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.
# S3 method for default
weightedCor(x, env, fossil, method = c("rda", "cca"),
test = TRUE, type = c("simulate", "permute"), sim = 999,
verbose = TRUE, ...)# S3 method for 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", ...)
The plot
method produces a plot on the current
device. weightedCor()
returns a list with the following
components:
numeric; the observed weighted and standard correlation.
data frame; containing the training set WA Optima, axis 1 species scores, and mean abundance for each species.
the fitted constrained ordination.
the fitted WA model.
the ordination method used.
the null distribution produced. NULL
if argument
test
was FALSE
.
numeric; the number of simulations or permutations used to test the observed correlations.
the type of test performed.
the deparsed version of env
argument. Used for
plotting.
the matched function call.
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
.
training set response, a vector usually of environmental data.
matrix of fossil/core species/proxy data for which a reconstruction is sought.
constrained ordination method. One of "rda"
and
"cca"
. Currently only "rda"
is supported.
logical; should the observed correlation be tested?
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.
numeric; number of simulations or permutations to permform as part of the test
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.
logical; should the null distribution plotted be of the weighted or normal correlation.
numeric; the size of the largest bubble in inches. See
symbols
and argument inches
for details.
graphical parameters with their usual meaning.
The border and fill colours for the histogram bars.
The colour of the bubbles drawn on the bubble plot.
The colour of the indicator for the observed correlation.
Gavin L. Simpson
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.
wa
for details on fitting weighted average models.
data(ImbrieKipp, SumSST, V12.122)
Cor <- weightedCor(ImbrieKipp, env = SumSST,
fossil = V12.122, type = "simulate", sim = 49)
Cor
plot(Cor)
plot(Cor, type = "null")
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