matbysurveylist: Generate List of Distance Matrix Between Observations, for...
In mbtyers/riverdist: River Network Distance Computation and Applications

matbysurveylist

R Documentation

Generate List of Distance Matrix Between Observations, for All Individuals

Description

Returns a list of matrices, each giving the river distance, direction, or upstream travel distance between all observations of one unique fish. This function is principally intended for producing an object to plot in plotmatbysurveylist.

Usage

matbysurveylist(
  unique,
  survey,
  seg,
  vert,
  rivers,
  indiv = NULL,
  method = "upstream",
  flowconnected = FALSE,
  net = FALSE,
  stopiferror = TRUE,
  algorithm = NULL
)

Arguments

`unique`	A vector of unique 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.
`indiv`	A vector of unique individuals to use. Accepting the default (`NULL`) will result in a matrix being returned for all unique individuals.
`method`	Which general method to use. Setting `method="distance"` will compute distance for each pair of observation, setting `method="direction"` will compute direction between each pair of observation, and setting `method="upstream"` will compute directional (upstream) distance between each pair of observation. Defaults to `"upstream"`.
`flowconnected`	Optional parameter to pass to the distance or direction calculation. Defaults to `FALSE`.
`net`	Optional parameter to pass to the distance or direction calculation. Defaults to `FALSE`.
`stopiferror`	Optional parameter to pass to the distance or direction calculation. Defaults to `TRUE`.
`algorithm`	Optional parameter to pass to the distance or direction calculation. Defaults to `NULL`.

Value

A list with each element corresponding to a unique fish. Each list element is the output from either riverdistancematbysurvey, riverdirectionmatbysurvey, or upstreammatbysurvey.

Note

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

Examples

data(Gulk, smallset)
matbysurveylist <- matbysurveylist(unique=smallset$id, survey=smallset$flight, seg=smallset$seg, 
   vert=smallset$vert, rivers=Gulk)
plotmatbysurveylist(matbysurveylist)
plotmatbysurveylist(matbysurveylist,type="confint")
plotmatbysurveylist(matbysurveylist,type="dotplot")
   
data(fakefish)
# matbysurveylist <- matbysurveylist(unique=fakefish$fish.id, survey=fakefish$flight, 
#   seg=fakefish$seg, vert=fakefish$vert, rivers=Gulk)
# plotmatbysurveylist(matbysurveylist)

mbtyers/riverdist documentation built on Jan. 16, 2024, 12:34 a.m.