EstConefor: Estimation of connectivity indexes from CONEFOR
In connectscape/Makurhini: Makurhini: Analyzing landscape connectivity

EstConefor

R Documentation

Estimation of connectivity indexes from CONEFOR

Description

Use the CONEFOR command line to estimate probabilistic and binary connectivity indexes

Usage

EstConefor(
  nodeFile,
  coneforpath = NULL,
  connectionFile,
  typeconnection,
  typepairs,
  index,
  thdist,
  multdist = NULL,
  conprob = NULL,
  onlyoverall = TRUE,
  LA = NULL,
  nrestauration = FALSE,
  prefix = NULL,
  write = NULL
)

Arguments

`nodeFile`	`character`. Node file name. If the `prefix` parameter is used, then use the prefix name.
`coneforpath`	`character`. Path to Conefor 2.6 with command line interface (for more details and download http://www.conefor.org/coneforsensinode.html). Example, "C:/Users/coneforWin64.exe".
`connectionFile`	`character`. Connection file name. If prefix is true use the prefix name.
`typeconnection`	`character`. Indicate if it is distance (dist), probability (prob), adjacency (adj).
`typepairs`	`character`. `"all"` if all pairs of patches are in the distances file and `"notall"` if only they are the most important connections.
`index`	`character`. Select Binary index (CCP, LCP, IIC, BC, BCIIC, NC, NL, H) or Probabilistic (F, AWF, PC, BCPC).
`thdist`	`numeric`. Distance threshold to establish connections.
`multdist`	`numeric`. Multiple distance threshold to establish connections (meters). The minimum (min) and maximum (max) distance values to be calculated need to be specified, as well as the value by which the distance value must be increased (step) starting from min until max is reached, e.g. `multdist = c(min=10000, max=100000, step=10000)`.
`conprob`	`numeric`. If a probabilistic index is selected, indicate the probability of connection under the selected distance threshold, e.g., 0.5 that is 50 percentage of probability connection.
`onlyoverall`	`logical`. Estimate only overall index, default `TRUE`.
`LA`	`numeric`. Maximum landscape attribute.
`nrestauration`	`logical`. If `TRUE` Indicates that there are nodes to add to the initial landscape -restauration effect-. The nodeFile needs a third column with values of 0 or 1 indicating for each node whether it already exists in the landscape (1) or is a candidate to be added to the landscape (0).The onlyoverall option have to be `FALSE`.
`prefix`	`character`. Used in case of processing several sites at once.
`write`	`character`. Full path direction of the folder.

Value

Four .txt files: "overall_indices", "results_all_EC(PC)", "results_all_overall_indices" y "node_importance".

References

Saura, S. & Torné, J. 2012. Conefor 2.6 user manual (May 2012). Universidad Politécnica de Madrid. Available at www.conefor.org.

Examples

## Not run: 
library(Makurhini)
setwd("~")
EstConefor(nodeFile = "nodes.txt",
          coneforpath = "C:/Users/coneforWin64.exe",
          connectionFile = "dist.txt",
          typeconnection = "dist",
          typepairs = "notall",
          index = "PC",
          thdist = 30000, multdist = NULL,
          conprob = 0.5,
          onlyoverall = FALSE, LA = NULL,
          nrestauration = FALSE,
          prefix= NULL, write = NULL)

## End(Not run)

connectscape/Makurhini documentation built on Jan. 12, 2025, 8:16 p.m.