ecofind: Find ecotone locations and widths
In dpritchard/dgmisc: Miscellaneous R functions for research

Description Usage Arguments Details Value Author(s) References Examples

Finds ecotones based on species composition via DCA

ecofind(veg, dist, window=5, axis_no=1)

## S3 method for class 'ecofind'
plot(x, scaling=0.5, plot_info=TRUE, 
    plot_se=TRUE, plot_cngpts=TRUE, spp_no=2, 
    plot_lab=NA, ...)

`veg`	A matrix of community data. Must be compatible with `decorana`
`dist`	A vector. Quadrat distances along transect. Must have `nrow(veg)` values.
`window`	An odd integer. Defines the width of the moving window.
`axis_no`	An integer. Which DCA axis to use for derivative calculations?
`x`	An object of class ecofind.
`scaling`	Arbitary scaling factor for plotting 1st and 2nd derivatives. See Details.
`plot_info`	A logical. Should the legend and other info be plotted?
`plot_se`	A logical. Should the 1.96*se lines be drawn?
`plot_cngpts`	A logical. Should the 2nd derivitive changepoints be drawn?
`spp_no`	An integer. Species with occurances <= to this are excluded from the plot.
`plot_lab`	A string. If present it is printed at the top of the figure.
`...`	Other arguments. Not used

This function impliments the ecotone-finding methods of Walker et al. (2003), as used by Brownstein et al. (2013). In essence it first performs a detrended correspondance analysis on the community matrix in veg and then caclulates the 1st and 2nd derivitives of the DCA axis defined by axis_no versus distance along the transect (provided by dist). The plot method presents this information in a helpful (but not publication-ready) way.

See decorana for more information on the DCA, but it is assumed that veg has rows = quadrats and columns = species. Here we use the site scores returned by scores.decorana which implicitly scales the DCA axes by a constant.

Changepoints are identified by changes in sign of the 2nd derivative which happen outside 1.96 times the standard error of the 2nd derivative (the 'threshold'). These changepoints are provided as a conveniance to the user, but are not based on any hard-and-fast rule. Careful interpretation by the user is still required.

Unlike Walker et al. (2003) we do not allow the window to get smaller near the ends of the transect, leading to NA's at transect extremes.

A list of class ecofind with the following items:

`result`	A named matrix, with columns: distance, dcaN, first_derivative, second_derivative and sd_change_pt. Where the 'N' of dcaN is the axis specified by `axis_no`.
`func_meta`	A named vector, with items: window and axis_no
`veg`	The original `veg` matix passed to ecofind
`dist`	The original `dist` vector passed to ecofind

Gretchen Brownstein, Daniel Pritchard

Walker, S., Wilson, J. B., Steel, J. B., Rapson, G. L., Smith, B., King, W. M., and Cottam, Y. H. 2003. Properties of ecotones: Evidence from five ecotones objectively determined from a coastal vegetation gradient. Journal of Vegetation Science, 14: 579–590. http://dx.doi.org/10.1111/j.1654-1103.2003.tb02185.x