| Title: | Segment-Based Migration Detection Algorithm |
|---|---|
| Description: | Detection of migration events and segments of continuous residence based on irregular time series of location data as published in Chi et al. (2020) <doi:10.1371/journal.pone.0239408>. |
| Authors: | Johannes Mast [aut, cre] (Author of R code and wrappers, <https://orcid.org/0000-0001-6595-5834>), Guanghua Chi [aut] (Developer of the Algorithm, <https://orcid.org/0000-0003-0430-7483>), German Aerospace Center DLR [cph, fnd] |
| Maintainer: | Johannes Mast <[email protected]> |
| License: | Apache License (>= 2) |
| Version: | 0.1.1 |
| Built: | 2024-11-05 06:16:30 UTC |
| Source: | CRAN |
A three step algorithm to identify segments of continuous presence within trace data
detect_segments( locs, times, param_min_days = 2, param_prop_days = 0.05, param_window_size_days = 20, param_ol_min_frac = 1, return_intermediate_results = FALSE )detect_segments( locs, times, param_min_days = 2, param_prop_days = 0.05, param_window_size_days = 20, param_ol_min_frac = 1, return_intermediate_results = FALSE )
locs |
(character). A vector containing locations corresponding to |
times |
(POSIXct). A vector containing timestamps corresponding to |
param_min_days |
(Optional) numeric. The minimum length in days of a segment. Smaller segments will be eliminated during stage 1. Default is |
param_prop_days |
(Optional) numeric. The minimum fraction of days in a segment during which a user must have been observed at a location. Segments with a smaller proportion will be eliminated. Default is |
param_window_size_days |
(Optional) numeric. The minimum forward window size in days for step 1. Observations separated by a smaller timespan will be connected. Default is |
param_ol_min_frac |
(Optional) numeric. In step 3, do not remove the overlapped segment if the place it belongs to is the mode during the period of overlap and if the place contains more than this fraction of all occurrences. Default is 1 meaning that no segments can persist at overlaps. |
return_intermediate_results |
(Optional) logical. Should the results of Step 1 and 2 be returned as well? If |
The first step in detecting migration requires detecting periods of time when an individual is continuously present in a single location, allowing for some margin of travel from that location (Chi et al., 2020).
These segments are identified from the time series of locs and times in a
three-step procedure:
Step 1: Identify contiguous segments, with no gap exceeding param_window_size_days days,
where the individual is present for at least param_prop_days percent of days in the segment,
and the total length of the segment is at least param_min_days,
Step 2: Merge segments if there are no segments in other locations between them.,
Step 3: Prune overlapping time from segments,
when an individual is associated with segments in multiple locations at a single point in time.
overlapping segments may be allowed to persist if they
contain at least param_ol_min_frac of all observations during the overlap period.
A tibble containing the detected segments as interval with their location as Character.
Johannes Mast [email protected], based on the algorithm by Guanghua Chi [email protected]
Chi, Guanghua, Fengyang Lin, Guangqing Chi, and Joshua Blumenstock. 2020. “A General Approach to Detecting Migration Events in Digital Trace Data.” Edited by Song Gao. PLOS ONE 15 (10): e0239408. https://doi.org/10.1371/journal.pone.0239408.
trace <- MigrationDetectR::example_trace # Detect segments segments <- detect_segments( locs = trace$location, times = trace$timestamp, param_min_days = 3, param_prop_days = 0.06, param_window_size_days = 7, param_ol_min_frac= 0.5) nrow(segments) # check the number of detected segments head(segments) # check the segmentstrace <- MigrationDetectR::example_trace # Detect segments segments <- detect_segments( locs = trace$location, times = trace$timestamp, param_min_days = 3, param_prop_days = 0.06, param_window_size_days = 7, param_ol_min_frac= 0.5) nrow(segments) # check the number of detected segments head(segments) # check the segments
A dataset containing trace of a fictional migrant in the form of location - timestamp pairs.
example_traceexample_trace
A tibble with 200 rows and 2 variables:
POSIXct timestamps of observations
Locations of observations for one of four places (Rivendell, Tatooine, Shangri-La, Narnia)
Find the optimal point in time to split a migration interval
find_best_split(locs, times, movement, from, to)find_best_split(locs, times, movement, from, to)
locs |
character, A vector of the locations of occurrences. |
times |
POSIXct, A vector of the occurrences corresponding timestamps. |
movement |
A lubridate interval for which the best split is to be found. |
from |
character, the name of the location the |
to |
character, the name of the location the |
The function checks which occurrences by locs and times fall within the interval given by movement.
It then tries to find the optimal point in time to split the interval, using the following two criteria:
The point which minimizes the number of misclassified days, i.e., the number of days when the migrant
appears at to before the migration date and days when the migrant appears at
from after the migration date.
In cases where multiple days yield the same number of misclassifications, we select the last timestamp as the migration date
A tibble of 2 fields:
split_time, a lubridate date time which indicates the time of the optimal split found
split_correctness, a numeric date time which indicates the split's ratio of the wrongly assigned days to the correctly assigned days
Johannes Mast [email protected], based on the algorithm by Guanghua Chi [email protected]
Chi, Guanghua, Fengyang Lin, Guangqing Chi, and Joshua Blumenstock. 2020. “A General Approach to Detecting Migration Events in Digital Trace Data.” Edited by Song Gao. PLOS ONE 15 (10): e0239408. https://doi.org/10.1371/journal.pone.0239408.
identify_migrations
identify_migrations( segs, locs, min_res_length = 90, occurrence_locs = NULL, occurrence_times = NULL, verbose = TRUE )identify_migrations( segs, locs, min_res_length = 90, occurrence_locs = NULL, occurrence_times = NULL, verbose = TRUE )
segs |
A vector of interval, a vector of intervals which indicate residence segments, such as detected by detect_segments. |
locs |
A vector of Character, locations which correspond to |
min_res_length |
(Optional) Numeric. A vector of days indicating the minimum number of days for |
occurrence_locs |
(Optional) Character. See |
occurrence_times |
(Optional) If provided along with the matching |
verbose |
(Optional) logical. Output optional messages? Default is |
A tibble containing the detected true relocations, if any. Contains the fields:
from Character, the location from which the relocations started.
to Character, the location from which the relocations started.
movement_interval interval of the transitionary period, starting with the end of the prior residency and ending with the start of the new residency.
movement_length The duration of the transitionary period in seconds.
movement_midrange The midpoint of the transitionary period.
If occurrence_locs and occurrence_times were provided, find_best_split will be used to detect the optimum split time, and the following columns will be added:
split_time, a POSIXct which indicates the time of the optimal split.
split_correctness, a numeric which as a quality measure of splot_time reports the split's ratio of wrongly assigned days to the correctly assigned days.
Johannes Mast [email protected], based on the algorithm by Guanghua Chi [email protected]
Chi, Guanghua, Fengyang Lin, Guangqing Chi, and Joshua Blumenstock. 2020. “A General Approach to Detecting Migration Events in Digital Trace Data.” Edited by Song Gao. PLOS ONE 15 (10): e0239408. https://doi.org/10.1371/journal.pone.0239408.
trace <- MigrationDetectR::example_trace # Detect segments segments <- detect_segments( locs = trace$location, times = trace$timestamp, param_min_days = 3, param_prop_days = 0.06, param_window_size_days = 7) nrow(segments) # check the number of detected segments migrations <- identify_migrations( segs = segments$segments, locs = segments$locs, min_res_length = 90, occurrence_locs = trace$location, occurrence_times = trace$timestamp ) nrow(migrations) # check the number of identified migrations head(migrations) # check the detected migrationstrace <- MigrationDetectR::example_trace # Detect segments segments <- detect_segments( locs = trace$location, times = trace$timestamp, param_min_days = 3, param_prop_days = 0.06, param_window_size_days = 7) nrow(segments) # check the number of detected segments migrations <- identify_migrations( segs = segments$segments, locs = segments$locs, min_res_length = 90, occurrence_locs = trace$location, occurrence_times = trace$timestamp ) nrow(migrations) # check the number of identified migrations head(migrations) # check the detected migrations
Implementation of Migration detection algorithm, published by Chi et al. (2020) in A general approach to detecting migration events in digital trace data (doi:10.1371/journal.pone.0239408 )
Compared to the reference, this implementation works at the precision of seconds rather than days. At the expense of speed, it is applicable at finer timescales.
The segment detector has the additional option to allow for one of several overlapping segments to persist if it contains the majority of occurrences during the overlap period.
First, transform your data into the format required by the package: Two aligned vectors, one with locations and one with timestamps. Use the detect_segments function to identify segments of continuous residence. Then, use the identify_migrations function on the segments to detect migrations. To optionally determine the best split time, pass the original locations and timestamps vectors.
Johannes Mast (R Implementation)
Guanghua Chi (Developer of the Algorithm)