R: Get stream distance matrices from an 'SSN' object

ssn_get_stream_distmat {SSN2}

R Documentation

Get stream distance matrices from an `SSN` object

Description

Extracts the stream network distance matrices for the observation or prediction data from an SSN object.

Usage

ssn_get_stream_distmat(x, name = "obs")

Arguments

`x`	An `SSN` object
`name`	Internal name of the dataset in the object `x`. For observed values, this will always be "obs", the default. To get a stream network distance matrix for a prediction data set, the name of the dataset must be given, in quotes.

Details

The internal name for observed data in objects of class SSN is "obs" and it is the default. If another name is specified, it must represent a prediction data set in the SSN object. For SSN objects, these names are obtained using the call names(x$preds).

Note that these are not traditional symmetric distance matrices. First, distances in an SSN object represent stream distance, or hydrologic distance, which is the distance between two locations when movement is restricted to the branching stream network. Another important difference is the distance matrices for SSN objects contain the downstream only stream distance between two locations, making them asymmetric. This asymmetry provides a way to store two types of spatial relationships based on stream distance:

Flow-connected: Water flows from an upstream site to a downstream site.
Flow-unconnected: Two sites reside on the same stream network, but do not share flow.

For example, if two sites are flow-connected the downstream distance from the upstream site to the downstream site is > 0, while the downstream distance between the downstream site and the upstream site = 0. For flow-unconnected sites, the downstream distance represents the distance from each site to the closest downstream junction and will be > 0 in both directions. Direction is preserved, with columns representing the FROM site and rows representing the TO site. Row and column names correspond to the unique point identifier "pid" for each site. From this matrix, it is also possible to get total stream distance (downstream + upstream) between any two sites on the same network (see examples for additional details).

Stream distances are only calculated within a network and so the asymmetric matrices are also stored by network. For observation data, a single square matrix of distances is returned for each network, with the names based on the netID value (e.g. "dist.net1", "dist.net2", etc.). However, two distance matrices ("a" and "b") are required to store the downstream only distance between observed and prediction sites. The label "a" represents the downstream stream distance from prediction sites to observation sites, and the label "b" represents the distance from observation sites to predictions sites. Thus, the list of prediction matrices are labeled "dist.net1.a" for the downstream only distance from prediction sites in the columns, to observation sites in the rows, for the first network. A prediction matrix labeled "dist.net1.b" contains downstream distances from observation sites in the columns to prediction sites in the rows, for the first network. The downstream only distance matrices for observations and predictions will be rectangular, unless the number of observation and prediction locations are equal. If the argument amongPreds = TRUE was used in the function ssn_create_distmat, then the distance between prediction sites themselves is also returned, using the same labelling convention as for among observation sites. That is, the matrices for each network will be labeled "dist.net1", "dist.net2", etc., for the first and second network, etc.

Value

A list of asymmetric downstream only stream distance matrices, by network.

References

Ver Hoef, J.M. and Peterson, E.E. (2010) A moving average approach to spatial statistical models of stream networks. The Journal of the American Statistical Association, 105(489), 22–24

Examples

## For this example only, copy MiddleFork04.ssn directory to R's
## temporary directory
copy_lsn_to_temp()
## Create an SSN object with prediction sites
mf04p <- ssn_import(paste0(tempdir(), "/MiddleFork04.ssn"),
  predpts = "pred1km", overwrite = TRUE
)

## Create distance matrices for obs x obs, obs x preds, and preds x
## preds
## Not run: 
ssn_create_distmat(mf04p,
  predpts = "pred1km", among_predpts = TRUE,
  overwrite = TRUE
)

## End(Not run)

## Check names of prediction datasets
names(mf04p$preds)

## Get list of stream distance matrices for observations
dist_obs <- ssn_get_stream_distmat(mf04p)
## Display structure of list and names of the matrices
str(dist_obs)
names(dist_obs)
## Look at first 5 rows and columns in asymmetric
## downstream only distance matrix for netID == 1
dist_obs$dist.net1[1:5, 1:5]

## Create symmetric total stream distance matrix between
## observations
strdist_2 <- dist_obs$dist.net2 + t(dist_obs$dist.net2)
strdist_2[5:10, 5:10]

## Get maximum downstream only distance between
## observations on netID == 2
a.mat <- pmax(dist_obs$dist.net2, t(dist_obs$dist.net2))
a.mat[5:10, 5:10]

## Get minimum downstream only distance between observations. If
## minimum distance == 0, sites are flow-connected
b.mat <- pmin(dist_obs$dist.net2, t(dist_obs$dist.net2))
b.mat[5:10, 5:10]

## Get distance matrices for pred1km
dist_pred1km <- ssn_get_stream_distmat(mf04p, name = "pred1km")
str(dist_pred1km)
names(dist_pred1km)
## Look at first 5 rows and columns of downstream only distances
## FROM prediction sites TO observed sites on netID == 1
dist_pred1km$dist.net1.a[1:5, 1:5]

## Look at downstream only stream distances among prediction
## sites in pred1km on netID == 1. This is useful for block
## prediction
dist_pred1km$dist.net1[1:5, 1:5]

[Package SSN2 version 0.2.0 Index]

Get stream distance matrices from an SSN object