Input data standards

File organization

Recording files must be organized as follows:

  • All audio should be stored in a single main folder.

  • The required file name format is: DEPLOYMENTID_DATE_HOUR.wav.

Optional recommendation: Within the main folder, create a subfolder for each deployment, named after the corresponding deployment.

Example:

/SONABIO-23-256
   /MC001
      MC001_20250529_133000.wav
      MC001_20250529_134000.wav
   /MC002
      MC002_20250529_133500.wav
      MC002_20250529_134500.wav

Field deployment sheet

This file provides metadata collected during the field deployment. It should be an Excel file named field_deployments_sheet.xlsx, with the below column names in the first row. See the tutorial data for an example.

Field Name

Description

Required

Unique

Type

Example

deploymentID

Unique identifier for the deployment. Required for tracking and referencing specific deployments.

✅

✅

string

DEP001

latitude

Latitude of the deployment location in decimal degrees (WGS84). Range: -90 to 90.

✅

float

5.2704

longitude

Longitude of the deployment location in decimal degrees (WGS84). Range: -180 to 180.

✅

float

2.3849

recorderModel

Manufacturer and model of the recorder, formatted as manufacturer-model.

✅

string

Audiomoth v1.2.0

recorderConfiguration

Detailed settings used for data collection (e.g., microphone type, recording schedule).

✅

string

record 1 minute every 29 minutes, internal microphone

locationID

Unique code that refers unambiguously to a location record. One locationID per latitude-longitude pair.

✅

string

LOC001

locationName

Name assigned to the deployment location for easy reference.

string

Finca La Esperanza

recorderHeight

Height (in meters) at which the recorder was deployed. Not to be combined with recorderDepth. Range: >0.

float

1.2

habitat

Brief description of the habitat at the deployment location.

string

Humid tropical rainforest

setupBy

Name or identifier of the individual or organization responsible for deploying the recorder.

string

Juan Gómez

deploymentComments

Additional comments or observations related to the deployment.

string

Traffic noise during installation

Target species

An optional target_species.csv with a single column (scientificName) listing one species per row. Species must be a subset of the model’s output labels. If the file is empty, no filtering is applied to detections.

Output data standards

To manage data collected during PAM analyses and facilitate exchange with biodiversity repositories, we implemented a standard called pamDP. This standard was adapted from camtrapDP (Bubnicki et al., 2023), preserving as much as possible while incorporating specific requirements for PAM. The data is stored in 3 main tables in csv format:

  • deployments.csv: Stores metadata about each deployment, including location, time frame, and recorder details.

  • media.csv: Contains information about recorded media files, such as file paths, timestamps, and technical metadata.

  • observations.csv: Records detected observations from media, including species identification, timestamps, and confidence scores.

Deployments

The deployments.csv table tracks information about sensor placements, such as location, duration, and recording settings.

Field Name

Description

Required

Unique

Type

Example

deploymentID

Unique identifier for the deployment. Required for tracking and referencing specific deployments.

✅

✅

string

DEP001

locationID

Identifier for the deployment location, either globally unique or dataset-specific.

✅

string

LOC001

locationName

Name assigned to the deployment location for easy reference.

string

Finca La Esperanza

latitude

Latitude of the deployment location in decimal degrees (WGS84). Range: -90 to 90.

✅

float

5.2704

longitude

Longitude of the deployment location in decimal degrees (WGS84). Range: -180 to 180.

✅

float

2.3849

coordinateUncertainty

Radius (in meters) representing the horizontal positional uncertainty of the deployment location. Leave blank if unknown. Range: > 0

float

100

deploymentStart

Date and time when the deployment started, formatted as ISO 8601 (YYYY-MM-DDThh:mm:ssZ or with timezone offset).

✅

datetime

2020-03-01T22:00:00Z

deploymentEnd

Date and time when the deployment ended, formatted as ISO 8601 (YYYY-MM-DDThh:mm:ssZ or with timezone offset).

✅

datetime

2020-04-01T22:00:00Z

setupBy

Name or identifier of the individual or organization responsible for deploying the recorder.

string

Juan Gómez

recorderID

Unique identifier of the audio recorder used (e.g., serial number).

✅

string

G02345

recorderModel

Manufacturer and model of the recorder, formatted as manufacturer-model.

✅

string

Audiomoth v1.2.0

recorderDelay

Time (in seconds) after a detection during which further activity is ignored. Minimum value: 0. Range: >0.

float

120

recorderHeight

Height (in meters) at which the recorder was deployed. Not to be combined with recorderDepth. Range: >0.

float

1.2

recorderDepth

Depth (in meters) at which the recorder was deployed. Not to be combined with recorderHeight. Range: >0.

float

4.8

recorderTilt

Vertical tilt angle of the recorder in degrees. -90° (downward), 0° (horizontal), 90° (upward). Range: (min -90, max 90)

float

87

recorderHeading

Horizontal orientation of the recorder in degrees, measured clockwise from north (0° = north, 90° = east, etc.). Range: 0 to 360.

float

225

recorderConfiguration

Detailed settings used for data collection (e.g., microphone type, recording schedule).

✅

string

record 1 minute every 29 minutes, internal microphone

detectionDistance

Maximum distance (in meters) at which the recorder reliably detects activity. Typically measured via playback experiments. Range: >0.

float

9.5

timestampIssues

Indicates whether timestamps in media resources have known issues (e.g., unknown timezone, AM/PM switch).

string

unknown timezone, am/pm switch

baitUse

Specifies whether bait was used during deployment. Additional details can be provided in deploymentTags or deploymentComments.

binary

featureType

Type of feature associated with the deployment (e.g., road, trail, water source).

enum

waterSource

habitat

Brief description of the habitat at the deployment location.

string

Humid tropical rainforest

deploymentGroups

Groups associated with the deployment (e.g., spatial arrays, temporal sessions). Multiple values separated by |, formatted as key:value pairs where applicable.

string

season:winter 2020 | grid:A1

deploymentTags

Tags associated with the deployment. Multiple values separated by |, optionally formatted as key:value pairs.

string

land cover:forest | bait:food

deploymentComments

Additional comments or observations related to the deployment.

string

traffic noise during installation

Media

The media.csv table contains references to audio or visual recordings used for classification.

Field Name

Description

Required

Unique

Type

Example

mediaID

Unique identifier for the media file.

✅

✅

string

MEDIA001

deploymentID

Identifier of the deployment associated with the media file (foreign key to deployments.deploymentID).

✅

string

DEP001

captureMethod

Method used to capture the media file.

enum: activityDetection, timeLapse

timeLapse

timestamp

Date and time when the media file was recorded, formatted as ISO 8601 with a timezone.

✅

string

2020-03-24T11:21:46Z

filePath

URL or relative path to the media file (external hosting or local package).

✅

string

https://colecciones.humboldt.org.co/rec/sonidos/IAvH-CSA-20439/G001_20211110_060000.WAV

filePublic

TRUE if the media file is publicly accessible; leave blank if private (e.g., for privacy protection).

✅

binary

TRUE

fileName

Name of the media file. Useful for sorting files chronologically within a deployment (by timestamp first, then fileName).

✅

string

AUDIO_001.wav

fileMediatype

Media type following the IANA format.

✅

string

audio/wav

sampleRate

Sampling rate of the audio file in Hertz.

✅

float

44.050

bitDepth

Bit depth (precision) of audio samples, in bits.

✅

integer

16

fileLength

Duration of the audio file in seconds.

✅

float

60

numChannels

Number of audio channels.

✅

int

1

favorite

TRUE if the media file is considered of interest (e.g., an exemplar sound).

binary

TRUE

mediaComments

Notes or remarks about the media file (e.g., “corrupted file”).

string

corrupted file

Observations

The observations.csv table stores classified occurrences of species or events, including metadata like behavior, vocalization details, and classification confidence.

Field Name

Description

Required

Unique

Type

Example

observationID

Unique observation identifier.

✅

✅

string

obs1

deploymentID

Deployment identifier (foreign key).

✅

✅

string

dep1

mediaID

Media file identifier (foreign key, only for media-based).

✅

string

media1

eventID

Event identifier linking observations.

✅

string

sequence1

observationLevel

Classification level: media (file-based) or event.

✅

string

media

observationType

Observation category (enum: animal, human voice, vehicle, silence, rain, wind, unknown, unclassified).

✅

string

animal

scientificName

Scientific name of observed species.

string

Ramphastos tucanus

count

Number of individuals (>1).

int

5

lifeStage

Age class (enum: adult, subadult, juvenile).

string

juvenile

sex

Sex (female, male).

enum: female, male

female

behavior

Primary sound-related behavior.

string

duet

vocalActivity

Vocalization intensity (1=Low, 2=Moderate, 3=High).

int

1

individualID

Unique individual identifier.

string

RD123

individualPositionRadius

Distance from recorder (m, >0).

float

6.81

bboxTime

Start time of vocalization in seconds. Range >0.

✅

float

3.5

bboxFrequency

Start frequency in Hertz. Range >0.

float

1500

bboxDuration

Duration of vocalization in seconds. Range >0.

float

10.4

bboxBandwidth

Vocalization bandwidth in Hertz. Range >0.

float

5400

classificationMethod

Classification method (human or machine).

string

human

classifiedBy

Name/ID of classifier (human or AI).

string

BirdNET v2.3

classificationTimestamp

Classification date/time (ISO 8601).

datetime

2020-08-22T10:25:19Z

classificationProbability

Confidence level. Range: 0-1.

float

0.95

observationTags

Tags (e.g., key:value format).

string

signalToNoise:high

observationComments

Additional notes.

string

Loud unknown bird vocalization

References

  • Bubnicki JW, Norton B, Baskauf SJ, Bruce T, Cagnacci F, Casaer J, Churski M, Cromsigt JPGM, Farra SD, Fiderer C, Forrester TD, Hendry H, Heurich M, Hofmeester TR, Jansen PA, Kays R, Kuijper DPJ, Liefting Y, Linnell JDC, Luskin MS, Mann C, Milotic T, Newman P, Niedballa J, Oldoni D, Ossi F, Robertson T, Rovero F, Rowcliffe M, Seidenari L, Stachowicz I, Stowell D, Tobler MW, Wieczorek J, Zimmermann F, Desmet P (2023). Camtrap DP: an open standard for the FAIR exchange and archiving of camera trap data. Remote Sensing in Ecology and Conservation. https://doi.org/10.1002/rse2.374