eventEval: Evaluate Detected Events with Known Event Sources and Times

In jonkatz2/monitoR: Acoustic Template Detection in R

Evaluate Detected Events with Known Event Sources and Times

Description

Evaluate whether the detected events are True +, True -, False +, or False - detections by comparing the results to a table of events with known sources and times (such as annotations from viewSpec). Events to evaluate may be either directly from an object of class detectionList, a csv file or data frame resulting from a call to getPeaks or getDetections, or a data frame downloaded from an acoustics database. A value for score.cutoff must be supplied to distinguish between True + and False -, even if assessing all peaks.

Usage

eventEval(detections, what = "detections", which.one, standard, 
score.cutoff = 11, tol = 1)

Arguments

detections	An object of class detectionList, a csv file, or data frame containing detection results. See Details.
what	If a detectionList object is supplied for detections the character value of either "detections" (default; all peaks above the score cutoff) or all "peaks" may be selected.
which.one	If the detection process involved multiple templates only one may be selected for evaluation. Value can be either character (identifying the template name), or numerical (identifying the position in names(detections['template']). See Details.
standard	The "standard" is the results from annotation with viewSpec (i.e. Gold Standard) containing the source and time of each event. Can be a data frame or a file path to a csv file.
score.cutoff	If no template is supplied a score.cutoff can be supplied to evaluate false negatives.
tol	Numeric value for tolerance, with units seconds. If a detected event is within this value (actually +/- 0.5 x tol), the events are assumed to co-occur and be of the same origin.

Details

Little checking is performed to ensure that evaluation is possible based on the values for detections and standard. The standard must contain the fields c("start.time", "end.time", "min.frq", "max.frq", "name"). Objects are assumed to be from an acoustics database if they contain the fields c("fldTime", "fldScore", "fldTemplateName"). Data frames are assumed to be objects formerly of class detectionList if they contain the fields c("time", "score", "template").

Results from only one template from one survey may be evaluated in each call to eventEval.

Value

The detections data frame with an outcome field appended.

Note

eventEval performs the evaluation by merging the detections and standard data frames, ordering by time, and checking to see which rows occur within a value of tol to the row above. True + are defined as a detected event that co-occurrs in time with an event from the standard AND scores above or equal to the score.cutoff. Such an event that scores below the score.cutoff is classified as a False -. False - events may also be the product of an event from the standard failing to co-occur with any detected events. True - events don't co-occur with any standard events, and False + events similarly don't co-occur with standard events but score above or equal to the score.cutoff.

Author(s)

Jon Katz

See Also

The function timeAlign operates similarly, but rather than evaluate a set of detections against a standard it merges detections from multiple templates and retains only the co-occurring detections with the highest scores.

Examples

# Load data
data(btnw)
data(survey)

# Write Wave objects to file (temporary directory used here)
btnw.fp <- file.path(tempdir(), "btnw.wav")
survey.fp <- file.path(tempdir(), "survey2010-12-31_120000_EST.wav")
writeWave(btnw, btnw.fp)
writeWave(survey, survey.fp)

# Make a template
btemp <- makeBinTemplate(btnw.fp, frq.lim = c(2, 8), select = "auto", name = "btnw1", buffer =
                         4, amp.cutoff = -31, binary = TRUE)

# Binary point matching
scores <- binMatch(survey = survey.fp, templates = btemp, time.source = "fileinfo")

# Isolate peaks
pks <- findPeaks(scores)

# Evaluate peaks
data(survey_anno)

survey_anno <- survey_anno[survey_anno['name'] == 'BTNW', ]  # Extract the "BTNW" rows

peaks <- getPeaks(pks) 

eval <- eventEval(detections = peaks, standard = survey_anno, score.cutoff = 15)

jonkatz2/monitoR documentation built on March 27, 2024, 4:39 p.m.