Random, neighbour, environment deletion analysis for transfer function models

Calculates effect of deleting sites from training set at random, from a geographic neighbourhood, or from an environmental neighbourhood. A simple graphical technique for gauging the effect of spatial autocorrelation on the transfer function model.

Usage

# S3 method for class 'RNE'
plot(x, which = 1, ylim, ...)

rne(
  y,
  env,
  geodist,
  fun,
  neighbours,
  subsets = c(1, 0.75, 0.5, 0.25, 0.1),
  ...
)

Arguments

x

RNE object to be plotted

which

Which column of the results to plot eg if more than one WAPLS component is calculated

ylim

Y-limits of the plot

...

Arguments passed to fun

y

Community data, or distance object, or distance matrix

env

Environmental variable

geodist

Matrix of geographical distances between sites

fun

Transfer function

neighbours

Neighbourhood radii

subsets

Proportion of sites to retain in random deletion

Value

Returns an RNE object, list with two components

random

Performance with random deletion.

neighbour

Performance with deletion by neighbourhood, or environment

Details

Finds the leave-one-out transfer function performance if sites are deleted at random, from a neighbourhood zone, or by deleting environmentally close sites.

Prior to version 2.1, this function would repeat the random removal 10 times to reduce variance in results. This is no longer done as the variance is small for large training sets, it took a long time, and treats one treatment of the data differently.

Functions

• plot(RNE): Plot RNE object

References

Telford, R. J. and Birks, H. J. B. (2009) Evaluation of transfer functions in spatially structured environments. Quaternary Science Reviews 28: 1309–1316. doi:10.1016/j.quascirev.2008.12.020

Author

Richard Telford Richard.Telford@bio.uib.no

Examples

require(rioja)
require(sf)
#> Loading required package: sf
#> Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE
data(arctic.env)
data(arctic.pollen)

# using just the first 100 sites so that code runs quickly
# (about 15 seconds for all 828 sites)

# convert environmental data into an sf object
arctic.env <- st_as_sf(
  x = arctic.env,
  coords = c("Longitude", "Latitude"),
  crs = 4326
)

# find great circle distances and remove units
arctic.dist <- st_distance(arctic.env[1:100, ]) |>
  units::set_units("km") |>
  units::set_units(NULL)

# rne
arctic.rne <- rne(
  y = arctic.pollen[1:100, ], env = arctic.env$tjul[1:100],
  geodist = arctic.dist, fun = MAT, neighbours = c(0, 200),
  subsets = c(1, .5), k = 5
)
#> random subset =  1
#> Cross-validating:
#> 
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#> random subset =  0.5
#> Cross-validating:
#> 
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#> 10.50.2270959392529170.1324043560606420.271963178842680.1579988229325
#> neighbourhood =  0 km
#> Cross-validating:
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#> Cross-validating:
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#> neighbourhood =  200 km
#> Cross-validating:
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#> Cross-validating:
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plot(arctic.rne)

#> $r
#>      prop    r2.N05
#> [1,]  1.0 0.2270959
#> [2,]  0.5 0.1324044
#> 
#> $n
#>                           N05
#> [1,]   0 0.01010101 0.2270959
#> [2,] 200 0.13474747 0.1367883
#> 
#> $e
#>        N05        N05 
#> 0.22709594 0.03720974 
#>