R: Stepacross as Flexible Shortest Paths or Extended...

stepacross {vegan} | R Documentation

## Stepacross as Flexible Shortest Paths or Extended Dissimilarities

### Description

Function `stepacross` tries to replace dissimilarities with shortest paths stepping across intermediate sites while regarding dissimilarities above a threshold as missing data (`NA`). With `path = "shortest"` this is the flexible shortest path (Williamson 1978, Bradfield & Kenkel 1987), and with `path = "extended"` an approximation known as extended dissimilarities (De'ath 1999). The use of `stepacross` should improve the ordination with high beta diversity, when there are many sites with no species in common.

### Usage

    stepacross(dis, path = "shortest", toolong = 1, trace = TRUE, ...)

### Arguments

`dis` | Dissimilarity data inheriting from class `dist` or a an object, such as a matrix, that can be converted to a dissimilarity matrix. Functions `vegdist` and `dist` are some functions producing suitable dissimilarity data.
`path` | The method of stepping across (partial match) Alternative `"shortest"` finds the shortest paths, and `"extended"` their approximation known as extended dissimilarities.
`toolong` | Shortest dissimilarity regarded as `NA`. The function uses a fuzz factor, so that dissimilarities close to the limit will be made `NA`, too.
`trace` | Trace the calculations.
`...` | Other parameters (ignored).

### Details

Williamson (1978) suggested using flexible shortest paths to estimate dissimilarities between sites which have nothing in common, or no shared species. With `path = "shortest"` function `stepacross` replaces dissimilarities that are `toolong` or longer with `NA`, and tries to find shortest paths between all sites using remaining dissimilarities. Several dissimilarity indices are semi-metric which means that they do not obey the triangle inequality d[ij] <= d[ik] + d[kj], and shortest path algorithm can replace these dissimilarities as well, even when they are shorter than `toolong`.

De'ath (1999) suggested a simplified method known as extended dissimilarities, which are calculated with `path = "extended"`. In this method, dissimilarities that are `toolong` or longer are first made `NA`, and then the function tries to replace these `NA` dissimilarities with a path through single stepping stone points. If not all `NA` could be replaced with one pass, the function will make new passes with updated dissimilarities as long as all `NA` are replaced with extended dissimilarities. This mean that in the second and further passes, the remaining `NA` dissimilarities are allowed to have more than one stepping stone site, but previously replaced dissimilarities are not updated. Further, the function does not consider dissimilarities shorter than `toolong`, although some of these could be replaced with a shorter path in semi-metric indices, and used as a part of other paths. In optimal cases, the extended dissimilarities are equal to shortest paths, but they may be longer.

As an alternative to defining too long dissimilarities with parameter `toolong`, the input dissimilarities can contain `NA`s. If `toolong` is zero or negative, the function does not make any dissimilarities into `NA`. If there are no `NA`s in the input and `toolong = 0`, `path = "shortest"` will find shorter paths for semi-metric indices, and `path = "extended"` will do nothing. Function `no.shared` can be used to set dissimilarities to `NA`.

If the data are disconnected or there is no path between all points, the result will contain `NA`s and a warning is issued. Several methods cannot handle `NA` dissimilarities, and this warning should be taken seriously. Function `distconnected` can be used to find connected groups and remove rare outlier observations or groups of observations.

Alternative `path = "shortest"` uses Dijkstra's method for finding flexible shortest paths, implemented as priority-first search for dense graphs (Sedgewick 1990). Alternative `path = "extended"` follows De'ath (1999), but implementation is simpler than in his code.

### Value

Function returns an object of class `dist` with extended dissimilarities (see functions `vegdist` and `dist`). The value of `path` is appended to the `method` attribute.

### Note

The function changes the original dissimilarities, and not all like this. It may be best to use the function only when you really must: extremely high beta diversity where a large proportion of dissimilarities are at their upper limit (no species in common).

Semi-metric indices vary in their degree of violating the triangle inequality. Morisita and Horn–Morisita indices of `vegdist` may be very strongly semi-metric, and shortest paths can change these indices very much. Mountford index violates basic rules of dissimilarities: non-identical sites have zero dissimilarity if species composition of the poorer site is a subset of the richer. With Mountford index, you can find three sites i, j, k so that d[ik] = 0 and d[jk] = 0, but d[ij] > 0. The results of `stepacross` on Mountford index can be very weird. If `stepacross` is needed, it is best to try to use it with more metric indices only.

### Author(s)

Jari Oksanen

### References

Bradfield, G.E. & Kenkel, N.C. (1987). Nonlinear ordination using flexible shortest path adjustment of ecological distances. Ecology 68, 750–753.

De'ath, G. (1999). Extended dissimilarity: a method of robust estimation of ecological distances from high beta diversity data. Plant Ecol. 144, 191–199.

Sedgewick, R. (1990). Algorithms in C. Addison Wesley.

Williamson, M.H. (1978). The ordination of incidence data. J. Ecol. 66, 911-920.

### See Also

Function `distconnected` can find connected groups in disconnected data, and function `no.shared` can be used to set dissimilarities as `NA`. See `swan` for an alternative approach. Function `stepacross` is an essential component in `isomap` and `cophenetic.spantree`.

### Examples

    # There are no data sets with high beta diversity in vegan, but this
    # should give an idea.
    data(dune)
    dis <- vegdist(dune)
    edis <- stepacross(dis)
    plot(edis, dis, xlab = "Shortest path", ylab = "Original")
    ## Manhattan distance have no fixed upper limit.
    dis <- vegdist(dune, "manhattan")
    is.na(dis) <- no.shared(dune)
    dis <- stepacross(dis, toolong=0)

[Package vegan version 2.4-3 Index]