BaRanking: Barrier permeability quantification

In wx-ecology/BaBA: Barrier Behavior Analysis (BaBA)

Barrier permeability quantification

Description

Evaluating permeabilities of all barrier segments based on the results of the Barrier Behavior Analysis (BaBA). Returns an sf MULTILINESTRING object depicting the permeability index value for each barrier segment with at least min_total_enc encounters, as well as the number of each type of encounter event that occured near each segment, the total number of encounter events (total_enc) for each barrier segment, and the number of unique individuals (unique_ind) that encountered each barrier segment).

Usage

BaRanking(classification, 
barrier, 
d, 
Barrier_ID,
min_total_enc = 0, 
index_fun = expression(((Bounce + Back_n_forth + Trace + Trapped)/total_enc) * unique_ind),
show_plot = F)

Arguments

classification	Classification results from the BaBA function (obtained with $classification)
barrier	same sf LINESTRING or MULTILINESTRING object representing barrier locations used when running the BaBA function. More see details.
d	barrier buffer size used in BaBA function.
Barrier_ID	The column name from the barrier object that indicate barrier ID.
min_total_enc	minimum number of encounters to consider when calculating ranking index. More see details.
index_fun	expression for quantifying permeability of each barrier. More in details.
show_plot	logical, TRUE if the barrier map colored by permeability should be printed.

Details

Classified barrier encounter events will be counted for the barrier segments at which the events occured. If the input barrier contains a few very long segments, users may want to break them into shorter sections so permeabilities will be examined for each smaller section.

Depending on animal movement distributions, the barrier segments may only be encountered a few times, or not at all. In this case, there may not be sufficient information to accurately quantify permeabilities of rarely encountered barriers. min_total_enc is used to filter out barriers with insufficient encounter events from the permeability index calculation.

Depending on management goal and animal ecology/biology, index_fun can be an expression regarding the total encounter events total_enc, the number of unique individuals affected unique_ind, and/or the occurence any of the six barrier behaviors (Bounce, Trace, Back_n_forth, Quick_Cross, Avergae_Movement, or Trapped) regarding to each barrier segment. Default is set to be the ratio of counts of altered behavior events (Bounce + Back_n_forth + Trace + Trapped) to counts of total encounter events (total_enc, weighted by the number of unique individuals that interacted with a given barrier segment. The result of this expression is scaled to range from 0 to 1 using equation:

function(x){(x-min(x))/(max(x)-min(x))}

NOTE: due to the scaling of the permeability index from 0-1, index values are context-specific and cannot be compared across studies or with different input data, other than as a relative indicator of permeability.

Value

an object of class sf with MULTILINESTRING geometry containing one row per barrier ID, and columns with information on:

Quick_Cross, Bounce, unknown, Avergae_movement, Trace, Back_n_forth, Trapped	total counts per barrier segment of the corresponding barrier behavior event type.
unique_ind	number of unique individuals that encountered the given barrier segment.
total_enc	total number of encounters for the given barrier segment.
index	permeability ranking index as calculated by index_fun and transformed to a scale of 0 to 1.

Author(s)

Wenjing Xu [e-mail] and Valentine Herrmann [e-mail]

References

Xu W, Dejid N, Herrmann V, Sawyer H, Middleton AD. Barrier Behaviour Analysis (BaBA) reveals extensive effects of fencing on wide-ranging ungulates. J Appl Ecol. 2020;00:1–9. https://doi.org/10.1111/1365-2664.13806

Examples

# load data
data(fences)
data(pronghorn)

# run BaBA function to classify barrier behaviors
results_prong <- BaBA(animal = pronghorn, barrier = fences, d = 110, max_cross = 4)

# rank barriers with default evaluation expression
fence_ranking <- BaRanking(classification = results_prong$classification,
  barrier = fences, d = 110, Barrier_ID = "FID_Fence0", min_total_enc = 5,
  show_plot = TRUE)  

wx-ecology/BaBA documentation built on April 13, 2025, 12:07 a.m.