Indicator.nonEqual: Calculated the non group-equalised habitat indicator value...
In Zabados/PhiCor: PhiCor: Calculating the Phi coefficient of Association

Description Usage Arguments Value Author(s) References See Also Examples

This function calculates the non group-equalised version of the habitat indicator value (IndVal) De Cáceres and Legendre (2009). This is useful alone to calculate the non group-equalised version for a single habitat of interest among multiple other habitats.

1	Indicator.nonEqual(CorIndexTargetVarInput)

CorIndexTargetVarInput

a custom class "CorIndexVar" containing all values from from both CorIndex and CorIndex.TargetVar

IndVal - a floating point number between 0 and 1.

Jordan Chetcuti

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).

PhiCor

    #Builing on the examples from \link[PhiCor]{CorIndex.TargetVar}
    #Using the included dataframe Species1
    Inputs_species1 = CorIndex(InDataframe = Species1, speciesbinary = 'Species1', weighted = 'Proportion', group = 'HabId', 'LocationID')
    Inputs_species1$nkoverNk
    #Using CorIndex.TargetVar, the input is the output of Indicator. In this case we are interested in
    #habitat 1 (using the ID for the habitat)
    Inputs_species1_hab1 = Indicator.TargetVar(Inputs_species1, 1)

    species1_hab1_Phi = Indicator.nonEqual(Inputs_species1_hab1)



    #Using the included dataframe Species2
    #If you wanted the analysis to be non-weighted.
    Species2Unweight = Species2[which(Species2$Proportion==1),]
    #This analysis is then the unweighted version of the analysis. SquareID is not needed.
    Inputs_species2 =  CorIndex(InDataframe = Species2Unweight, speciesbinary = 'Species2', weighted = 'Proportion', group = 'HabId')
    names(Inputs_species2)

    #Looking at habitat 4
    Inputs_species2_hab4 = Indicator.TargetVar(Inputs_species2, 4)

    species2_hab4_IndVal = Indicator.nonEqual(Inputs_species2_hab4)