assign {plantTracker} | R Documentation |
Tracks genets through time
Description
This function tracks individual organisms through time, but only
for one species in one quadrat. It is designed for use within the
trackSpp
function, and is not intended for use on its own.
Usage
assign(
dat,
inv,
dorm,
buff,
buffGenet,
clonal,
flagSuspects = FALSE,
shrink = 0.1,
dormSize = 0.05,
inheritsFromTrackSpp = FALSE,
nearEdgeBox = NULL,
...
)
Arguments
dat |
An sf data.frame of the same format as
This function will add columns called "basalArea_ramet", "trackID", "age", "size_tplus1", "recruit" and "survives_tplus1", so 'dat' should not contain columns with these names. |
inv |
An integer vector that contains all of years in which this quadrat (or other unique spatial area) was sampled. Years must be ordered sequentially. |
dorm |
A numeric vector of length 1, indicating the number of years this species is allowed to go dormant, i.e. be absent from the map but be considered the same individual when it reappears. This must be an integer greater than or equal to 0. |
buff |
A numeric vector of length 1 that is greater than or equal to
zero, indicating how far (in the same units as spatial values in 'dat') a
polygon can move from year |
buffGenet |
A numeric vector of length 1 that is greater than or equal
to zero, indicating how close (in the same units as spatial values in 'dat')
polygons must be to one another in the same year to be grouped as a genet
(if 'clonal' argument = TRUE). This argument is passed to
the |
clonal |
A logical argument of length 1, indicating whether this species is allowed to be clonal or not (i.e. if multiple polygons (ramets) can be grouped into one individual (genet)). If clonal = TRUE, the species is allowed to be clonal, and if clonal = FALSE, the species is not allowed to be clonal. |
flagSuspects |
A logical argument of length 1, indicating whether
observations that are 'suspect' will be flagged. The default is
|
shrink |
A single numeric value. This value is only used when
|
dormSize |
A single numeric value. This value is only used when
|
inheritsFromTrackSpp |
A logical argument that is only applicable when 'assign()' is used internally in 'trackSpp()'. |
nearEdgeBox |
An sf data frame indicating the bounding box of the quadrat. This argument is only used if 'assign()' is used internally in 'trackSpp()'. |
... |
Other arguments passed on to methods. Not currently used. |
Details
see trackSpp
for details of arguments and usage.
See Also
trackSpp()
, which is a wrapper for the assign()
function that
applies it over many species and quadrats. The assign()
function uses the
groupByGenet()
function to group ramets into genets
(if 'clonal' argument = TRUE).