matbysurveylist: 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
)

Value

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

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.

Author

Matt Tyers

Examples

Run this code

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)