ord_bc: Bray-Curtis ordination, aka polar ordination

In phytomosaic/ecole: ecole: School of Ecology Package

Description

Bray-Curtis ordination.

Usage

ord_bc(
  x,
  method = "bray",
  endmethod = c("var_reg", "BC_orig", "PCORD_orig"),
  ends = c(NA, NA),
  ...
)

Arguments

x	array, where rows = SUs and cols = variables such as environmental or traits values.
method	dissimilarity index, passed to 'vegan::vegdist'.
endmethod	Endpoint selection method. ''var_reg'' is the variance regression method now default in PC-ORD (McCune and Mefford 2017). ''BC_orig'' is Bray-Curtis original method of selecting most-distant SUs. ''PCORD_orig'' is the deprecated method from PC-ORD, whereby the first endpoint has the greatest sum of distances from other sites, and the second endpoint has the greatest distance from the first endpoint.
ends	Numeric, index two sample units as endpoints on first axis (optional). Endpoints in higher dimensions then selected by 'endmethod'.
...	further arguments not currently passed to other functions.

Details

Bray-Curtis ordination. See references.

Value

List containing items:
- sumtab: summary table containing for each axis: sums-of-squares of residual distances, percent variance explained, and sample units selected as endpoints.
- scores: ordination scores.

References

Beals, E.W. 1984. Bray-Curtis ordination: an effective strategy for analysis of multivariate ecological data. Advances in Ecological Research 14: 1-55.

Bray, J.R., and J.T. Curtis. 1957. An ordination of the upland forest communities of southern Wisconsin. Ecological Monographs 27: 325-349.

McCune, B. and E.W. Beals. 1993. History of the development of Bray-Curtis ordination. Pgs 67-80 in J.S. Fralish, R.P. McIntosh, and O.L. Loucks (eds). John T. Curtis: Fifty Years of Wisconsin Plant Ecology, Wisconsin Academy of Science, Arts, and Letters, Madison, WI.

McCune, B., and M.J. Mefford. 2017. PC-ORD. Multivariate Analysis of Ecological Data. Version 7. MjM Software Design, Gleneden Beach, OR.

Examples

data(smoky, package='ecole')
spe <- smoky$spe
o1 <- ord_bc(spe, method='bray', endmethod='BC_orig')
o2 <- ord_bc(spe, method='bray', endmethod='BC_orig', ends=c(1,12))
ecole::set_par(2)
plot(scores(o1), type='n')
text(scores(o1))
plot(scores(o2), type='n')
text(scores(o2))

phytomosaic/ecole documentation built on Jan. 2, 2022, 11:24 p.m.