PhiCor-package: Package for calculation the Weighted Phi Coefficient of...
In Zabados/PhiCor: PhiCor: Calculating the Phi coefficient of Association
Description
Details
Author(s)
References
See Also
Description
This package can be used to calculate the weighted phi coeficient of
association using a weighting for habitats within a location, or
can calculate the unweighted original version from
De Cáceres and Legendre (2009) by using a weighting of one.
The package also allows the group-equalised version to be run.
Details
The Phi Coefficent of association gives the habitat preference, or
site fidelity of habitat sites.
The main function in PhiCor is CorIndex.all.plusP.
This will calculate all phi corelation of association values and
purmutate to give p-values.
The other Phi coefficent functions are useful in testing or calculating only part
of the full outputs from CorIndex.all.plusP:
-
CorIndex calculates the inputs that don't change between habitats.
-
CorIndex.TargetVar calculates the additional input specific to a habitat.
-
CorIndex.groupEqual calculates the group-equalised phi for a habitat.
-
CorIndex.nonEqual calculates the non group-equalised phi for a habitat.
-
CorIndex.xPerm returns the null phi distribution for a habitat.
-
CorIndex.all returns the non and group-equalised phi values for all habitats
without p-values and is therefore quicker.
Weighted habitat indicator values (IndVal) can also be calculated, but these have not been tested in
the way that the phi coefficent has been.
The main function for calculating IndVal is Indicator.all.plusP
These functions are useful in testing or calculating only part
of the full outputs from Indicator.all.plusP:
-
Indicator.nonEqual Calculated the non group-equalised habitat indicator value (IndVal).
-
Indicator.groupEqual Calculated the group-equalised species indicator value (IndVal).
-
Indicator.xPerm Permutates and calculates for each permutation both the non and
group-equalised species indicator value (IndVal).
-
The functions lookup and FilePathInTree
might be used elsewhere.
Author(s)
Jordan Chetcuti
References
De Cáceres, M., & Legendre, P. (2009). Associations between species and groups of sites: indices and statistical inference. Ecology, 90(12), 3566–3574.
Chetcuti, J., Kunin, W. E. & Bullock, J. M. A weighting method to improve habitat association analysis: tested on British carabids. Ecography (Cop.). 42, 1395–1404 (2019).
See Also
Useful links:
Zabados/PhiCor documentation built on Oct. 9, 2021, 1:24 a.m.
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Description Details Author(s) References See Also
Description
This package can be used to calculate the weighted phi coeficient of association using a weighting for habitats within a location, or can calculate the unweighted original version from De Cáceres and Legendre (2009) by using a weighting of one. The package also allows the group-equalised version to be run.
Details
The Phi Coefficent of association gives the habitat preference, or site fidelity of habitat sites.
The main function in PhiCor is CorIndex.all.plusP. This will calculate all phi corelation of association values and purmutate to give p-values.
The other Phi coefficent functions are useful in testing or calculating only part of the full outputs from CorIndex.all.plusP:
-
CorIndex calculates the inputs that don't change between habitats.
-
CorIndex.TargetVar calculates the additional input specific to a habitat.
-
CorIndex.groupEqual calculates the group-equalised phi for a habitat.
-
CorIndex.nonEqual calculates the non group-equalised phi for a habitat.
-
CorIndex.xPerm returns the null phi distribution for a habitat.
-
CorIndex.all returns the non and group-equalised phi values for all habitats without p-values and is therefore quicker.
Weighted habitat indicator values (IndVal) can also be calculated, but these have not been tested in the way that the phi coefficent has been. The main function for calculating IndVal is Indicator.all.plusP These functions are useful in testing or calculating only part of the full outputs from Indicator.all.plusP:
-
Indicator.nonEqual Calculated the non group-equalised habitat indicator value (IndVal).
-
Indicator.groupEqual Calculated the group-equalised species indicator value (IndVal).
-
Indicator.xPerm Permutates and calculates for each permutation both the non and group-equalised species indicator value (IndVal).
The functions lookup and FilePathInTree might be used elsewhere.
Author(s)
Jordan Chetcuti
References
De Cáceres, M., & Legendre, P. (2009). Associations between species and groups of sites: indices and statistical inference. Ecology, 90(12), 3566–3574.
Chetcuti, J., Kunin, W. E. & Bullock, J. M. A weighting method to improve habitat association analysis: tested on British carabids. Ecography (Cop.). 42, 1395–1404 (2019).
See Also
Useful links:
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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