PAMpal (version 1.4.4)

markAnnotated: Mark Detections as Annotated

Description

Marks detections within an AcousticStudy as being within the bounds of an annotation box. Annotations can either be read in from the "Spectrogram Annotation" module of PAMguard, or supplied as a separate dataframe. Detections must be entirely contained within the annotation bounds.

Usage

markAnnotated(
  x,
  anno = NULL,
  tBuffer = 0,
  fBuffer = 0,
  table = "Spectrogram_Annotation"
)

Value

the same object as x, but detectors have additional columns added

Arguments

x

an AcousticStudy object

anno

annotations to read from. If NULL, will be read in from the PAMguard database. If a data.frame, must have columns start and end in UTC, and column id. Can additionally have columns fmin and fmax to apply frequency bounds (values in Hz).

tBuffer

additional buffer value to add on to annotation time bounds in seconds. If a single number, the number of seconds to extend the bounds by on the start and end of each annotation. Can also be a vector of two to extend different values on the start and end. This can be useful if original bounding boxes were drawn very close to the desired detections since any small portion of a signal outside the box will cause it to be excluded.

fBuffer

additional buffer value to add to annotation frequency bounds in Hz. If a single number, the number of Hz to extend bounds by on lower and upper end of boxes. Can also be a vector of two to extend different values on lower and upper bounds. This can be useful if original bounding boxes were drawn very close to the desired detections since any small portion of a signal outside the box will cause it to be excluded.

table

if anno is NULL, the name of the "Spectrogram Annotation" module table within the database.

Author

Taiki Sakai

Details

This adds new columns inAnno and annoId to all detector dataframes within the AcousticStudy. inAnno is a logical flag whether or not a given detection was fully contained in any annotation bounding box, and annoId lists the IDs of the boxes it matched. A detection is considered within an annotation only if it is entirely within the time and frequency bounds of the annotation. For GPL and whistle detections, the min and max frequency values are used. For click detections, only the peak frequency is used. For cesptrum detections, frequency bounds are ignored.

Examples

data(exStudy)
annotation <- data.frame(start = min(getWhistleData(exStudy)$UTC),
                         fmin = c(16000, 17000),
                         fmax = c(17000, 18000))
annotation$end <- annotation$star + 1
exStudy <- markAnnotated(exStudy, annotation)
getWhistleData(exStudy)[c('UTC', 'duration', 'freqMin', 'freqMax', 'inAnno', 'annoId')]