upstreamseq {riverdist} | R Documentation |
Upstream Distance Between Sequential Observations
Description
Returns a matrix of distance with direction by unique fish between sequential surveys. The mouth (lowest point) segment and vertex must be specified (see setmouth). A plotting method is provided for the output; see plotseq.
Usage
upstreamseq(
unique,
survey,
seg,
vert,
rivers,
logical = NULL,
flowconnected = FALSE,
net = FALSE,
stopiferror = TRUE,
algorithm = NULL
)
Arguments
unique |
A vector of identifiers for each fish. |
survey |
A vector of identifiers for each survey. It is recommended to use a numeric or date format (see as.Date) to preserve survey order. |
seg |
A vector of river locations (segment component). |
vert |
A vector of river locations (vertex component). |
rivers |
The river network object to use. |
logical |
A boolean vector that can be used for subsetting - if used,
|
flowconnected |
If |
net |
Whether to calculate net upstream distance (net=TRUE) or total distance (net=FALSE, default). |
stopiferror |
Whether or not to exit with an error if a route cannot be
found. If this is set to |
algorithm |
Which route detection algorithm to use ( |
Value
A data frame of upstream distances (numeric), with rows defined by unique fish and columns defined by observation increment (1 to 2, 2 to 3, etc.) See upstream for additional information.
Note
Returns either net upstream distance (net=TRUE) or total distance (net=FALSE, default). See upstream.
Building routes from the river mouth to each river network segment and/or distance lookup tables will greatly reduce computation time (see buildsegroutes).
Author(s)
Matt Tyers
See Also
Examples
data(Gulk, fakefish)
# Mouth must be specified
Gulk$mouth$mouth.seg <- 1
Gulk$mouth$mouth.vert <- 1
upstreamseq(unique=fakefish$fish.id, survey=fakefish$flight, seg=fakefish$seg,
vert=fakefish$vert, rivers=Gulk)
seqbysurvey <- upstreamseq(unique=fakefish$fish.id, survey=fakefish$flight.date, seg=fakefish$seg,
vert=fakefish$vert, rivers=Gulk)
seqbysurvey
plotseq(seqbysurvey)