Description Usage Arguments Details Value Author(s) Examples
Subsamples temporal records of different entities to a data set which only includes records that occur at predefined and equally spaced synchronization events. A subsample is created for each possible combination of entities (unless restricted by argument minEntities, maxEntities or mustEntities).
1 2 3 4 5 6 7 8 9 10 11 12 | syncSubsample(
x,
startSearch = min(as.character(x$study.local.timestamp)),
endSearch = max(as.character(x$study.local.timestamp)),
syncIntervalSecs = 3600,
syncAccuracySecs = 60,
minEntities = 2,
maxEntities = length(unique(x$individual.local.identifier)),
mustEntities = NULL,
completeSyncsOnly = TRUE,
fast = TRUE
)
|
x |
a data frame with the following columns (further columns are allowed, but will be ignored): individual.local.identifier: character, entity ID study.local.timestamp: character, time of format "YYYY-MM-DD HH:MM:SS" Such a data frame can be created by importing data from www.movebank.org. If the output is to be processed with function utm.easting: numeric, planar x coordinate. Although the name indicates UTM coordinates other planar coordinate systems are also allowed. utm.northing: analogue to utm.easting |
startSearch |
character, time of format "YYYY-MM-DD HH:MM:SS" as the start time for the creation of synchronization events. Default is the minimum timestamp in the data. |
endSearch |
analogue to startSearch. |
syncIntervalSecs |
numeric, interval between synchronization events in seconds. (e.g., 60*60*24*3 defines a three day interval) |
syncAccuracySecs |
numeric, accuracy for synchronization events in seconds. (e.g., 60*60*2 defines a two hour accuracy) |
minEntities |
numeric, minimum number of entities to be included in the synchronization events. |
maxEntities |
analogue to minEntities |
mustEntities |
character, vector of IDs of entities which have to be included in the synchronization events. |
completeSyncsOnly |
boolean, if TRUE (default) only events will appear in the output where each entity of a given combination of entities has a record. If FALSE also events with no records for some entities will appear in the output. |
fast |
boolean, if TRUE (default) synchronized subsamples are created only for those combinations of entities that seem to be the most prominent in the input data. If FALSE synchronized subsamples are created for all combinations of entities in the input data. See details. |
The synchronization events are created with a start time as the first synchronization event (argument startSearch) and an interval between following synchronization events. Each synchronization event has an accuracy. All records of a given combination of entities which fall into synchronization events + - accuracy are selected for the subsample. If there is more than one record for an entity in a synchronization event + - accuracy the record that is closest to the synchronization event is selected. The arguments startSearch, syncIntervalSecs and syncAccuracySecs must be chosen with respect to the input data in order to get good synchronization results.
Running the function with fast = FALSE one can find the combination of entities with the maximum number of synchronization events. However, an input data set with more then 8 to 10 entities should be processed with fast = TRUE. Otherwise the calculations can take a long time. (For input data with 10 entities there are more than 1000 possible combinations of entities.)
The synchronization events are numbered from 1 to n. These numbers
are referred to as sync IDs. If no records are present at a given
synchronization event the ID for this event will not appear in the
output subsample. Thus the sync IDs in the subsample show if
subsequent pairs of synchronized events exist (e.g., sync ID
1 and 2, sync ID 2 and 3, ...). Such pairs can be used to calculate
the Movement Coordination Index, see function mci
.
List, returns a list with 3 elements named overview, data, and entities.
overview |
An overview of the synchronized subsamples for all possible combinations of entities. Each row refers to the respective element in the data and entities lists (see below). E.g., for the data described in row 1 see <output>$data[[1]] and <output>$entities[[1]]. The overview table contains the following columns: numberOfEntities: the number of entities used for creating the subsample numberOfSyncs: number of synchronized events in the subsample numberOfSubsequentSyncs: number subsequent synchronized events (see details) firstEvent: time of first synchronization event lastEvent: analogue to lastEvent syncIntervalSecs: interval used for creating the synchronization events syncAccuracySecs: accuracy of the synchronization events |
data |
A list containing the subsampled data described in the overview. The subsamples have the same columns as the input data set plus the additional columns syncTime and syncID for the time and ID of the synchronization events respectively. |
entities |
A list containing the entity combinations used for creating the synchronized subsamples. |
Martin Rimmler (maintainer, martin.rimmler[AT]gmail.com), Thomas Mueller
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | # load example data
data(gazelleRelocations)
# subsample sychronal events
syncRelocs <- syncSubsample(x = gazelleRelocations,
startSearch = "2007-09-05 00:00:00",
syncIntervalSecs = 3600*24*16,
syncAccuracySecs = 3600*24)
# show results overview
syncRelocs$overview
# show first subsample
syncRelocs$data[[1]]
# show entities of first subsample
syncRelocs$entities[[1]]
|
numberOfEntities numberOfSyncs numberOfSubsequentSyncs firstEvent
1 3 20 19 2007-09-21 00:00:00
2 2 21 20 2007-09-05 00:00:00
lastEvent syncIntervalSecs syncAccuracySecs
1 2008-07-21 00:00:00 1382400 86400
2 2008-07-21 00:00:00 1382400 86400
individual.local.identifier sex study.local.timestamp utm.easting
296 602189A female 2007-09-21 00:01:06 868.6244
1017 602190A female 2007-09-21 00:00:36 773.6690
1703 602191A female 2007-09-21 00:01:05 917.1640
325 602189A female 2007-10-07 00:01:36 990.8651
1042 602190A female 2007-10-07 00:01:23 755.7416
1732 602191A female 2007-10-07 00:01:23 903.9009
354 602189A female 2007-10-23 00:01:06 1024.8414
1071 602190A female 2007-10-23 00:00:37 752.4900
1761 602191A female 2007-10-23 00:00:37 924.2670
382 602189A female 2007-11-08 00:01:07 1026.5730
1100 602190A female 2007-11-08 00:00:37 753.5425
1790 602191A female 2007-11-08 00:00:36 899.7673
411 602189A female 2007-11-24 00:02:55 1003.2585
1129 602190A female 2007-11-24 00:00:37 797.3807
1819 602191A female 2007-11-24 00:00:37 903.8494
440 602189A female 2007-12-10 00:01:25 920.8909
1158 602190A female 2007-12-10 00:00:37 762.9527
1848 602191A female 2007-12-10 00:00:37 900.1156
469 602189A female 2007-12-26 00:01:06 919.5677
1187 602190A female 2007-12-26 00:00:36 762.9914
1877 602191A female 2007-12-26 00:00:54 851.4206
498 602189A female 2008-01-11 00:01:59 920.2279
1216 602190A female 2008-01-11 00:00:36 865.5521
1906 602191A female 2008-01-11 00:00:36 870.9232
527 602189A female 2008-01-27 00:01:24 928.8176
1241 602190A female 2008-01-27 00:00:54 874.1118
1934 602191A female 2008-01-27 00:00:55 870.2210
556 602189A female 2008-02-12 00:01:24 921.2901
1270 602190A female 2008-02-12 00:00:37 858.0300
1963 602191A female 2008-02-12 00:00:36 871.7373
584 602189A female 2008-02-28 00:01:36 929.5734
1298 602190A female 2008-02-28 00:00:36 848.4739
1991 602191A female 2008-02-28 00:00:36 876.9959
613 602189A female 2008-03-15 00:01:07 855.4991
1327 602190A female 2008-03-15 00:00:37 815.5586
2020 602191A female 2008-03-15 00:00:38 845.2368
642 602189A female 2008-03-31 00:01:07 853.9082
1356 602190A female 2008-03-31 00:00:36 791.4997
2049 602191A female 2008-03-31 00:00:36 841.0786
671 602189A female 2008-04-16 00:01:06 855.0381
1385 602190A female 2008-04-16 00:00:37 775.0580
2078 602191A female 2008-04-16 00:00:37 783.5925
700 602189A female 2008-05-02 00:01:07 864.9775
1414 602190A female 2008-05-02 00:00:37 783.6780
2107 602191A female 2008-05-02 00:00:36 770.5648
729 602189A female 2008-05-18 00:01:06 806.0905
1443 602190A female 2008-05-18 00:00:55 751.4969
2136 602191A female 2008-05-18 00:00:55 731.4883
758 602189A female 2008-06-03 00:01:36 726.9916
1472 602190A female 2008-06-03 00:01:06 754.8515
2165 602191A female 2008-06-03 00:00:37 732.2616
787 602189A female 2008-06-19 00:01:30 739.4487
1501 602190A female 2008-06-19 00:00:36 717.0156
2193 602191A female 2008-06-19 00:00:37 739.1495
816 602189A female 2008-07-05 00:01:06 739.9709
1529 602190A female 2008-07-05 00:00:36 725.1178
2222 602191A female 2008-07-05 00:00:36 833.6769
845 602189A female 2008-07-21 00:01:06 705.9033
1558 602190A female 2008-07-21 00:02:54 765.6336
2249 602191A female 2008-07-21 00:00:36 827.8880
utm.northing syncTime syncID
296 8.4769285 2007-09-21 00:00:00 2
1017 99.7631819 2007-09-21 00:00:00 2
1703 1.1800951 2007-09-21 00:00:00 2
325 -23.7448037 2007-10-07 00:00:00 3
1042 77.1102179 2007-10-07 00:00:00 3
1732 -21.2891750 2007-10-07 00:00:00 3
354 0.4283062 2007-10-23 00:00:00 4
1071 37.1992453 2007-10-23 00:00:00 4
1761 -2.6430089 2007-10-23 00:00:00 4
382 -5.7979426 2007-11-08 00:00:00 5
1100 65.0410094 2007-11-08 00:00:00 5
1790 54.0532827 2007-11-08 00:00:00 5
411 -29.2462839 2007-11-24 00:00:00 6
1129 7.4197984 2007-11-24 00:00:00 6
1819 -5.2550889 2007-11-24 00:00:00 6
440 -28.5854525 2007-12-10 00:00:00 7
1158 44.8249933 2007-12-10 00:00:00 7
1848 18.2143795 2007-12-10 00:00:00 7
469 -25.3032006 2007-12-26 00:00:00 8
1187 47.6699155 2007-12-26 00:00:00 8
1877 46.6907330 2007-12-26 00:00:00 8
498 -29.5446199 2008-01-11 00:00:00 9
1216 45.0077978 2008-01-11 00:00:00 9
1906 51.0186619 2008-01-11 00:00:00 9
527 75.0626745 2008-01-27 00:00:00 10
1241 40.9828750 2008-01-27 00:00:00 10
1934 8.6134759 2008-01-27 00:00:00 10
556 96.6658472 2008-02-12 00:00:00 11
1270 59.3454940 2008-02-12 00:00:00 11
1963 16.6419720 2008-02-12 00:00:00 11
584 95.0585246 2008-02-28 00:00:00 12
1298 56.8100273 2008-02-28 00:00:00 12
1991 16.7781858 2008-02-28 00:00:00 12
613 121.1242833 2008-03-15 00:00:00 13
1327 91.4343483 2008-03-15 00:00:00 13
2020 42.1241798 2008-03-15 00:00:00 13
642 120.2420628 2008-03-31 00:00:00 14
1356 96.9159246 2008-03-31 00:00:00 14
2049 29.4148220 2008-03-31 00:00:00 14
671 139.9985102 2008-04-16 00:00:00 15
1385 118.7530515 2008-04-16 00:00:00 15
2078 45.8216335 2008-04-16 00:00:00 15
700 127.7193656 2008-05-02 00:00:00 16
1414 106.8296195 2008-05-02 00:00:00 16
2107 48.4988737 2008-05-02 00:00:00 16
729 123.5455528 2008-05-18 00:00:00 17
1443 94.7381720 2008-05-18 00:00:00 17
2136 94.4009178 2008-05-18 00:00:00 17
758 121.4424120 2008-06-03 00:00:00 18
1472 81.3692060 2008-06-03 00:00:00 18
2165 105.5935767 2008-06-03 00:00:00 18
787 110.5419733 2008-06-19 00:00:00 19
1501 107.4216213 2008-06-19 00:00:00 19
2193 112.4938891 2008-06-19 00:00:00 19
816 112.5189079 2008-07-05 00:00:00 20
1529 109.6719842 2008-07-05 00:00:00 20
2222 56.9699256 2008-07-05 00:00:00 20
845 120.1732331 2008-07-21 00:00:00 21
1558 61.0669027 2008-07-21 00:00:00 21
2249 60.0322339 2008-07-21 00:00:00 21
[1] "602189A" "602190A" "602191A"
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