Combine Occasions Or Detectors
Use these methods to combine data from multiple occasions or multiple detectors in a
traps object, creating a new data set and possibly converting
between detector types.
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## S3 method for class 'traps' reduce(object, newtraps = NULL, span = NULL, rename = FALSE, ...) ## S3 method for class 'capthist' reduce(object, newtraps = NULL, span = NULL, rename = FALSE, newoccasions = NULL, by = 1, outputdetector = detector(traps(object)), select = "last", dropunused = TRUE, verify = TRUE, sessions = NULL, ...)
list in which each component is a vector of subscripts for detectors to be pooled
numeric maximum span in metres of new detector
logical; if TRUE the new detectors will be numbered from 1, otherwise a name will be constructed from the old detector names
list in which each component is a vector of subscripts for occasions to be pooled
number of old occasions in each new occasion
character value giving detector type for output
character value for method to resolve conflicts
logical, if TRUE any never-used detectors are dropped
logical, if TRUE the
vector of session indices or names (optional)
other arguments passed by reduce.traps to hclust
Grouping may be specified explicitly via
span is specified a clustering of detector sites will be
hclust and detectors will be assigned to
cutree. The default algorithm in
is complete linkage, which tends to yield compact, circular clusters;
each will have diameter less than or equal to
The first component of
newoccasions defines the columns of
object for new occasion 1, the second for new occasion 2, etc. If
newoccasions is NULL then all occasions are output. Subscripts in a
newoccasions that do not match an occasion in the input
are ignored. When the output detector is one of the trap types
(‘single’, ‘multi’), reducing capture occasions can result in locational
ambiguity for individuals caught on more than one occasion, and for
single-catch traps there may also be conflicts between individuals at
the same trap. The method for resolving conflicts among ‘multi’
detectors is determined by
select which should be one of ‘first’,
‘last’ or ‘random’. With ‘single’ detectors
select is ignored and
the method is: first, randomly select* one trap per animal per day;
second, randomly select* one animal per trap per day; third, when
collapsing multiple days use the first capture, if any, in each
Usage data in the
traps attribute are also pooled if present;
usage is summed over contributing occasions and detectors. If there is
no 'usage' attribute in the input, and
outputdetector is one of
'count', 'polygon', 'transect' and 'telemetry', a homogeneous (all-1's)
'usage' attribute is first generated for the input.
* i.e., in the case of a single capture, use that capture; in the case of multiple ‘competing’ captures draw one at random.
newoccasions is not provided then old occasions are grouped into
new occasions as indicated by the
by argument. For example, if
there are 15 old occasions and
by = 5 then new occasions will be
formed from occasions 1:5, 6:10, and 11:15. A warning is given when the
number of old occasions is not a multiple of
by as then the final
new occasion will comprise fewer old occasions.
dropunused = TRUE has the possibly unintended effect of dropping
whole occasions on which there were no detections.
A special use of the
by argument is to combine all occasions into
one for each session in a multi-session dataset. This is done by setting
by = "all".
An object of class traps with detectors combined according to
span. The new object has an attribute
‘newtrap’, a vector of length equal to the original number of
detectors. Each element in newtrap is the index of the new detector to
which the old detector was assigned (see Examples).
The object has no clusterID or clustertrap attribute.
An object of class capthist with number of occasions (columns) equal to
length(newoccasions); detectors may simulataneously be aggregated
reduce.traps. The detector type is inherited from
unless a new type is specified with the argument
The argument named ‘columns’ was renamed to ‘newoccasions’ in version 2.5.0, and arguments were added to reduce.capthist for the pooling of detectors. Old code should work as before if all arguments are named and ‘columns’ is changed.
The reduce method may be used to re-assign the detector type (and
hence data format) of a capthist object without combining occasions or
detectors. Set the
and leave others at their default values.
Automated clustering can produce unexpected outcomes. In particular,
there is no guarantee that clusters will be equal in size. You should
inspect the results of reduce.traps especially when using
reduce.traps is not implemented for polygons or transects.
discretize converts polygon data to
point-detector (multi, proximity or count) data.
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tempcapt <- sim.capthist (make.grid(nx = 6, ny = 6), nocc = 6) class(tempcapt) pooled.tempcapt <- reduce(tempcapt, newocc = list(1,2:3,4:6)) summary (pooled.tempcapt) pooled.tempcapt2 <- reduce(tempcapt, by = 2) summary (pooled.tempcapt2) ## collapse multi-session dataset to single-session 'open population' onesess <- join(reduce(ovenCH, by = "all")) summary(onesess) # group detectors within 60 metres plot (traps(captdata)) plot (reduce(captdata, span = 60), add = TRUE) # plot linking old and new old <- traps(captdata) new <- reduce(old, span = 60) newtrap <- attr(new, "newtrap") plot(old, border = 10) plot(new, add = TRUE, detpar = list(pch = 16), label = TRUE) segments (new$x[newtrap], new$y[newtrap], old$x, old$y)