weightedCor: Weighted correlation test of WA reconstruction

Description

Weighted correlation between WA optima from training set and axis 1 scores of constrained ordination fitted to fossil data with WA model predictions for fossil samples as constraints.

Usage

## S3 method for class 'default':
weightedCor(x, env, fossil, method = c("rda", "cca"),
            test = TRUE, type = c("simulate", "permute"), sim = 999,
            verbose = TRUE, ...)
## S3 method for class 'weightedCor':
plot(x,
     type = c("bubble", "null"),
     weighted = TRUE,
     size = 0.25,
     xlab = paste(x$env, "WA Optima"),
     ylab = "Axis 1 Score",
     xlim,
     main = "",
     sub = NULL,
     border = "gray75",
     col = "gray75",
     obscol = "red",
     fg = "black", ...)

Arguments

training set covariates, a matrix-like object usually of species/proxy data. For the plot method, an object of class "weightedCor", the result of a call to weightedCor.

env

training set response, a vector usually of environmental data.

fossil

matrix of fossil/core species/proxy data for which a reconstruction is sought.

method

constrained ordination method. One of "rda" and "cca". Currently only "rda" is supported.

test

logical; should the observed correlation be tested?

type

the type of test to apply. One of "simulate" or "permute". The latter is currently not implemented. For the plot method, the type of plot to produce.

sim

numeric; number of simulations or permutations to permform as part of the test

verbose

logical; should the progress of the test be shown via a progress bar?

...

arguments passed to other methods. In the case of the plot method, additional graphical parameters can be supplied.

weighted

logical; should the null distribution plotted be of the weighted or normal correlation.

size

numeric; the size of the largest bubble in inches. See symbols and argument inches for details.

xlim,xlab,ylab,main,sub

graphical parameters with their usual meaning.

border, col

The border and fill colours for the histogram bars.

The colour of the bubbles drawn on the bubble plot.

obscol

The colour of the indicator for the observed correlation.

Value

The plot method produces a plot on the current device. weightedCor() returns a list with the following components:
wtdCorrel,Correlnumeric; the observed weighted and standard correlation.
datadata frame; containing the training set WA Optima, axis 1 species scores, and mean abundance for each species.
ordthe fitted constrained ordination.
modelthe fitted WA model.
methodthe ordination method used.
ndistthe null distribution produced. NULL if argument test was FALSE.
simnumeric; the number of simulations or permutations used to test the observed correlations.
typethe type of test performed.
envthe deparsed version of env argument. Used for plotting.
callthe matched function call.

References

Telford R.J. and Birks, H.J.B. (2011) A novel method for assessing the statistical significance of quantitative reconstructions inferred from biotic assemblages. Quanternary Science Reviews 30:1272-1278.

Examples

Run this code

data(ImbrieKipp, SumSST, V12.122)

Cor <- weightedCor(ImbrieKipp, env = SumSST,
                   fossil = V12.122, type = "simulate", sim = 49)
Cor

plot(Cor)
plot(Cor, type = "null")