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Compute flights from stationary periods

Source: R/stap2flight.R
stap2flight.Rd

Convert a stationary period data.frame stap into a flight data.frame or list. Flight are computed as the difference between the end of a stationary period to the start of the next one. Because the pressure/acceleration is labelled for "in flight", the bird was already in flight before the first label and after the last label. We account for this by adding to all flights duration half the temporal resolution of the sensor.

You can compute the flight between specific stationary periods using include_stap_id. In this case, the flight duration is computed as the sum of individual flights in between.

You can return the flight as a data.frame or as a list if you want to retrieve the information of all individual flight between the include_stap_id.

Usage

stap2flight(
  stap,
  include_stap_id = NULL,
  format = "df",
  units = "hours",
  return_numeric = TRUE
)

Arguments

stap

a stationary period data.frame (see tag_label_stap()).

include_stap_id

vector of the stationary period stap_id to consider in the flight. Default is to use stap$stap_id[stap$include] or stap$stap_id if model is not available in stap.

format

character to return a list "list" or a data.frame "df" (see description)

units

character string. Units in which the results are desired. Can be abbreviated. See difftime()

return_numeric

logical to return the duration as a numeric rather than with a duration format.

Value

A list or a data.frame (see description) containing

  • start: Start time of the (first) flight

  • end: End time of the (last) flight

  • stap_id_s: Source stap_id (i.e, start)

  • stap_id_t: Target stap_id (i.e, end)

  • duration: (Sum of the) duration of flight(s)

  • (n: Number of flights) The value in brackets are only for the data.frame

Examples

setwd(system.file("extdata", package = "GeoPressureR"))
tag <- tag_create("18LX", quiet = TRUE) |> tag_label(quiet = TRUE)

# By default, return a data.frame of all individual flights
knitr::kable(stap2flight(tag$stap))
#> 
#> 
#> |start               |end                 | stap_s| stap_t| duration|  n|
#> |:-------------------|:-------------------|------:|------:|--------:|--:|
#> |2017-08-04 19:47:30 |2017-08-04 23:17:30 |      1|      2| 3.500000|  1|
#> |2017-08-05 19:27:30 |2017-08-06 02:52:30 |      2|      3| 7.416667|  1|
#> |2017-08-06 19:12:30 |2017-08-07 03:12:30 |      3|      4| 8.000000|  1|
#> |2017-08-07 19:12:30 |2017-08-08 00:12:30 |      4|      5| 5.000000|  1|

# Compute the total flight between stap 1,3 and 5. Sum flight duration in between.
knitr::kable(stap2flight(tag$stap, include_stap_id = c(1, 3, 5)))
#> 
#> 
#> |   |start               |end                 | stap_s| stap_t| duration|  n|
#> |:--|:-------------------|:-------------------|------:|------:|--------:|--:|
#> |1  |2017-08-04 19:47:30 |2017-08-06 02:52:30 |      1|      3| 10.91667|  2|
#> |3  |2017-08-06 19:12:30 |2017-08-08 00:12:30 |      3|      5| 13.00000|  2|

# Can also return as a list of data.frame to access individual flights information.
knitr::kable(stap2flight(tag$stap,
  include_stap_id = c(1, 3, 5), format = "list",
  units = "secs"
))
#> 
#> 
#> |start               |end                 | stap_s| stap_t| duration|
#> |:-------------------|:-------------------|------:|------:|--------:|
#> |2017-08-04 19:47:30 |2017-08-04 23:17:30 |      1|      2|    12600|
#> |2017-08-05 19:27:30 |2017-08-06 02:52:30 |      2|      3|    26700|
#> 
#> |   |start               |end                 | stap_s| stap_t| duration|
#> |:--|:-------------------|:-------------------|------:|------:|--------:|
#> |3  |2017-08-06 19:12:30 |2017-08-07 03:12:30 |      3|      4|    28800|
#> |4  |2017-08-07 19:12:30 |2017-08-08 00:12:30 |      4|      5|    18000|