Extract tibble_df and text message from activitylog object - r

Question

I have the code below
library(bupar)
library(daqapo)
hospital<-hospital
hospital %>%
rename(start = start_ts,
complete = complete_ts) -> hospital
hospital %>%
convert_timestamps(c("start","complete"), format = dmy_hms) -> hospital
hospital %>%
activitylog(case_id = "patient_visit_nr",
activity_id = "activity",
resource_id = "originator",
timestamps = c("start", "complete")) -> hospital
hospital %>%
detect_time_anomalies()
which gives
*** OUTPUT ***
For 5 rows in the activity log (9.43%), an anomaly is detected.
The anomalies are spread over the activities as follows:
# A tibble: 3 × 3
activity type n
<chr> <chr> <int>
1 Registration negative duration 3
2 Clinical exam zero duration 1
3 Trage negative duration 1
Anomalies are found in the following rows:
# Log of 10 events consisting of:
3 traces
3 cases
5 instances of 3 activities
5 resources
Events occurred from 2017-11-21 11:22:16 until 2017-11-21 19:00:00
# Variables were mapped as follows:
Case identifier: patient_visit_nr
Activity identifier: activity
Resource identifier: originator
Timestamps: start, complete
# A tibble: 5 × 10
patient_visit_nr activity originator start complete triagecode specialization .order durat…¹ type
<dbl> <chr> <chr> <dttm> <dttm> <dbl> <chr> <int> <dbl> <chr>
1 518 Registration Clerk 12 2017-11-21 11:45:16 2017-11-21 11:22:16 4 PED 1 -23 nega…
2 518 Registration Clerk 6 2017-11-21 11:45:16 2017-11-21 11:22:16 4 PED 2 -23 nega…
3 518 Registration Clerk 9 2017-11-21 11:45:16 2017-11-21 11:22:16 4 PED 3 -23 nega…
4 520 Trage Nurse 17 2017-11-21 13:43:16 2017-11-21 13:39:00 5 URG 4 -4.27 nega…
5 528 Clinical exam Doctor 1 2017-11-21 19:00:00 2017-11-21 19:00:00 3 TRAU 5 0 zero…
# … with abbreviated variable name ¹​duration
from this output I would like to extract the text message
For 5 rows in the activity log (9.43%), an anomaly is detected.
The anomalies are spread over the activities as follows:
and also in another object the tibble
activity type n
<chr> <chr> <int>
1 Registration negative duration 3
2 Clinical exam zero duration 1
3 Trage negative duration 1

Answer 1

The string you are trying to obtain is a message, and though it is possible to capture a message, it's not that straightforward. You can easily generate it by emulating a couple of lines within the function though.
If you store the result of detect_time_anomalies:
anomalies <- hospital %>% detect_time_anomalies()
Then you can generate the message like this:
paste0("For ", nrow(anomalies), " rows in the activity log (",
round(nrow(anomalies)/nrow(hospital) * 100, 2),
"%), an anomaly is detected.")
#> [1] "For 5 rows in the activity log (9.43%), an anomaly is detected."
Similarly, you can obtain the output table like this:
anomalies %>%
group_by(activity, type) %>%
summarize(n = n()) %>%
arrange(desc(n))
#> # A tibble: 3 x 3
#> activity type n
#> <chr> <chr> <int>
#> 1 Registration negative duration 3
#> 2 Clinical exam zero duration 1
#> 3 Trage negative duration 1
Created on 2022-12-13 with reprex v2.0.2