needs input of integer, is the lower value of the radius range to be used
step_value	integer or numeric, is the step value to be used between these two values
limit	needs input of integer: is the value above which distances between sites will not be stored
radius_unit	is either 1 for meter or 1000 for km; applied to all input values

Details

data = A data.frame, with the format and example data below:

PlcIndex,Easting,Northing

1,350350,233050

2,354700,260200

3,358700,238900

PlcIndex is an assigned index number to distinguish the points. This does not need to be sequential and can for example be drawn from a source database.

Easting and Northing are self-explanatory, and are to the metre. (Note that additional columns, if any, will be ignored).

distance_table is set to be NULL as a default, which means, using the data input (coordinates) a distance matrix is calculated using Euclidean distance. If not NULL, the data frame given here needs to adhere to this format and example values:

ID1, ID2, d12

1,2,12.1

1,3,14.2

2,3,2.9

ID1 and ID2 are point IDs (i.e. the PlcIndex values) and

d12 denotes the weighted distance between them, if a non-euclidian distance is to be used.

upper_radius is an integer, the upper value of the radius range to be used.

lower_radius is an integer, the lower value of the radius range to be used.

step_value is numeric or integer and the step value to be used between lower and upper radius.

limit is an integer, the value above which distances will not be calculated between sites.

radius_unit is either 1 for meter or 1000 for km for all input radii.

Exported are in the folder "working_data": tables (csv) with the input-data, the list of PlcIndex, null_entries and duplicate_entries to be used by following functions.

In the folder "analysis_results" the tables (csv) analysis_by_radius and member_cluster_by_radius are exported. They will be used by the following functions as well, but may also be useful for other applications, therefore they are considered analysis results. For more information and a code and data example please check the vignette "percolation".

Value

the function generates the data files analysis_by_radius.csv and member_cluster_by_radius.csv

Author(s)

Simon Maddison

Sophie C. Schmidt

Elsa Arcaute

SCSchmidt/percopackage documentation built on May 2, 2020, 12:14 p.m.