R Code for Extracting Independent Events

[Nia Smith]

Dear camtrapR Community,

I hope you are all doing well?

I apologize for asking a question slightly unrelated to the group... I don't have anywhere else to ask.. I have a camera trapping data set which I would like to extract only the independent events from. With independence taken at 30 minutes. Could anyone please be so kind to help me find such code? My data is not in the normal camtrapR format, and basically just in a normal R dataframe with the following columns: Station, Date, Time, Species, and DateTimeOriginal.

The code below is the closest I can get, but it's not quite right... It deletes more records than it should...

#####################################################

# Fake data:
df <- structure(
  list(
    spp = c("X", "X", "X", "X", "X", "X", "X", "X", "X", "Y", "Y", "Y", "Y", "Y", "Y", "Y", "Z", "Z", "Z", "Z", "Z", "Z", "Z"),
    loc = c(1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 2, 3, 3, 3, 4, 2, 3, 3, 3, 3, 3, 4),
    date_time = structure(c(1609451755, 1609452355, 1609581600, 1609582202, 1609583403, 1609585204, 1609668005, 1609538155, 1609841700, 1609495204, 1609583406, 1609668000, 1609539071, 1609756205, 1609758001, 1609581600, 1609668067, 1609451793, 1609452213, 1609452633, 1609495200, 1609626404, 1609581600), tzone = "", class = c("POSIXct", "POSIXt")),
    date = structure(c(18627, 18628, 18629, 18629, 18629, 18629, 18630, 18628, 18632, 18628, 18629, 18630, 18629, 18631, 18631, 18629, 18630, 18627, 18628, 18628, 18628, 18630, 18629), class = "Date"),
    time = c("23:55:55", "00:05:55", "12:00:00", "12:10:02", "12:30:03", "13:00:04", "12:00:05", "23:55:55", "12:15:00", "12:00:04", "12:30:06", "12:00:00", "00:11:11", "12:30:05", "13:00:01", "12:00:00", "12:01:07", "23:56:33", "00:03:33", "00:10:33", "12:00:00", "00:26:44", "12:00:00")),
  row.names = c(NA, -23L), class = "data.frame")

#####################################################

# Bad code
df %>%
  arrange(date_time) %>%
  group_by(spp, loc) %>%
  filter(
    as.integer(
      difftime(date_time, lag(date_time), units = 'secs')
    ) > 1800 | row_number() == 1) %>%
  ungroup()
#####################################################

Any guidance would be well appreciated! Thanks!

:)

Best Wishes,

Nia

[Juergen Niedballa]

Hi Nia, 

search in the forum for the keyword "assessTemporalIndependence". It is an internal function of camtrapR that can be used for filtering a record table by time differences. It's not a pretty solution and doesn't do any of the checks that camtrapR normally does, but it seems to work. 

Based on your code, here's an example. 

colnames(df) <- c("Species", "Station", "DateTimeOriginal", "Date", "Time")

df$Station <- as.character(df$Station)

df_filt <- camtrapR:::assessTemporalIndependence(df, 

                                      deltaTimeComparedTo = "lastIndependentRecord",

                                      stationCol = "Station",

                                      camerasIndependent = FALSE,

                                      columnOfInterest = "Species",

                                      minDeltaTime = 30)    # minutes

You may also want to look at the difference between deltaTimeComparedTo = "lastIndependentRecord" and "lastRecord". For more details on that, see ?recordTable

Please don't use any assessTemporalIndependence scripts files I may have attached to previous threads. Better to install the latest version of camtrapR and then use the internal function with camtrapR:::assessTemporalIndependence()

Is the output what you'd expect? Seemed ok at first glance, but please check thoroughly. 

Best regards,

Jürgen