riverdist (version 0.17.0)

upstreamseq: 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
)

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.

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, upstreamseq() will only return pairwise distances in which a specified condition is met.

flowconnected

If TRUE, only returns distance if the input segments are flow-connected. Defaults to FALSE.

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 FALSE and a route cannot be found, the function will return NA in the appropriate entry. Defaults to TRUE. See detectroute.

algorithm

Which route detection algorithm to use ("Dijkstra", "sequential", or "segroutes"). If left as NULL (the default), the function will automatically make a selection. See detectroute for more details.

Author

Matt Tyers

See Also

upstream, plotseq

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)