Open
Description
A part of a deployment can be invalid. E.g. a storm happens and the tree with the camera trap falls. All observations after this event are invalid.
This has implications for:
- deploymentEnd
- observations and media
- metadata
There are two options:
- users code this themselves, and can be helped with a vignette
- a new function to mutate deployments
User case:
library(camtrapdp)
raw_data <- example_dataset()
#> ✔ Updating temporal and spatial scopes in metadata based on data.
deploymentID_storm <- "62c200a9"
new_deploymentEnd <- as.POSIXct("2021-04-02 17:31:00", tz = "Europe/Brussels")
# inspect raw data
deployments(raw_data) %>%
dplyr::select(deploymentID, deploymentStart, deploymentEnd)
#> # A tibble: 4 × 3
#> deploymentID deploymentStart deploymentEnd
#> <chr> <dttm> <dttm>
#> 1 00a2c20d 2020-05-30 02:57:37 2020-07-01 09:41:41
#> 2 29b7d356 2020-07-29 05:29:41 2020-08-08 04:20:40
#> 3 577b543a 2020-06-19 21:00:00 2020-06-28 23:33:22
#> 4 62c200a9 2021-03-27 20:38:18 2021-04-18 21:25:00
observations(raw_data) %>%
dplyr::filter(deploymentID == deploymentID_storm) %>%
dplyr::summarise(last_eventEnd = max(eventEnd))
#> # A tibble: 1 × 1
#> last_eventEnd
#> <dttm>
#> 1 2021-04-18 21:25:00
media(raw_data) %>%
dplyr::filter(deploymentID == deploymentID_storm) %>%
dplyr::summarise(last_timestamp = max(timestamp))
#> # A tibble: 1 × 1
#> last_timestamp
#> <dttm>
#> 1 2021-04-18 21:25:00
# mutate deploymentEnd
clean_data <- raw_data
camtrapdp::deployments(clean_data) <-
camtrapdp::deployments(clean_data) %>%
dplyr::mutate(
deploymentEnd =
as.POSIXct(
dplyr::if_else(
deploymentID == deploymentID_storm,
new_deploymentEnd,
deploymentEnd
)
)
)
# Identify observations and media to remove
to_remove <-
clean_data %>%
camtrapdp::filter_observations(deploymentID == deploymentID_storm, eventEnd >= new_deploymentEnd)
#> Warning: There was 1 warning in `dplyr::filter()`.
#> ℹ In argument: `eventEnd >= new_deploymentEnd`.
#> Caused by warning in `.check_tzones()`:
#> ! 'tzone' attributes are inconsistent
observations_to_remove <- observations(to_remove)
media_to_remove <- media(to_remove)
# Update observations and media
observations(clean_data) <-
observations(clean_data) %>%
dplyr::anti_join(observations_to_remove)
#> Joining with `by = join_by(observationID, deploymentID, mediaID, eventID,
#> eventStart, eventEnd, observationLevel, observationType, cameraSetupType,
#> scientificName, count, lifeStage, sex, behavior, individualID,
#> individualPositionRadius, individualPositionAngle, individualSpeed, bboxX,
#> bboxY, bboxWidth, bboxHeight, classificationMethod, classifiedBy,
#> classificationTimestamp, classificationProbability, observationTags,
#> observationComments, taxon.taxonID, taxon.taxonRank, taxon.vernacularNames.eng,
#> taxon.vernacularNames.nld)`
media(clean_data) <-
media(clean_data) %>%
dplyr::anti_join(media_to_remove)
#> Joining with `by = join_by(mediaID, deploymentID, captureMethod, timestamp,
#> filePath, filePublic, fileName, fileMediatype, exifData, favorite,
#> mediaComments, eventID)`
# inspect clean data
deployments(clean_data) %>%
dplyr::select(deploymentID, deploymentStart, deploymentEnd)
#> # A tibble: 4 × 3
#> deploymentID deploymentStart deploymentEnd
#> <chr> <dttm> <dttm>
#> 1 00a2c20d 2020-05-30 02:57:37 2020-07-01 11:41:41
#> 2 29b7d356 2020-07-29 05:29:41 2020-08-08 06:20:40
#> 3 577b543a 2020-06-19 21:00:00 2020-06-29 01:33:22
#> 4 62c200a9 2021-03-27 20:38:18 2021-04-02 17:31:00
observations(clean_data) %>%
dplyr::filter(deploymentID == deploymentID_storm) %>%
dplyr::summarise(last_eventEnd = max(eventEnd))
#> # A tibble: 1 × 1
#> last_eventEnd
#> <dttm>
#> 1 2021-03-31 22:59:21
media(clean_data) %>%
dplyr::filter(deploymentID == deploymentID_storm) %>%
dplyr::summarise(last_timestamp = max(timestamp))
#> # A tibble: 1 × 1
#> last_timestamp
#> <dttm>
#> 1 2021-03-31 22:59:21
# The last observation is a couple of days before the storm (new deploymentEnd)
# (Update metadata in assignment functions is not merged with main branch yet)
clean_data <- clean_data %>%
camtrapdp:::update_temporal() %>%
camtrapdp:::update_taxonomic()Created on 2024-10-15 with reprex v2.1.1