Description Usage Arguments Details Value See Also Examples
Function calculating fourth corner analysis between sample attributes (environmental variables) and species attributes (traits) and testing it by row based, column based or max permutation test.
1 2 3 4 5 6 7 8 9 10 | test_fourth(env, com = NULL, traits = NULL, cwm = NULL, perm = 499,
test = "max", parallel = NULL, p.adjust.method = p.adjust.methods,
adjustP = FALSE)
## S3 method for class 'testFOURTH'
print(x, digits = max(3, getOption("digits") - 3),
missing.summary = FALSE, ...)
## S3 method for class 'testFOURTH'
coef(object, ...)
|
env |
Vector, matrix or data frame with sample attributes (environemntal variables). |
com |
Matrix of data frame with species composition data. |
traits |
Vector, matrix or data frame with species attributes (traits) |
cwm |
An object of the class |
perm |
Number of permutations. |
test |
Vector of character values. Which test should be conducted? Partial match to |
parallel |
NULL (default) or integer number. Number of cores for parallel calculation of modified permutation test. Maximum number of cores should correspond to number of available cores on the processor. |
p.adjust.method |
A string indicating the method of P-value adjustement, see |
adjustP |
Logical, default FALSE. Should be the P-values adjusted? If |
x, object |
object of the class |
digits |
number of digits reported by |
missing.summary |
Logical; should be the summary of values missing in |
... |
Other arguments for |
Environmental variables, species composition and traits can be provided in two ways: either each object separately, using arguments env
, com
and traits
, or using only env
and cwm
; in the later case, the function extract
is used to extract the com
and traits
from the cwm
object.
Specific issue related to weighted mean is the case of missing species attributes. In current implementation, species with missing species attributes are removed from sample x species matrix prior to permutation of species attributes among species.
Function test_fourth
returns the list of the class "testFOURTH"
(with print
and summary
methods), which contains the following items:
call
Function call.
out
Data frame with results of calculation; first two columns contain the original fourth corner metric (r_fc
) and its Chessel transformation (r_ch
); following columns contain some of the following results of permutation tests: P.row
, P.col
and P.max
. If adjustP = TRUE
, the last column contains P values adjusted by p.adjust
function.
miss
List with missing values of env
, traits
or cwm
(the last provided for compatibility with test_cwm
function and refers to samples which, after removing missing traits
values, do not contain any species.)
param
Setting of input parameters (perm
and test
).
1 2 3 4 5 |
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