Status of each site x species cell for the community matrices

Classifies each site x species cell of the calibration by whether its detections can enter a community matrix, separating the absence of a species from a calibration that does not work:

Usage

cell_status(fit, validations, p_min = 0.95, min_n = 15)

Arguments

fit

Model returned by fit_calibration().

validations

Table returned by read_validations(), the clips the model was fitted to.

p_min

Calibrated probability that makes a detection reliable, as in detection_history().

min_n

Minimum number of reviewed clips in a cell.

Value

A tibble with one row per site x species: site, species, n_reviewed, n_tp, max_confidence (highest reviewed score), threshold (lowest grid score at which the calibrated probability reaches p_min; NA if never), status and reason. The grid contains both observed endpoints and steps of 0.01 within the reviewed range.

Details

• "reliable": the calibrated curve reaches p_min within the range of reviewed scores of the cell, and the cell has at least min_n reviewed clips;

• "probably_absent": clips were reviewed but none was a true positive. The species can enter the matrix with zeros at that site;

• "unreliable": true positives were reviewed, but the curve never reaches p_min within the reviewed scores, or the cell has fewer than min_n reviewed clips, or no clip at all was reviewed. A zero in such a cell could be a false negative.

suggest_core_species() keeps the species without unreliable cells. The final choice of core species remains with the analyst.