Sick_tree_errors: Sick tree error calculator

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

Description

Calculate errors in automated detection of declining trees using visual inspection data as reference.

Usage

Sick_tree_errors(r_pred_dir, tile = "ALL", prefix, vuln_classes,
  training_pnt_filename, radius = 2, field_name, abs_samp = 100,
  minthresh = 0, maxthresh = 1, stepthresh = 0.05, parallel = F,
  nWorkers = 4, data_outp_dir = NULL)

Arguments

r_pred_dir	A directory where binary .tifs predicting presence as 1 and absence as 0 can be found for multiple tiles
tile	path to a txtfile with the names of the tile you want to execute If you want to run all the images of r_pred_dir, leave it empty. Default is 'ALL'
prefix	Prefix that you want to add to the output file. EX: NorthPortugal NorthPortugal-> -sicktree_performance_dfs.rdsdata
vuln_classes	A list of the classes you want to model. The list can contain one or more vectors. Each vector represents a seperate vegetation class and response variable for the model and the vector elements are synonyms used to describe that class. The fist place in each vector will be used in the output name used to store the calibrated model, so it should not contain spaces. The other places should appear as attributes in the field 'field_name' of pnts.
training_pnt_filename	Full path to the SpatialPointsDataFrame of which one field contains the vuln_classes
radius	The radius within which a presence point must be found for it to be considered 'correct'. Default is True
field_name	Character. The field in AOI.filename that contains the vuln_classes
abs_samp	How many 'absence' pixels should be randomly selected from each tile to evaluate the absences? Default is 100.
minthresh	The minimum cut-off number you want to use, Default = 0
maxthresh	The maximum cut-off number you want to use, Default = 1
stepthresh	The step used to create de sequences of threshold from the minthresh to the max thresh. Default = 0.05
parallel	Should the code be run in parallel using the doParallel package? Default is FALSE.
nWorkers	If running the ocde in parallel, how many workers should be used? Default is 4.
data_outp_dir	The folder to save the sampled data to. No data is saved is data_outp_dir is NULL. Default is NULL.

Value

A data frame with commission and ommission errors and sample sizes of presence and absence

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