Estimation of connectivity indexes from CONEFOR

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

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 prefix is true use the prefix name
coneforpath	character. Path to Conefor 2.6 with command line interface (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 vector. 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 files .txt:"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

if (FALSE) {
setwd("~")
EstConefor(nodeFile = "nodes.txt",
          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)
}