R: Mixed-variables coefficient of distance

dist.ktab {ade4} | R Documentation

## Mixed-variables coefficient of distance

### Description

The mixed-variables coefficient of distance generalizes Gower's general coefficient of distance to allow the treatment of various statistical types of variables when calculating distances. This is especially important when measuring functional diversity. Indeed, most of the indices that measure functional diversity depend on variables (traits) that have various statistical types (e.g. circular, fuzzy, ordinal) and that go through a matrix of distances among species.

### Usage

    dist.ktab(x, type, option = c("scaledBYrange", "scaledBYsd", "noscale"),
    scann = FALSE, tol = 1e-8)
    ldist.ktab(x, type, option = c("scaledBYrange", "scaledBYsd",
    "noscale"), scann = FALSE, tol = 1e-8)
    kdist.cor(x, type, option = c("scaledBYrange", "scaledBYsd", "noscale"),
    scann = FALSE, tol = 1e-8, squared = TRUE)
    prep.fuzzy(df, col.blocks, row.w = rep(1, nrow(df)), labels = paste("F",
    1:length(col.blocks), sep = ""))
    prep.binary(df, col.blocks, labels = paste("B", 1:length(col.blocks), sep = ""))
    prep.circular(df, rangemin = apply(df, 2, min, na.rm = TRUE), rangemax =
    apply(df, 2, max, na.rm = TRUE))

### Arguments

`x` | Object of class `ktab` (see details)
`type` | Vector that provide the type of each table in x. The possible types are "Q" (quantitative), "O" (ordinal), "N" (nominal), "D" (dichotomous), "F" (fuzzy, or expressed as a proportion), "B" (multichoice nominal variables, coded by binary columns), "C" (circular). Values in type must be in the same order as in x.
`option` | A string that can have three values: either "scaledBYrange" if the quantitative variables must be scaled by their range, or "scaledBYsd" if they must be scaled by their standard deviation, or "noscale" if they should not be scaled. This last option can be useful if the the values have already been normalized by the known range of the whole population instead of the observed range measured on the sample. If x contains data from various types, then the option "scaledBYsd" is not suitable (a warning will appear if the option selected with that condition).
`scann` | A logical. If TRUE, then the user will have to choose among several possible functions of distances for the quantitative, ordinal, fuzzy and binary variables.
`tol` | A tolerance threshold: a value less than tol is considered as null.
`squared` | A logical, if TRUE, the squared distances are considered.
`df` | Objet of class data.frame
`col.blocks` | A vector that contains the number of levels per variable (in the same order as in `df`)
`row.w` | A vector of row weigths
`labels` | the names of the traits
`rangemin` | A numeric corresponding to the smallest level where the loop starts
`rangemax` | A numeric corresponding to the highest level where the loop closes

### Details

When preparing the object of class `ktab` (object x), variables of type "Q", "O", "D", "F", "B" and "C" should be of class `numeric` (the class `ordered` is not yet considered by `dist.ktab`); variables of type "N" should be of class `character` or `factor`

### Value

The functions provide the following results:

`dist.ktab` | returns an object of class `dist`;
`ldist.ktab` | returns a list of objects of class `dist` that correspond to the distances between species calculated per trait;
`kdist.cor` | returns a list of three objects: "paircov" provides the covariance between traits in terms of (squared) distances between species; "paircor" provides the correlations between traits in terms of (squared) distances between species; "glocor" provides the correlations between the (squared) distances obtained for each trait and the global (squared) distances obtained by mixing all the traits (= contributions of traits to the global distances);
`prep.binary and prep.fuzzy` | returns a data frame with the following attributes: col.blocks specifies the number of columns per fuzzy variable; col.num specifies which variable each column belongs to;
`prep.circular` | returns a data frame with the following attributes: max specifies the number of levels in each circular variable.

### Author(s)

Sandrine Pavoine pavoine@mnhn.fr

### References

Pavoine S., Vallet, J., Dufour, A.-B., Gachet, S. and Daniel, H. (2009) On the challenge of treating various types of variables: Application for improving the measurement of functional diversity. Oikos, 118, 391–402. doi: 10.1111/j.1600-0706.2008.16668.x

Appendix available at: http://www.oikosjournal.org/sites/oikosjournal.org/files/appendix/o16668.pdf http://www.oikosjournal.org/sites/oikosjournal.org/files/appendix/o16668_files.zip

### See Also

`daisy` in the case of ratio-scale (quantitative) and nominal variables; and `woangers` for an application.

### Examples

    # With fuzzy variables
    data(bsetal97)

    w <- prep.fuzzy(bsetal97$biol, bsetal97$biol.blo)
    w[1:6, 1:10]
    ktab1 <- ktab.list.df(list(w))
    dis <- dist.ktab(ktab1, type = "F")
    as.matrix(dis)[1:5, 1:5]

    ## Not run:
    # With ratio-scale and multichoice variables
    data(ecomor)

    wM <- log(ecomor$morpho + 1) # Quantitative variables
    wD <- ecomor$diet
    # wD is a data frame containing a multichoice nominal variable
    # (diet habit), with 8 modalities (Granivorous, etc)
    # We must prepare it by prep.binary
    head(wD)
    wD <- prep.binary(wD, col.blocks = 8, label = "diet")
    wF <- ecomor$forsub
    # wF is also a data frame containing a multichoice nominal variable
    # (foraging substrat), with 6 modalities (Foliage, etc)
    # We must prepare it by prep.binary
    head(wF)
    wF <- prep.binary(wF, col.blocks = 6, label = "foraging")
    # Another possibility is to combine the two last data frames wD and wF as
    # they contain the same type of variables
    wB <- cbind.data.frame(ecomor$diet, ecomor$forsub)
    head(wB)
    wB <- prep.binary(wB, col.blocks = c(8, 6), label = c("diet", "foraging"))
    # The results given by the two alternatives are identical
    ktab2 <- ktab.list.df(list(wM, wD, wF))
    disecomor <- dist.ktab(ktab2, type= c("Q", "B", "B"))
    as.matrix(disecomor)[1:5, 1:5]
    contrib2 <- kdist.cor(ktab2, type= c("Q", "B", "B"))
    contrib2

    ktab3 <- ktab.list.df(list(wM, wB))
    disecomor2 <- dist.ktab(ktab3, type= c("Q", "B"))
    as.matrix(disecomor2)[1:5, 1:5]
    contrib3 <- kdist.cor(ktab3, type= c("Q", "B"))
    contrib3

    # With a range of variables
    data(woangers)

    traits <- woangers$traits
    # Nominal variables 'li', 'pr', 'lp' and 'le'
    # (see table 1 in the main text for the codes of the variables)
    tabN <- traits[,c(1:2, 7, 8)]
    # Circular variable 'fo'
    tabC <- traits[3]
    tabCp <- prep.circular(tabC, 1, 12)
    # The levels of the variable lie between 1 (January) and 12 (December).
    # Ordinal variables 'he', 'ae' and 'un'
    tabO <- traits[, 4:6]
    # Fuzzy variables 'mp', 'pe' and 'di'
    tabF <- traits[, 9:19]
    tabFp <- prep.fuzzy(tabF, c(3, 3, 5), labels = c("mp", "pe", "di"))
    # 'mp' has 3 levels, 'pe' has 3 levels and 'di' has 5 levels.
    # Quantitative variables 'lo' and 'lf'
    tabQ <- traits[, 20:21]
    ktab1 <- ktab.list.df(list(tabN, tabCp, tabO, tabFp, tabQ))
    distrait <- dist.ktab(ktab1, c("N", "C", "O", "F", "Q"))
    is.euclid(distrait)
    contrib <- kdist.cor(ktab1, type = c("N", "C", "O", "F", "Q"))
    contrib
    dotchart(sort(contrib$glocor), labels = rownames(contrib$glocor)[order(contrib$glocor[, 1])])

    ## End(Not run)

[Package ade4 version 1.7-19 Index]