Fix 288 and 279 #289
Fix 288 and 279 #289
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The new mica datapackage example requires some changes to make meaningful example of setting minDeltaTime to remove not independent observations.
Column added in 201737e
Multiply by ten actually or in character terms adding a zero
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@MartijnUH: could you please check the two functions in your use cases? |
Co-Authored-By: Peter Desmet <[email protected]>
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camtraptor/tests/testthat/test-get_cam_op.R Lines 74 to 77 in 3af4488 It's a real shame testthat has no real expectation for matrices, |
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easier to read and slight performance benefit
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I've left some questions out of interest for @damianooldoni to have a look at when it suits him. Any changes I felt necessary I've made myself. I looked at the functionality as best as I could, but will depend on @MartijnUH to check if it suits the teams needs.
Great job Damiano!
| record_table <- get_record_table(mica) | ||
| expected_colnames <- c("Station", | ||
| "Species", | ||
| "n", | ||
| "DateTimeOriginal", | ||
| "Date", | ||
| "Time", | ||
| "delta.time.secs", | ||
| "delta.time.mins", | ||
| "delta.time.hours", | ||
| "delta.time.days", | ||
| "Directory", | ||
| "FileName" | ||
| ) | ||
| testthat::expect_identical(names(record_table), expected_colnames) |
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| record_table <- get_record_table(mica) | |
| expected_colnames <- c("Station", | |
| "Species", | |
| "n", | |
| "DateTimeOriginal", | |
| "Date", | |
| "Time", | |
| "delta.time.secs", | |
| "delta.time.mins", | |
| "delta.time.hours", | |
| "delta.time.days", | |
| "Directory", | |
| "FileName" | |
| ) | |
| testthat::expect_identical(names(record_table), expected_colnames) | |
| expect_named( | |
| get_record_table(mica), | |
| c( | |
| "Station", | |
| "Species", | |
| "n", | |
| "DateTimeOriginal", | |
| "Date", | |
| "Time", | |
| "delta.time.secs", | |
| "delta.time.mins", | |
| "delta.time.hours", | |
| "delta.time.days", | |
| "Directory", | |
| "FileName" | |
| ) | |
| ) |
| deltaTimeComparedTo = "lastRecord" | ||
| )) %>% | ||
| nrow() | ||
| testthat::expect_true(nrow_delta_10000 < nrow_delta_0) |
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Did you know about:
testthat::expect_lt()
These comparison expectations have slightly nicer failure messages
https://testthat.r-lib.org/reference/comparison-expectations.html
| mica_dup <- mica | ||
| # create duplicates at 2020-07-29 05:46:48, location: B_DL_val 5_beek kleine vijver | ||
| # use 3rd observation as the first two are unknown or blank (= no animal) | ||
| mica_dup$data$observations[,"sequenceID"] <- mica_dup$data$observations$sequenceID[3] |
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I would use purrr::chuck for this, because I find it more readable. But it's a matter of preference. Good job documenting by the way!
purrr::pluck is careful, and will fail silently, purrr::chuck will trow (chuck) an error when the index doesn't exist, another advantage.
| get_record_table(mica, | ||
| minDeltaTime = 60, | ||
| mica_dependent <- mica | ||
| mica_dependent$data$observations[4,"timestamp"] <- lubridate::as_datetime("2020-07-29 05:55:00") |
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I tend to use lubridate::dmy_hms() for character vectors, is there an advantage to lubridate::as_datetime()?
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| ### Session and camera IDs | ||
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| You can specify the column containing the camera IDs to be added to the station names following the camtrapR's convention: `Station__CAM_CameraID`. Only the row names are shown: |
| "it must be one of the deployments column names." | ||
| ) | ||
| ) | ||
| camera_values <- package$data$deployments[[camera_col]] |
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I'd personally use purrr::chuck() for this so I throw an error when I try to access an index that doesn't exist. I'm not really sure what the base behaviour is in this case. Ok to leave like this.
| output <- output %>% | ||
| dplyr::left_join(n_media, | ||
| by = "sequenceID" | ||
| ) | ||
| testthat::expect_equal(output$len, output$n) | ||
| testthat::expect_equal(output$len, output$n_media) |
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n_media is a integer vector, and len is a double vector. Is this intentional?
This PR solves:
get_record_table#279get_cam_op: allowsessionColargument to addsessionIDinstationNamecolumn as in camtrapR #288Also, some examples of
get_record_tablehave been updated as the last version ofmicadatapackage we are using do not contain observations made in quick succession. Same holds true for the correspondent unit-tests.