Description Usage Arguments Value Note Author(s) See Also Examples
Computes weighted average optima and tolerance ranges from species abundances and values of the environment.
1 2 3 4 5 6 7 8 |
x |
Species data matrix or data frame. |
env |
Numeric; variable for which optima or tolerances are required. |
boot, nboot |
logical ( |
alpha |
numeric; 1 - |
useN2 |
logical; should Hill's N2 values be used to produce un-biased tolerances? |
... |
Arguments passed to other methods. |
Both functions return a named vector containing the WA optima or
tolerances for the environmental gradient specified by env
.
Objects of class "optima"
or "tolerance"
can be coerced
to data frames using methods for as.data.frame
.
Gavin L. Simpson
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ## Load the Imbrie & Kipp data and
## summer sea-surface temperatures
data(ImbrieKipp)
data(SumSST)
## WA optima
(opt <- optima(ImbrieKipp, SumSST))
## WA tolerances
(tol <- tolerance(ImbrieKipp, SumSST, useN2 = TRUE))
## caterpillar plot
caterpillarPlot(opt, tol)
## convert to data frame
as.data.frame(opt)
as.data.frame(tol)
## bootstrap WA optima - 100 resamples too low for SD & pCI
bopt <- optima(ImbrieKipp, SumSST, boot = TRUE, nboot = 100)
head(bopt)
|
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