upstreamseq: Upstream Distance Between Sequential Observations

In mbtyers/riverdist: River Network Distance Computation and Applications

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, 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.

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

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)

mbtyers/riverdist documentation built on Nov. 12, 2024, 1:05 p.m.