All the functionality of the morts package is accessible with the
residences(), morts(),
infrequent(), mortsplot(), and
review() functions, addressed in the other vignettes. Many
of these functions rely on output from additional functions. As you are
exploring your data, you may want to run these additional functions to
better dig through and understand your data. The drift()
and season() functions are respectively addressed in the Drift
and Seasonality
vignettes. Here, we address the stationchange(),
resmax(), and resmaxcml() functions.
stationchange() function
The thresholds in morts() rely on identifying the most
recent station or location change of each animal, because it is assumed
that the animal was alive before this most recent movement. To explore
the most recent station changes for each animal, the user can can call
stationchange() directly. The arguments are used in the
same manner as for morts(). Drift may also be applied with
the argument drift=TRUE. See the Drift
vignette for more information on the other drift arguments.
station_change<-stationchange(data=events,type="mort",ID="ID",station="Station.Name",
drift=TRUE,ddd=ddd,units="days",from.station="From",to.station="To")The output of stationchange() is a dataframe with one
row for each animal ID. The residence event information (start, end,
duration) is for the event that marks the most recent station change
(i.e., the start is when the movement occurred).
| ResidenceStart | Station.Name | ID | ResidenceEnd | ResidenceLength.days |
|---|---|---|---|---|
| 2005-06-25 21:26:12 | 10 | A | 2005-06-26 09:01:17 | 0.4826968 |
| 2005-07-01 05:28:31 | 1 | B | 2005-07-01 05:28:31 | 0.0000000 |
| 2004-06-19 15:31:47 | 9 | C | 2004-06-19 19:10:01 | 0.1515509 |
| 2004-08-31 16:48:00 | 5 | D | 2004-08-31 17:38:18 | 0.0349306 |
| 2004-07-15 21:09:22 | 5 | E | 2004-10-12 21:44:11 | 89.0241782 |
| 2005-06-28 21:12:58 | 1 | F | 2005-10-09 20:28:05 | 102.9688310 |
resmax() function
The threshold for morts() when method is
“last”, “any”, or “all” is determined by identifying the longest
residence event that occurred before a station change. If there are some
animals with very long resident events that are not identified as
potential mortalities by morts(), you may want to look at
the longest living residence events to explore how the threshold is
being identified. This can be done by calling the resmax()
function directly.
Note that stationchange() must be run beforehand, and
the output provided in the argument stnchange.
If drift was applied in generating the residence events, the
drift argument specifies whether drift events should be
included in resmax(). If drift was not applied or if
drift="morts" in morts(), then you should
include drift=FALSE. If drift="threshold" or
drift="both" in morts(), then you should
include drift=TRUE. See the Drift
vignette for more information on applying drift.
The output of resmax() is a dataframe with one row for
each animal ID. The residence event information is for the event that
has the longest duration and occurred before the most recent station
change for that animal.
resmax_example<-resmax(data=events,ID="ID",station="Station.Name",
res.start="ResidenceStart",residences="ResidenceLength.days",
stnchange=station_change,drift=FALSE)| ResidenceStart | Station.Name | ID | ResidenceEnd | ResidenceLength.days |
|---|---|---|---|---|
| 2003-09-24 16:56:36 | 1 | A | 2003-10-11 17:15:47 | 17.0133218 |
| 2003-09-13 13:25:38 | 4 | C | 2003-10-07 16:26:06 | 24.1253241 |
| 2003-08-16 22:35:23 | 1 | G | 2003-08-18 12:05:20 | 1.5624653 |
| 2003-01-31 19:47:16 | 8 | I | 2003-02-06 18:59:34 | 5.9668750 |
| 2002-08-26 07:18:12 | 8 | J | 2002-08-26 22:01:00 | 0.6130556 |
| 2003-01-16 18:55:12 | 8 | K | 2003-02-08 16:31:25 | 22.9001505 |
resmaxcml() function
The threshold for morts() when the method
is “cumulative” or “any” is determined by finding the longest cumulative
residence event that occurred before a station change. Cumulative
residence events are the length of time between when an animal was first
detected at a station and when it was last detected at the same station,
ignoring any gaps in detection. You may wish to explore the cumulative
residence events that contribute to determining this threshold. This can
be done by calling the resmaxcml() function directly.
Note that stationchange() must be run beforehand, and
the output provided in the argument stnchange.
If you have applied drift by using drift="threshold" or
drift="both" in morts(), then you should apply
drift using the drift() function and use the output as the
input for the data argument in resmaxcml().
See the Drift
vignette for more information on applying drift.
resmaxcml_example<-resmaxcml(data=events,ID="ID",station="Station.Name",
res.start="ResidenceStart",res.end="ResidenceEnd",
residences="ResidenceLength.days",units="days",
stnchange=station_change)The output of resmaxcml() is similar to that from
resmax(), except there is one row for each cumulative
residence event (not just the longest event). This means that there may
be more than one row for each animal ID.
| ResidenceStart | Station.Name | ID | ResidenceEnd | ResidenceLength.days |
|---|---|---|---|---|
| 2003-09-21 23:49:45 | 11 | A | 2003-09-22 00:08:18 | 0.0128819 days |
| 2003-09-22 00:20:28 | 1 | A | 2004-06-24 01:15:25 | 276.0381597 days |
| 2004-06-24 17:30:42 | 14 | A | 2004-06-24 17:30:42 | 0.0000000 days |
| 2004-06-24 20:37:18 | 8 | A | 2004-06-24 21:39:34 | 0.0432407 days |
| 2004-06-25 05:48:34 | 2 | A | 2004-06-25 06:47:40 | 0.0410417 days |
| 2004-06-26 04:49:31 | 10 | A | 2004-07-01 07:41:36 | 5.1195023 days |