R: Matrix Permutation Algorithms for Presence-Absence and Count...

permat {vegan} | R Documentation

## Matrix Permutation Algorithms for Presence-Absence and Count Data

### Description

Individual (for count data) or incidence (for presence-absence data) based null models can be generated for community level simulations. Options for preserving characteristics of the original matrix (rows/columns sums, matrix fill) and restricted permutations (based on strata) are discussed in the Details section.

### Usage

    permatfull(m, fixedmar = "both", shuffle = "both", strata = NULL,
        mtype = "count", times = 99, ...)
    permatswap(m, method = "quasiswap", fixedmar="both", shuffle = "both",
        strata = NULL, mtype = "count", times = 99,
        burnin = 0, thin = 1, ...)
    ## S3 method for class 'permat'
    print(x, digits = 3, ...)
    ## S3 method for class 'permat'
    summary(object, ...)
    ## S3 method for class 'summary.permat'
    print(x, digits = 2, ...)
    ## S3 method for class 'permat'
    plot(x, type = "bray", ylab, xlab, col, lty,
        lowess = TRUE, plot = TRUE, text = TRUE, ...)
    ## S3 method for class 'permat'
    lines(x, type = "bray", ...)
    ## S3 method for class 'permat'
    as.ts(x, type = "bray", ...)
    ## S3 method for class 'permat'
    as.mcmc(x)

### Arguments

`m` | A community data matrix with plots (samples) as rows and species (taxa) as columns.
`fixedmar` | character, stating which of the row/column sums should be preserved (`"none", "rows", "columns", "both"`).
`strata` | Numeric vector or factor with length same as `nrow(m)` for grouping rows within strata for restricted permutations. Unique values or levels are used.
`mtype` | Matrix data type, either `"count"` for count data, or `"prab"` for presence-absence type incidence data.
`times` | Number of permuted matrices.
`method` | Character for method used for the swap algorithm (`"swap"`, `"tswap"`, `"quasiswap"`, `"backtrack"`) as described for function `make.commsim`. If `mtype="count"` the `"quasiswap"`, `"swap"`, `"swsh"` and `"abuswap"` methods are available (see details).
`shuffle` | Character, indicating whether individuals (`"ind"`), samples (`"samp"`) or both (`"both"`) should be shuffled, see details.
`burnin` | Number of null communities discarded before proper analysis in sequential (`"swap", "tswap"`) methods.
`thin` | Number of discarded permuted matrices between two evaluations in sequential (`"swap", "tswap"`) methods.
`x, object` | Object of class `"permat"`
`digits` | Number of digits used for rounding.
`ylab, xlab, col, lty` | graphical parameters for the `plot` method.
`type` | Character, type of plot to be displayed: `"bray"` for Bray-Curtis dissimilarities, `"chisq"` for Chi-squared values.
`lowess, plot, text` | Logical arguments for the `plot` method, whether a locally weighted regression curve should be drawn, the plot should be drawn, and statistic values should be printed on the plot.
`...` | Other arguments passed to `simulate.nullmodel` or methods.

### Details

The function `permatfull` is useful when matrix fill is allowed to vary, and matrix type is `count`. The `fixedmar` argument is used to set constraints for permutation. If `none` of the margins are fixed, cells are randomised within the matrix. If `rows` or `columns` are fixed, cells within rows or columns are randomised, respectively. If `both` margins are fixed, the `r2dtable` function is used that is based on Patefield's (1981) algorithm. For presence absence data, matrix fill should be necessarily fixed, and `permatfull` is a wrapper for the function `make.commsim`. The `r00, r0, c0, quasiswap` algorithms of `make.commsim` are used for `"none", "rows", "columns", "both"` values of the `fixedmar` argument, respectively

The `shuffle` argument only have effect if the `mtype = "count"` and `permatfull` function is used with `"none", "rows", "columns"` values of `fixedmar`. All other cases for count data are individual based randomisations. The `"samp"` and `"both"` options result fixed matrix fill. The `"both"` option means that individuals are shuffled among non zero cells ensuring that there are no cell with zeros as a result, then cell (zero and new valued cells) are shuffled.

The function `permatswap` is useful when with matrix fill (i.e. the proportion of empty cells) and row/columns sums should be kept constant. `permatswap` uses different kinds of swap algorithms, and row and columns sums are fixed in all cases. For presence-absence data, the `swap` and `tswap` methods of `make.commsim` can be used. For count data, a special swap algorithm ('swapcount') is implemented that results in permuted matrices with fixed marginals and matrix fill at the same time.

The 'quasiswapcount' algorithm (`method="quasiswap"` and `mtype="count"`) uses the same trick as Carsten Dormann's `swap.web` function in the package bipartite. First, a random matrix is generated by the `r2dtable` function retaining 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 2x2 submatrices (see 'swapcount' algorithm for details) to maintain row and column totals. This algorithm generates independent matrices in each step, so `burnin` and `thin` arguments are not considered. This is the default method, because this is not sequential (as `swapcount` is) so independence of subsequent matrices does not have to be checked.

The `swapcount` algorithm (`method="swap"` and `mtype="count"`) tries to find 2x2 submatrices (identified by 2 random row and 2 random column indices), that can be swapped in order to leave column and row totals and fill unchanged. First, the algorithm finds the largest value in the submatrix that can be swapped (d) and whether in diagonal or antidiagonal way. Submatrices that contain values larger than zero in either diagonal or antidiagonal position can be swapped. 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 doesn't change. This algorithm is sequential, subsequent matrices are not independent, because swaps modify little if the matrix is large. In these cases many burnin steps and thinning is needed to get independent random matrices. Although this algorithm is implemented in C, large burnin and thin values can slow it down considerably. WARNING: according to simulations, this algorithm seems to be biased and non random, thus its use should be avoided!

The algorithm `"swsh"` in the function `permatswap` is a hybrid algorithm. First, it makes binary quasiswaps to keep row and column incidences constant, then non-zero values are modified according to the `shuffle` argument (only `"samp"` and `"both"` are available in this case, because it is applied only on non-zero values). It also recognizes the `fixedmar` argument which cannot be `"both"` (vegan versions <= 2.0 had this algorithm with `fixedmar = "none"`).

The algorithm `"abuswap"` produces two kinds of null models (based on `fixedmar="columns"` or `fixedmar="rows"`) as described in Hardy (2008; randomization scheme 2x and 3x, respectively). These preserve column and row occurrences, and column or row sums at the same time. (Note that similar constraints can be achieved by the non sequential `"swsh"` algorithm with `fixedmar` argument set to `"columns"` or `"rows"`, respectively.)

Constraints on row/column sums, matrix fill, total sum and sums within strata can be checked by the `summary` method. `plot` method is for visually testing the randomness of the permuted matrices, especially for the sequential swap algorithms. If there are any tendency in the graph, higher `burnin` and `thin` values can help for sequential methods. New lines can be added to existing plot with the `lines` method.

Unrestricted and restricted permutations: if `strata` is `NULL`, functions perform unrestricted permutations. Otherwise, it is used for restricted permutations. Each strata should contain at least 2 rows in order to perform randomization (in case of low row numbers, swap algorithms can be rather slow). If the design is not well balanced (i.e. same number of observations within each stratum), permuted matrices may be biased because same constraints are forced on submatrices of different dimensions. This often means, that the number of potential permutations will decrease with their dimensions. So the more constraints we put, the less randomness can be expected.

The `plot` method is useful for graphically testing for trend and independence of permuted matrices. This is especially important when using sequential algorithms (`"swap", "tswap", "abuswap"`).

The `as.ts` method can be used to extract Bray-Curtis dissimilarities or Chi-squared values as time series. This can further used in testing independence (see Examples). The method `as.mcmc` is useful for accessing diagnostic tools available in the coda package.

### Value

Functions `permatfull` and `permatswap` return an object of class `"permat"` containing the the function call (`call`), the original data matrix used for permutations (`orig`) and a list of permuted matrices with length `times` (`perm`).

The `summary` method returns various statistics as a list (including mean Bray-Curtis dissimilarities calculated pairwise among original and permuted matrices, Chi-square statistics, and check results of the constraints; see Examples). Note that when `strata` is used in the original call, summary calculation may take longer.

The `plot` creates a plot as a side effect.

The `as.ts` method returns an object of class `"ts"`.

### Author(s)

Péter Sólymos, solymos@ualberta.ca and Jari Oksanen

### References

Original references for presence-absence algorithms are given on help page of `make.commsim`.

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.

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.

### See Also

For other functions to permute matrices: `make.commsim`, `r2dtable`, `sample`, `swap.web`.

For the use of these permutation algorithms: `oecosimu`, `adipart`, `hiersimu`.

For time-series diagnostics: `Box.test`, `lag.plot`, `tsdiag`, `ar`, `arima`

For underlying ‘low level’ implementation: `commsim` and `nullmodel`.

### Examples

    ## A simple artificial community data matrix.
    m <- matrix(c(
        1,3,2,0,3,1,
        0,2,1,0,2,1,
        0,0,1,2,0,3,
        0,0,0,1,4,3
        ), 4, 6, byrow=TRUE)
    ## Using the quasiswap algorithm to create a
    ## list of permuted matrices, where
    ## row/columns sums and matrix fill are preserved:
    x1 <- permatswap(m, "quasiswap")
    summary(x1)
    ## Unrestricted permutation retaining
    ## row/columns sums but not matrix fill:
    x2 <- permatfull(m)
    summary(x2)
    ## Unrestricted permutation of presence-absence type
    ## not retaining row/columns sums:
    x3 <- permatfull(m, "none", mtype="prab")
    x3$orig  ## note: original matrix is binarized!
    summary(x3)
    ## Restricted permutation,
    ## check sums within strata:
    x4 <- permatfull(m, strata=c(1,1,2,2))
    summary(x4)

    ## NOTE: 'times' argument usually needs to be >= 99
    ## here much lower value is used for demonstration

    ## Not sequential algorithm
    data(BCI)
    a <- permatswap(BCI, "quasiswap", times=19)
    ## Sequential algorithm
    b <- permatswap(BCI, "abuswap", fixedmar="col",
        burnin=0, thin=100, times=19)
    opar <- par(mfrow=c(2,2))
    plot(a, main="Not sequential")
    plot(b, main="Sequential")
    plot(a, "chisq")
    plot(b, "chisq")
    par(opar)
    ## Extract Bray-Curtis dissimilarities
    ## as time series
    bc <- as.ts(b)
    ## Lag plot
    lag.plot(bc)
    ## First order autoregressive model
    mar <- arima(bc, c(1,0,0))
    mar
    ## Ljung-Box test of residuals
    Box.test(residuals(mar))
    ## Graphical diagnostics
    tsdiag(mar)

[Package vegan version 2.4-3 Index]