Package 'camtrapdp'

Title: Read and Manipulate Camera Trap Data Packages
Description: Read and manipulate Camera Trap Data Packages ('Camtrap DP'). 'Camtrap DP' (<https://camtrap-dp.tdwg.org>) is a data exchange format for camera trap data. With 'camtrapdp' you can read, filter and transform data (including to Darwin Core) before further analysis in e.g. 'camtraptor' or 'camtrapR'.
Authors: Peter Desmet [aut, cre] (<https://orcid.org/0000-0002-8442-8025>, Research Institute for Nature and Forest (INBO)), Sanne Govaert [aut] (<https://orcid.org/0000-0002-8939-1305>, Research Institute for Nature and Forest (INBO)), Pieter Huybrechts [aut] (<https://orcid.org/0000-0002-6658-6062>, Research Institute for Nature and Forest (INBO)), Damiano Oldoni [aut] (<https://orcid.org/0000-0003-3445-7562>, Research Institute for Nature and Forest (INBO)), Research Institute for Nature and Forest (INBO) [cph] (https://www.vlaanderen.be/inbo/en-gb/), Research Foundation - Flanders [fnd] (https://lifewatch.be)
Maintainer: Peter Desmet <[email protected]>
License: MIT + file LICENSE
Version: 0.3.1.9000
Built: 2024-11-21 15:24:52 UTC
Source: https://github.com/inbo/camtrapdp

Help Index


Check a Camera Trap Data Package object

Description

Checks if an object is a Camera Trap Data Package object with the required properties.

Usage

check_camtrapdp(x)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

Value

x invisibly or an error.

Examples

x <- example_dataset()
check_camtrapdp(x) # Invisible return of x if valid

Get or set deployments

Description

deployments() gets the deployments from a Camera Trap Data Package object.

⁠deployments<-()⁠ is the assignment equivalent.

  • It should only be used within other functions, where the expected data structure can be guaranteed.

  • Metadata (x$spatial and x$temporal) are updated to match the assigned deployments.

Usage

deployments(x)

deployments(x) <- value

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

value

A data frame to assign as deployments.

Value

A tibble::tibble() data frame with deployments.

See Also

Other accessor functions: events(), locations(), media(), observations(), taxa()

Examples

x <- example_dataset()
# Get deployments
deployments(x)

# Set deployments (not recommended outside a function)
deployments(x) <- head(deployments(x), 1)

Get events

Description

Gets the (unique) events from the observations of a Camera Trap Data Package object. Only observations with observationLevel == "event" are considered.

Usage

events(x)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

Value

A tibble::tibble() data frame with the events, containing the following columns:

  • deploymentID

  • eventID

  • eventStart

  • eventEnd

See Also

Other accessor functions: deployments(), locations(), media(), observations(), taxa()

Examples

x <- example_dataset()
events(x)

Read the Camtrap DP example dataset

Description

Reads the Camtrap DP example dataset. This dataset is maintained and versioned with the Camtrap DP standard.

Usage

example_dataset()

Value

Camera Trap Data Package object.

Examples

example_dataset()

Filter deployments

Description

Subsets deployments in a Camera Trap Data Package object, retaining all rows that satisfy the conditions.

  • Media are filtered on associated deploymentID.

  • Observations are filtered on associated deploymentID.

  • Metadata (x$spatial, x$temporal and x$taxonomic) are updated to match the filtered deployments.

Usage

filter_deployments(x, ...)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

...

Filtering conditions, see dplyr::filter().

Value

x filtered.

See Also

Other filter functions: filter_media(), filter_observations()

Examples

x <- example_dataset()

# Filtering returns x, so pipe with deployments() to see the result
x %>%
  filter_deployments(deploymentID == "62c200a9") %>%
  deployments()

# Filtering on deployments also affects associated media and observations
x_filtered <- filter_deployments(x, deploymentID == "62c200a9")
media(x_filtered)
observations(x_filtered)

# Filtering on multiple conditions (combined with &)
x %>%
  filter_deployments(latitude > 51.0, longitude > 5.0) %>%
  deployments()

# Filtering on dates is easiest with lubridate
library(lubridate, warn.conflicts = FALSE)
x %>%
  filter_deployments(
    deploymentStart >= lubridate::as_date("2020-06-19"),
    deploymentEnd <= lubridate::as_date("2020-08-30")
  ) %>%
  deployments()

Filter media

Description

Subsets media in a Camera Trap Data Package object, retaining all rows that satisfy the conditions.

  • Deployments are not filtered.

  • Observations are filtered on associated mediaID (for media-based observations) and eventID (for event-based observations).

  • Metadata (x$taxonomic) are updated to match the filtered observations.

Usage

filter_media(x, ...)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

...

Filtering conditions, see dplyr::filter().

Value

x filtered.

See Also

Other filter functions: filter_deployments(), filter_observations()

Examples

x <- example_dataset()

# Filtering returns x, so pipe with media() to see the result
x %>%
  filter_media(captureMethod == "timeLapse") %>%
  media()

# Filtering on media also affects associated observations, but not deployments
x_filtered <- filter_media(x, favorite == TRUE)
observations(x_filtered)

# Filtering on multiple conditions (combined with &)
x %>%
  filter_media(captureMethod == "activityDetection", filePublic == FALSE) %>%
  media()

# Filtering on datetimes is easiest with lubridate
library(lubridate, warn.conflicts = FALSE)
x %>%
  filter_media(
    timestamp >= lubridate::as_datetime("2020-08-02 05:01:00"),
    timestamp <= lubridate::as_datetime("2020-08-02 05:02:00")
  ) %>%
  media()

Filter observations

Description

Subsets observations in a Camera Trap Data Package object, retaining all rows that satisfy the conditions.

  • Deployments are not filtered.

  • Media are filtered on associated mediaID (for media-based observations) and eventID (for event-based observations). Filter on observationLevel == "media" to only retain directly linked media.

  • Metadata (x$taxonomic) are updated to match the filtered observations.

Usage

filter_observations(x, ...)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

...

Filtering conditions, see dplyr::filter().

Value

x filtered.

See Also

Other filter functions: filter_deployments(), filter_media()

Examples

x <- example_dataset()

# Filtering returns x, so pipe with observations() to see the result
x %>%
  filter_observations(observationType == "animal") %>%
  observations()

# Filtering on observations also affects associated media, but not deployments
x %>%
  filter_observations(
    scientificName == "Vulpes vulpes",
    observationLevel == "event"
  ) %>%
  media()
x %>%
  filter_observations(
    scientificName == "Vulpes vulpes",
    observationLevel == "media"
  ) %>%
  media()

# Filtering on multiple conditions (combined with &)
x %>%
  filter_observations(
    deploymentID == "577b543a",
    scientificName %in% c("Martes foina", "Mustela putorius")
  ) %>%
  observations()

# Filtering on datetimes is easiest with lubridate
library(lubridate, warn.conflicts = FALSE)
x %>%
  filter_observations(
    eventStart >= lubridate::as_datetime("2020-06-19 22:00:00"),
    eventEnd <= lubridate::as_datetime("2020-06-19 22:10:00")
  ) %>%
  observations()

Get locations

Description

Gets the (unique) locations from the deployments of a Camera Trap Data Package object.

Usage

locations(x)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

Value

A tibble::tibble() data frame with the locations, containing the following columns:

  • locationID

  • locationName

  • latitude

  • longitude

  • coordinateUncertainty

See Also

Other accessor functions: deployments(), events(), media(), observations(), taxa()

Examples

x <- example_dataset()
locations(x)

Get or set media

Description

media() gets the media from a Camera Trap Data Package object.

⁠media<-()⁠ is the assignment equivalent.

  • It should only be used within other functions, where the expected data structure can be guaranteed.

Usage

media(x)

media(x) <- value

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

value

A data frame to assign as media.

Value

A tibble::tibble() data frame with media.

See Also

Other accessor functions: deployments(), events(), locations(), observations(), taxa()

Examples

x <- example_dataset()
# Get media
media(x)

# Set media (not recommended outside a function)
media(x) <- head(media(x), 1)

Merge two Camera Trap Data Packages

Description

Merges two Camera Trap Data Package objects into one.

Usage

merge_camtrapdp(x, y)

Arguments

x, y

Camera Trap Data Package objects, as returned by read_camtrapdp().

Value

A single Camera Trap Data Package object that is the combination of x and y.

Transformation details

Both x and y must have a unique dataset name x$name and y$name. This name is used to prefix identifiers in the data that occur in both datasets. For example:

  • x contains deploymentIDs c("a", "b").

  • y contains deploymentIDs c("b", "c").

  • Then merged xy will contain deploymentIDs c("a", "x_b", "y_b", "c").

Data are merged as follows:

  • Deployments are combined, with deploymentID kept unique.

  • Media are combined, with mediaID, deploymentID and eventID kept unique.

  • Observations are combined, with observationID, deploymentID, mediaID and eventID kept unique.

  • Additional resources are retained, with the resource name kept unique.

Metadata properties are merged as follows:

  • name: Removed.

  • id: Removed.

  • created: Set to current timestamp.

  • title: Removed.

  • contributors: Combined, with duplicates removed.

  • description: Combined as two paragraphs.

  • version: Set to 1.0.

  • keywords: Combined, with duplicates removed.

  • image: Removed.

  • homepage: Removed.

  • sources: Combined, with duplicates removed.

  • licenses: Combined, with duplicates removed.

  • bibliographicCitation: Removed.

  • project$id: Removed.

  • project$title: Combined.

  • project$acronym: Removed.

  • project$description: Combined as two paragraphs.

  • project$path: Removed.

  • project$samplingDesign: Sampling design of x.

  • project$captureMethod: Combined, with duplicates removed.

  • project$individuals: TRUE if one of the datasets has TRUE.

  • project$observationLevel: Combined, with duplicates removed.

  • coordinatePrecision: Set to the least precise coordinatePrecision.

  • spatial: Reset based on the new deployments.

  • temporal: Reset based on the new deployments.

  • taxonomic: Combined, with duplicates removed.

  • relatedIdentifiers: Combined, with duplicates removed.

  • references: Combined, with duplicates removed.

  • Custom properties of x are also retained.

See Also

Other transformation functions: round_coordinates(), shift_time(), write_dwc(), write_eml()

Examples

x <- example_dataset() %>%
  filter_deployments(deploymentID %in% c("00a2c20d", "29b7d356"))
y <- example_dataset() %>%
  filter_deployments(deploymentID %in% c("577b543a", "62c200a9"))
x$name <- "x"
y$name <- "y"
merge_camtrapdp(x, y)

Get or set observations

Description

observations() gets the observations from a Camera Trap Data Package object.

⁠observations<-()⁠ is the assignment equivalent.

  • It should only be used within other functions, where the expected data structure can be guaranteed.

  • Metadata (x$taxonomic) are updated to match the assigned observations.

Usage

observations(x)

observations(x) <- value

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

value

A data frame to assign as observations.

Value

A tibble::tibble() data frame with observations.

See Also

Other accessor functions: deployments(), events(), locations(), media(), taxa()

Examples

x <- example_dataset()
# Get the observations
observations(x)

# Set observations (not recommended outside a function)
observations(x) <- head(observations(x), 1)

Print a Camera Trap Data Package

Description

Prints a human-readable summary of a Camera Trap Data Package, as an extension of frictionless::print.datapackage().

Usage

## S3 method for class 'camtrapdp'
print(x, ...)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

...

Further arguments, they are ignored by this function.

Value

print() with a summary of the Camera Trap Data Package object.

Examples

x <- example_dataset()

# Print a summary
print(x)

# Print a summary after filtering
filter_deployments(x, deploymentID == "62c200a9")

Read a Camera Trap Data Package

Description

Reads files from a Camera Trap Data Package (Camtrap DP) into memory.

Usage

read_camtrapdp(file)

Arguments

file

Path or URL to a datapackage.json file.

Value

A Camera Trap Data Package object.

Assign taxonomic information

Camtrap DP metadata has a taxonomic property that can contain extra information for each scientificName found in observations. Such information can include higher taxonomy (family, order, etc.) and vernacular names in multiple languages.

This function will automatically include this taxonomic information in observations, as extra columns starting with taxon..

Assign eventIDs

Observations can contain two classifications at two levels:

Media-based observations (observationLevel = "media") are based on a single media file and are directly linked to it via mediaID.

Event-based observations (observationLevel = "event") are based on an event, defined as a combination of eventID, eventStart and eventEnd. This event can consist of one or more media files, but is not directly linked to these.

This function will automatically assign eventIDs to media, using media.deploymentID = event.deploymentID and ⁠eventStart <= media.timestamp <= eventEnd⁠. Note that this can result in media being linked to multiple events (and thus being duplicated), for example when events and sub-events were defined.

Update metadata

Camtrap DP metadata has a spatial and temporal property that contains the spatial and temporal coverage of the package respectively.

This function will automatically update the spatial and temporal scopes in metadata based on the data.

Examples

file <- "https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0/example/datapackage.json"
x <- read_camtrapdp(file)
x

Round coordinates to generalize camera trap locations

Description

Rounds deployment coordinates to a certain number of digits to fuzzy/generalize camera trap locations. This function can be used before publishing data in order to protect sensitive species and/or prevent theft of active cameras.

Usage

round_coordinates(x, digits)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

digits

Number of decimal places to round coordinates to (1, 2 or 3).

Value

x with chosen coordinatePrecision in metadata and rounded coordinates and calculated coordinateUncertainty in deployments.

Details

Rounding coordinates is a recommended method to generalize sensitive biodiversity information (see Section 4.2 in Chapman 2020). Use this function to do so for your data. Determine the category of sensitivity (see Section 2.2 in Chapman 2020) and choose the associated number of digits :

category sensitivity digits
category 1 extreme (do not publish)
category 2 high 1
category 3 medium 2
category 4 low 3
not sensitive not sensitive all (do not use this function)

The function will:

  1. Set the coordinatePrecision in the metadata (original values will be overwritten):

    digits coordinatePrecision
    1 0.1
    2 0.01
    3 0.001
  2. Round all coordinates in the deployments to the selected number of digits.

  3. Update the coordinateUncertainy (in meters) in the deployments. This uncertainty is based on the number of digits and the latitude, following Table 3 in Chapman & Wieczorek 2020:

    digits 0° latitude 30° latitude 60° latitude 85° latitude
    1 15691 m 14697 m 12461 m 11211 m
    2 1570 m 1470 m 1246 m 1121 m
    3 157 m 147 m 125 m 112 m

    If a coordinatePrecision is already present, the function will subtract the coordinateUncertainty associated with it before setting a new uncertainty (e.g. 0.001 to 0.01 = ⁠original value - 157 + 1570 m⁠). If ⁠original value⁠ is NA, the function will assume the coordinates were obtained by GPS and set ⁠original value = 30⁠.

See Also

Other transformation functions: merge_camtrapdp(), shift_time(), write_dwc(), write_eml()

Examples

x <- example_dataset()

# Original precision
x$coordinatePrecision

# Original coordinates and uncertainty
deployments(x)[c("latitude", "longitude", "coordinateUncertainty")]

# Round coordinates to 1 digit
x_rounded <- round_coordinates(x, 1)

# Updated coordinatePrecision
x_rounded$coordinatePrecision

# Updated coordinates and uncertainty (original 187 - 147 + 14697 = 14737)
deployments(x_rounded)[c("latitude", "longitude", "coordinateUncertainty")]

Shift date-times

Description

Shifts date-times for selected deployments (and associated media and observations) by a specified duration. This function can be used to correct date-time issues such as incorrectly set time zones.

  • Deployments: deploymentStart and deploymentEnd are updated and timestampIssues is set to FALSE.

  • Media: timestamp is updated.

  • Observations: eventStart and eventEnd are updated.

  • Metadata (x$temporal) are updated to match the new temporal scope.

Usage

shift_time(x, deployment_id, duration)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

deployment_id

One or more deploymentIDs.

duration

Difference between the current and new date-times. Provide as a lubridate::duration() or difftime.

Value

x with shifted date-times.

See Also

Other transformation functions: merge_camtrapdp(), round_coordinates(), write_dwc(), write_eml()

Examples

# Set desired duration between current and new date-times (e.g. 4 hours earlier)
library(lubridate, warn.conflicts = FALSE)
duration(-4, units = "hours")

# Or calculate one based on two date-times
current <- ymd_hms("2024-04-01T04:00:00", tz = "UTC")
new <- ymd_hms("2024-04-01T00:00:00", tz = "UTC")
duration <- as.duration(interval(current, new))

# Shift date-times for 2 deployments
x <- example_dataset()
x_shifted <- shift_time(x, c("00a2c20d", "29b7d356"), duration)

# Inspect results
deployments(x)[, c("deploymentID", "deploymentStart", "deploymentEnd")]
deployments(x_shifted)[, c("deploymentID", "deploymentStart", "deploymentEnd")]

Get taxa

Description

Gets the (unique) scientific names and associated taxonomic information from the observations of a Camera Trap Data Package object. Duplicate taxa (i.e. with the same scientificName) are removed, retaining the taxon with (first) a taxonID and (second) the most taxonomic information.

Usage

taxa(x)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

Value

A tibble::tibble() data frame with the taxonomic information, containing at least a scientificName column.

See Also

Other accessor functions: deployments(), events(), locations(), media(), observations()

Examples

x <- example_dataset()
taxa(x)

Get Camtrap DP version

Description

Extracts the version number used by a Camera Trap Data Package object. This version number indicates what version of the Camtrap DP standard was used.

Usage

version(x)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp(). Also works on a Frictionless Data Package, as returned by frictionless::read_package().

Details

The version number is derived as follows:

  1. The version attribute, if defined.

  2. A version number contained in x$profile, which is expected to contain the URL to the used Camtrap DP standard.

  3. x$profile in its entirety (can be NULL).

Value

Camtrap DP version number (e.g. 1.0).

Examples

x <- example_dataset()
version(x)

Write a Camera Trap Data Package to disk

Description

Writes a Camera Trap Data Package and its related Data Resources to disk as a datapackage.json and CSV files.

Usage

write_camtrapdp(x, directory, ...)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

directory

Path to local directory to write files to.

...

Further arguments, passed to frictionless::write_package() (e.g. compress = TRUE).

Value

datapackage.json and CSV files written to disk.

Examples

x <- example_dataset()

# Filter (and therefore change) the dataset
x <- filter_deployments(x, deploymentID == "00a2c20d")

# Write the Camera Trap Data Package to disk
write_camtrapdp(x, directory = "my_directory")

# Check files
list.files("my_directory")

# Clean up (don't do this if you want to keep your files)
unlink("my_directory", recursive = TRUE)

Transform a Camera Trap Data Package to a Darwin Core Archive

Description

Transforms a Camera Trap Data Package object to a Darwin Core Archive.

Usage

write_dwc(x, directory)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

directory

Path to local directory to write files to.

Value

CSV and meta.xml files written to disk. And invisibly, a list of data frames with the transformed data.

Transformation details

This function follows recommendations in Reyserhove et al. (2023) doi:10.35035/doc-0qzp-2x37 and transform data to:

Key features of the Darwin Core transformation:

  • The Occurrence core contains one row per observation (dwc:occurrenceID = observationID).

  • Only observations with observationType = "animal" and observationLevel = "event" are included, thus excluding observations that are (of) humans, vehicles, blanks, unknowns, unclassified and media-based.

  • Deployment information is included in the Occurrence core, such as location, habitat, dwc:samplingProtocol, deployment duration in dwc:samplingEffort and dwc:parentEventID = deploymentID as grouping identifier.

  • Event information is included in the Occurrence core, as event duration in dwc:eventDate and dwc:eventID = eventID as grouping identifier.

  • Media files are included in the Audubon/Audiovisual Media Description extension, with a foreign key to the observation. A media file that is used for more than one observation is repeated.

  • Metadata are used to set the following record-level terms:

    • dwc:datasetID: x$id.

    • dwc:datasetName: x$title.

    • dwc:collectionCode: first source in x$sources.

    • dcterms:license: license name (e.g. CC0-1.0) in x$licenses with scope data. The license name with scope media is used as dcterms:rights in the Audubon Media Description extension.

    • dcterms:rightsHolder: first contributor in x$contributors with role rightsHolder.

    • dwc:dataGeneralizations: set if x$coordinatePrecision is defined.

See Also

Other transformation functions: merge_camtrapdp(), round_coordinates(), shift_time(), write_eml()

Examples

x <- example_dataset()
write_dwc(x, directory = "my_directory")

# Clean up (don't do this if you want to keep your files)
unlink("my_directory", recursive = TRUE)

Transform a Camera Trap Data Package to EML

Description

Transforms the metadata of a Camera Trap Data Package object to an Ecological Metadata Language (EML) file.

Usage

write_eml(x, directory, derived_paragraph = TRUE)

Arguments

x

Camera Trap Data Package object, as returned by read_camtrapdp().

directory

Path to local directory to write files to.

derived_paragraph

If TRUE, a paragraph will be added to the abstract, indicating that data have been transformed using write_dwc().

Value

eml.xml file written to disk. And invisibly, an EML::eml object.

Transformation details

Metadata are derived from what is provided in x. The following properties are set:

  • title: Title as provided in x$title.

  • type: Set to Occurrence in keywords.

  • subtype: Set to Observation in keywords.

  • update frequency: Set to unknown.

  • description: Description as provided in x$description. If derived_paragraph = TRUE a generated paragraph is added, e.g.:

    Data have been standardized to Darwin Core using the camtrapdp R package and only include observations (and associated media) of animals. Excluded are records that document blank or unclassified media, vehicles and observations of humans.

  • license: License with scope data as provided in x$licenses.

  • creators: Contributors as provided in x$contributors, excluding those with roles rightsHolder and publisher.

  • contact: Contributors with role contact. If none exist, first creator.

  • metadata provider: Same as contact.

  • keywords: Keywords as provided in x$keywords.

  • geographic coverage: Bounding box as provided in x$spatial.

  • taxonomic coverage: Taxa as provided in x$taxonomic.

  • temporal coverage: Date range as provided in x$temporal.

  • project data: Title, acronym as identifier, description, and sampling design as provided in x$project.

  • alternative identifier: Identifier as provided in x$id. If this is a DOI, no new DOI will be created when publishing to GBIF.

  • external link: URL of the project as provided in x$project$path.

The following properties are not set:

  • publishing organization

  • associated parties

  • sampling methods

  • citations

  • collection data: not applicable.

See Also

Other transformation functions: merge_camtrapdp(), round_coordinates(), shift_time(), write_dwc()

Examples

x <- example_dataset()
(write_eml(x, directory = "my_directory"))

# Clean up (don't do this if you want to keep your files)
unlink("my_directory", recursive = TRUE)