R: Create an Object for Null Model Algorithms

commsim {vegan} | R Documentation

## Create an Object for Null Model Algorithms

### Description

The `commsim` function can be used to feed Null Model algorithms into `nullmodel` analysis. The `make.commsim` function returns various predefined algorithm types (see Details). These functions represent low level interface for community null model infrastructure in vegan with the intent of extensibility, and less emphasis on direct use by users.

### Usage

    commsim(method, fun, binary, isSeq, mode)
    make.commsim(method)
    ## S3 method for class 'commsim'
    print(x, ...)

### Arguments

`method` | Character, name of the algorithm.
`fun` | A function. For possible formal arguments of this function see Details.
`binary` | Logical, if the algorithm applies to presence-absence or count matrices.
`isSeq` | Logical, if the algorithm is sequential (needs burnin and thinning) or not.
`mode` | Character, storage mode of the community matrix, either `"integer"` or `"double"`.
`x` | An object of class `commsim`.
`...` | Additional arguments.

### Details

The function `fun` must return an array of `dim(nr, nc, n)`, and must take some of the following arguments:

- `x`: input matrix,

- `n`: number of permuted matrices in output,

- `nr`: number of rows,

- `nc`: number of columns,

- `rs`: vector of row sums,

- `cs`: vector of column sums,

- `rf`: vector of row frequencies (non-zero cells),

- `cf`: vector of column frequencies (non-zero cells),

- `s`: total sum of `x`,

- `fill`: matrix fill (non-zero cells),

- `thin`: thinning value for sequential algorithms,

- `...`: additional arguments.

You can define your own null model, but several null model algorithm are pre-defined and can be called by their name. The predefined algorithms are described in detail in the following chapters. The binary null models produce matrices of zeros (absences) and ones (presences) also when input matrix is quantitative. There are two types of quantitative data: Counts are integers with a natural unit so that individuals can be shuffled, but abundances can have real (floating point) values and do not have a natural subunit for shuffling. All quantitative models can handle counts, but only some are able to handle real values. Some of the null models are sequential so that the next matrix is derived from the current one. This makes models dependent from previous models, and usually you must thin these matrices and study the sequences for stability: see `oecosimu` for details and instructions.

See Examples for structural constraints imposed by each algorithm and defining your own null model.

### Value

An object of class `commsim` with elements corresponding to the arguments (`method`, `binary`, `isSeq`, `mode`, `fun`).

If the input of `make.comsimm` is a `commsim` object, it is returned without further evaluation. If this is not the case, the character `method` argument is matched against predefined algorithm names. An error message is issued if none such is found. If the `method` argument is missing, the function returns names of all currently available null model algorithms as a character vector.

### Binary null models

All binary null models preserve fill: number of presences or conversely the number of absences. The classic models may also preserve column (species) frequencies (`c0`) or row frequencies or species richness of each site (`r0`) and take into account commonness and rarity of species (`r1`, `r2`). Algorithms `swap`, `tswap`, `curveball`, `quasiswap` and `backtracking` preserve both row and column frequencies. Three first ones are sequential but the two latter are non-sequential and produce independent matrices. Basic algorithms are reviewed by Wright et al. (1998).

- `"r00"`: non-sequential algorithm for binary matrices that only preserves the number of presences (fill).

- `"r0", "r0_old"`: non-sequential algorithm for binary matrices that preserves the site (row) frequencies. Methods `"r0"` and `"r0_old"` implement the same method, but use different random number sequences; use `"r0_old"` if you want to reproduce results in vegan 2.0-0 or older using `commsimulator` (now deprecated).

- `"r1"`: non-sequential algorithm for binary matrices that preserves the site (row) frequencies, but uses column marginal frequencies as probabilities of selecting species.

- `"r2"`: non-sequential algorithm for binary matrices that preserves the site (row) frequencies, and uses squared column marginal frequencies as as probabilities of selecting species.

- `"c0"`: non-sequential algorithm for binary matrices that preserves species frequencies (Jonsson 2001).

- `"swap"`: sequential algorithm for binary matrices that changes the matrix structure, but does not influence marginal sums (Gotelli & Entsminger 2003). This inspects 2 by 2 submatrices so long that a swap can be done.

- `"tswap"`: sequential algorithm for binary matrices. Same as the `"swap"` algorithm, but it tries a fixed number of times and performs zero to many swaps at one step (according to the thin argument in the call). This approach was suggested by Miklós & Podani (2004) because they found that ordinary swap may lead to biased sequences, since some columns or rows are more easily swapped.

- `"curveball"`: sequential method for binary matrices that implements the ‘Curveball’ algorithm of Strona et al. (2014). The algorithm selects two random rows and finds the set of unique species that occur only in one of these rows. The algorithm distributes the set of unique species to rows preserving the original row frequencies. Zero to several species are swapped in one step, and usually the matrix is perturbed more strongly than in other sequential methods.

- `"quasiswap"`: non-sequential algorithm for binary matrices that implements a method where matrix is first filled honouring row and column totals, but with integers that may be larger than one. Then the method inspects random 2 by 2 matrices and performs a quasiswap on them. In addition to ordinary swaps, quasiswap can reduce numbers above one to ones preserving marginal totals (Miklós & Podani 2004). The method is non-sequential, but it accepts `thin` argument: the convergence is checked at every `thin` steps. This allows performing several ordinary swaps in addition to fill changing swaps which helps in reducing or removing the bias.

- `"backtracking"`: non-sequential algorithm for binary matrices that implements a filling method with constraints both for row and column frequencies (Gotelli & Entsminger 2001). The matrix is first filled randomly using row and column frequencies as probabilities. Typically row and column sums are reached before all incidences are filled in. After that begins "backtracking", where some of the points are removed, and then filling is started again, and this backtracking is done so may times that all incidences will be filled into matrix. The function may be very slow for some matrices. The results may be biased and should be inspected carefully before use.

### Quantitative Models for Counts with Fixed Marginal Sums

These models shuffle individuals of counts and keep marginal sums fixed, but marginal frequencies are not preserved. Algorithm `r2dtable` uses standard R function `r2dtable` also used for simulated P-values in `chisq.test`. Algorithm `quasiswap_count` uses the same, but preserves the original fill. Typically this means increasing numbers of zero cells and the result is zero-inflated with respect to `r2dtable`.

- `"r2dtable"`: non-sequential algorithm for count matrices. This algorithm keeps matrix sum and row/column sums constant. Based on `r2dtable`.

- `"quasiswap_count"`: non-sequential algorithm for count matrices. This algorithm is similar as Carsten Dormann's `swap.web` function in the package bipartite. First, a random matrix is generated by the `r2dtable` function preserving row and column sums. Then the original matrix fill is reconstructed by sequential steps to increase or decrease matrix fill in the random matrix. These steps are based on swapping 2 x 2 submatrices (see `"swap_count"` algorithm for details) to maintain row and column totals.

### Quantitative Swap Models

Quantitative swap models are similar to binary `swap`, but they swap the largest permissible value. The models in this section all maintain the fill and perform a quantitative swap only if this can be done without changing the fill. Single step of swap often changes the matrix very little. In particular, if cell counts are variable, high values change very slowly. Checking the chain stability and independence is even more crucial than in binary swap, and very strong `thin`ning is often needed. These models should never be used without inspecting their properties for the current data. These null models can also be defined using `permatswap` function.

- `"swap_count"`: sequential algorithm for count matrices. This algorithm find 2 x 2 submatrices that can be swapped leaving column and row totals and fill unchanged. The algorithm finds the largest value in the submatrix that can be swapped (d). Swap means that the values in diagonal or antidiagonal positions are decreased by d, while remaining cells are increased by d. A swap is made only if fill does not change.

- `"abuswap_r"`: sequential algorithm for count or nonnegative real valued matrices with fixed row frequencies (see also `permatswap`). The algorithm is similar to `swap_count`, but uses different swap value for each row of the 2 x 2 submatrix. Each step changes the the corresponding column sums, but honours matrix fill, row sums, and row/column frequencies (Hardy 2008; randomization scheme 2x).

- `"abuswap_c"`: sequential algorithm for count or nonnegative real valued matrices with fixed column frequencies (see also `permatswap`). The algorithm is similar as the previous one, but operates on columns. Each step changes the the corresponding row sums, but honours matrix fill, column sums, and row/column frequencies (Hardy 2008; randomization scheme 3x).

### Quantitative Swap and Shuffle Models

Quantitative Swap and Shuffle methods (`swsh` methods) preserve fill and column and row frequencies, and also either row or column sums. The methods first perform a binary `quasiswap` and then shuffle original quantitative data to non-zero cells. The `samp` methods shuffle original non-zero cell values and can be used also with non-integer data. The `both` methods redistribute individuals randomly among non-zero cells and can only be used with integer data. The shuffling is either free over the whole matrix, or within rows (`r` methods) or within columns (`c` methods). Shuffling within a row preserves row sums, and shuffling within a column preserves column sums. These models can also be defined with `permatswap`.

- `"swsh_samp"`: non-sequential algorithm for quantitative data (either integer counts or non-integer values). Original non-zero values values are shuffled.

- `"swsh_both"`: non-sequential algorithm for count data. Individuals are shuffled freely over non-zero cells.

- `"swsh_samp_r"`: non-sequential algorithm for quantitative data. Non-zero values (samples) are shuffled separately for each row.

- `"swsh_samp_c"`: non-sequential algorithm for quantitative data. Non-zero values (samples) are shuffled separately for each column.

- `"swsh_both_r"`: non-sequential algorithm for count matrices. Individuals are shuffled freely for non-zero values within each row.

- `"swsh_both_c"`: non-sequential algorithm for count matrices. Individuals are shuffled freely for non-zero values with each column.

### Quantitative Shuffle Methods

Quantitative shuffle methods are generalizations of binary models `r00`, `r0` and `c0`. The `_ind` methods shuffle individuals so that the grand sum, row sum or column sums are preserved. These methods are similar as `r2dtable` but with still slacker constraints on marginal sums. The `_samp` and `_both` methods first apply the correspongind binary model with similar restriction on marginal frequencies and then distribute quantitative values over non-zero cells. The `_samp` models shuffle original cell values and can therefore handle also non-count real values. The `_both` models shuffle individuals among non-zero values. The shuffling is over the whole matrix in `r00_`, and within row in `r0_` and within column in `c0_` in all cases.

- `"r00_ind"`: non-sequential algorithm for count matrices. This algorithm preserves grand sum and individuals are shuffled among cells of the matrix.

- `"r0_ind"`: non-sequential algorithm for count matrices. This algorithm preserves row sums and individuals are shuffled among cells of each row of the matrix.

- `"c0_ind"`: non-sequential algorithm for count matrices. This algorithm preserves column sums and individuals are shuffled among cells of each column of the matrix.

- `"r00_samp"`: non-sequential algorithm for count or nonnegative real valued (`mode = "double"`) matrices. This algorithm preserves grand sum and cells of the matrix are shuffled.

- `"r0_samp"`: non-sequential algorithm for count or nonnegative real valued (`mode = "double"`) matrices. This algorithm preserves row sums and cells within each row are shuffled.

- `"c0_samp"`: non-sequential algorithm for count or nonnegative real valued (`mode = "double"`) matrices. This algorithm preseerves column sums constant and cells within each column are shuffled.

- `"r00_both"`: non-sequential algorithm for count matrices. This algorithm preserves grand sum and cells and individuals among cells of the matrix are shuffled.

- `"r0_both"`: non-sequential algorithm for count matrices. This algorithm preserves grand sum and cells and individuals among cells of each row are shuffled.

- `"c0_both"`: non-sequential algorithm for count matrices. This algorithm preserves grand sum and cells and individuals among cells of each column are shuffled.

### Author(s)

Jari Oksanen and Peter Solymos

### References

Gotelli, N.J. & Entsminger, N.J. (2001). Swap and fill algorithms in null model analysis: rethinking the knight's tour. Oecologia 129, 281–291.

Gotelli, N.J. & Entsminger, N.J. (2003). Swap algorithms in null model analysis. Ecology 84, 532–535.

Hardy, O. J. (2008) Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community. Journal of Ecology 96, 914–926.

Jonsson, B.G. (2001) A null model for randomization tests of nestedness in species assemblages. Oecologia 127, 309–313.

Miklós, I. & Podani, J. (2004). Randomization of presence-absence matrices: comments and new algorithms. Ecology 85, 86–92.

Patefield, W. M. (1981) Algorithm AS159. An efficient method of generating r x c tables with given row and column totals. Applied Statistics 30, 91–97.

Strona, G., Nappo, D., Boccacci, F., Fattorini, S. & San-Miguel-Ayanz, J. (2014). A fast and unbiased procedure to randomize ecological binary matrices with fixed row and column totals. Nature Communications 5:4114 doi: 10.1038/ncomms5114.

Wright, D.H., Patterson, B.D., Mikkelson, G.M., Cutler, A. & Atmar, W. (1998). A comparative analysis of nested subset patterns of species composition. Oecologia 113, 1–20.

### See Also

See `permatfull`, `permatswap` for alternative specification of quantitative null models. Function `oecosimu` gives a higher-level interface for applying null models in hypothesis testing and analysis of models. Function `nullmodel` and `simulate.nullmodel` are used to generate arrays of simulated null model matrices.

### Examples

    ## write the r00 algorithm
    f <- function(x, n, ...)
        array(replicate(n, sample(x)), c(dim(x), n))
    (cs <- commsim("r00", fun=f, binary=TRUE,
        isSeq=FALSE, mode="integer"))

    ## retrieving the sequential swap algorithm
    (cs <- make.commsim("swap"))

    ## feeding a commsim object as argument
    make.commsim(cs)

    ## structural constraints
    diagfun <- function(x, y) {
        c(sum = sum(y) == sum(x),
            fill = sum(y > 0) == sum(x > 0),
            rowSums = all(rowSums(y) == rowSums(x)),
            colSums = all(colSums(y) == colSums(x)),
            rowFreq = all(rowSums(y > 0) == rowSums(x > 0)),
            colFreq = all(colSums(y > 0) == colSums(x > 0)))
    }
    evalfun <- function(meth, x, n) {
        m <- nullmodel(x, meth)
        y <- simulate(m, nsim=n)
        out <- rowMeans(sapply(1:dim(y)[3],
            function(i) diagfun(attr(y, "data"), y[,,i])))
        z <- as.numeric(c(attr(y, "binary"), attr(y, "isSeq"),
            attr(y, "mode") == "double"))
        names(z) <- c("binary", "isSeq", "double")
        c(z, out)
    }
    x <- matrix(rbinom(10*12, 1, 0.5)*rpois(10*12, 3), 12, 10)
    algos <- make.commsim()
    a <- t(sapply(algos, evalfun, x=x, n=10))
    print(as.table(ifelse(a==1,1,0)), zero.print = ".")

[Package vegan version 2.4-3 Index]