Add support for Camtrap DP 1.0

[peterdesmet]

Camtrap DP 1.0 has been released: https://github.com/tdwg/camtrap-dp/releases/tag/1.0. We're planning to update the Agouti export to Camtrap DP 1.0 directly (and not have 1.0-RC.1). Before we can release that Agouti export however, camtraptor needs to be updated to support 1.0, otherwise users won't be able to read the data.

• Update convert_to_0.1.6() and support 1.0 instead of 1.0-rc.1 (this version never made it to production in Agouti or IPT)
• observations.taxonID has been removed, downconvert by including in observations (leave empty)
• deployments.cameraDepth has been added, downconvert by removing it
• Update

  camtraptor/R/zzz.R

  Line 400 in db6c53a

  by = c("taxonID", "scientificName")

  to only join on scientificName (since Camtrap DP 1.0 no longer has taxonID)
• Downconvert media.captureMethod values activityDetection to motionDetection
• Downconvert project.catureMethod (in metadata) values activityDetection to motionDetection
• Pass all tests

[PietrH]

version is not supported ...

camtraptor/R/read_camtrap_dp.R

Lines 97 to 107 in db6c53a

	# check version is supported
	assertthat::assert_that(
	version %in% supported_versions,
	msg = paste0(
	glue::glue("Version {version} "),
	"is not supported. Supported versions: ",
	glue::glue_collapse(glue::glue("{supported_versions}"),
	sep = " ",
	last = " and "),
	".")
	)

convert_metadata_to_0.1.6():

camtraptor/R/zzz.R

Lines 431 to 484 in db6c53a

	#' Convert a Camtrap DP to version 0.1.6
	#'
	#' This conversion function takes as input a Camtrap DP and returns
	#'
	#' @param package Camera trap data package object.
	#' @param from Character identifying the version of `package`.
	#' @param media If `TRUE` (default), read media records into memory. If `FALSE`,
	#' ignore media file to speed up reading larger Camtrap DP packages.
	#' @noRd
	convert_to_0.1.6 <- function(package, from = "1.0-rc.1", media = TRUE){
	if (from == "0.1.6") {
	message(glue::glue("package's version: {from}. No conversion needed."))
	return(package)
	}
	# check version
	supported_versions <- c("1.0-rc.1")
	assertthat::assert_that(
	from %in% supported_versions,
	msg = paste0(
	"Only conversion from ",
	glue::glue_collapse(glue::glue("{supported_versions}"),
	sep = " ",
	last = " and "),
	" to 0.1.6 is supported."
	)
	)
	# check data slot is present in package
	assertthat::assert_that(
	"data" %in% names(package),
	msg = "Can't find `data` element in `package`."
	)
	# notify about conversion
	message(
	writeLines(
	c(
	"The dataset uses Camtrap DP version 1.0-rc.1, it has been converted to 0.1.6.",
	"See https://inbo.github.io/camtraptor/#camtrap-dp for details."
	)
	)
	)
	# convert metadata
	package <- convert_metadata_to_0.1.6(package, from)
	# convert deployments
	package <- convert_deployments_to_0.1.6(package, from)
	# convert media
	if (media) {
	package <- convert_media_to_0.1.6(package, from)
	}
	# convert observations
	package <- convert_observations_to_0.1.6(package, from)
	return(package)
	}

In the future we'll stack these functions, every incoming version will be upgraded to the next version serially from version to version.

Everything will internally be converted to the newest version.

At the moment the internal datamodel needs to be changed to v1.0 still.

---

What we want to change here is that convert_metadata_to_0.1.6() so it supports v1.0, and drop support for the rc since it's not in the wild.

In the future we want the internal data model to change to use the most recent version, but not for this issue.

[PietrH]

Differences between RC and v1.0

• taxonID has been removed from observations, we need to create this field for version v0.1.6
  How will we populate this field?

Peter proposes to leave it empty. So add it but leave it empty.

The function that links the taxonomy with the observations (add_taxonomic_info() -> get_species())

camtraptor/R/zzz.R

Line 400 in db6c53a

by = c("taxonID", "scientificName")

Needs to change to only join on scientificName

• Do we need additional tests? Unclear if all changes are covered

[PietrH]

example package to test on: https://github.com/tdwg/camtrap-dp/tree/main/example