Classify_maxent_output_based_on_error_stats: Classify maxent output to binary presence absence maps

In MartinezLaura/CanHeMonR.MaxEnt: Application of MaxEnt for canopy health monitoring through airbone image analysis.

Description

Classify maxent output to binary presence absence maps based on thresholds of pixel-level probability, expected minimum crown size, and clump size, finally outputs a polygon shapefile.

Usage

Classify_maxent_output_based_on_error_stats(r_pred_dir, tile = "ALL",
  max_permittable_cutoff_final = max_permittable_cutoff_final,
  max_permittable_cutoff_npix_final = max_permittable_cutoff_npix_final,
  max_area, res, outp_dir)

Arguments

r_pred_dir	A directory where binary .tifs predicting presence as 1 and absence as 0 can be found for multiple tiles
tile	Character vector. Names of tile(s) to run. 'ALL will run all tiles in r_pred_dir. Default is 'ALL'
max_permittable_cutoff_final	Cutoff-level for Maxent probability output. Typically produced by cut_off_selection.r
max_permittable_cutoff_npix_final	Cutoff-level for the nr of pixels (clumpsize) of presence that a circles of radius radius needs to contain to be maintained as presence. Typically produced by error_summaries.R
max_area	The maximum are aof a polygon, all the polygons above this area will be filtered
res	The resolution of the raster
outp_dir	The directory where you want to save the output shapefiles.

Value

A shapefile for each binarized raster file

See Also

Depends on: cut_off_selection.r

MartinezLaura/CanHeMonR.MaxEnt documentation built on May 17, 2019, 6:21 p.m.