R: Data formatting

crosstab {ecodist} | R Documentation

## Data formatting

### Description

Converts field data of the form site, species, observation into a site by species data frame.

### Usage

    crosstab(rowlab, collab, values, type = "sum", data, allrows, allcols,
    na.as.0 = TRUE, check.names = TRUE, ...)

### Arguments

`rowlab` | row labels, e.g. site names.
`collab` | column labels, e.g. species names.
`values` | data values.
`data` | optional data frame from which to take rowlab, collab and/or values.
`type` | function to use to combine data, one of "sum" (default), "min", "max", "mean", "count".
`allrows` | optional, list of all desired row names that may not appear in rowlab.
`allcols` | optional, list of all desired column names that may not appear in collab.
`na.as.0` | if TRUE, all NA values are replaced with 0.
`check.names` | if FALSE, data frame names are not checked for syntactic validity, so that they match the input categories. Otherwise make.names() is used to adjust them.
`...` | optional arguments to the function specified in type, such as na.rm=TRUE

### Details

Field data are often recorded as a separate row for each site-species combination. This function reformats such data into a data frame for further analysis based on unique row and column labels. The three vectors should all be the same length (including duplicates). The three vectors may also be provided as names of columns in the data frame specified by the data argument.

If allrows or allcols exists, rows and/or columns of zeros are inserted for any elements of allrows/allcols not present in rowlab/collab.

If values is missing the number of occurrences of combinations of rowlab and collab will be returned. Thus, crosstab(rowlab, collab) is equivalent to table(rowlab, collab).

If type is "count", the unique combinations of rowlab, collab and values will be returned.

### Value

data frame with rowlab as row headings, collab as columns, and values as the data.

### Author(s)

Sarah Goslee

### Examples

    # Make a random example
    plotnames <- rep(1:5, each = 6)
    speciesnames <- rep(c("A", "B", "C"), 10)
    freqdata <- runif(30)

    # number of samples of each species and plot
    crosstab(plotnames, speciesnames)

    # can use the data argument
    speciesdata <- data.frame(plots = plotnames, species = speciesnames,
      freq = freqdata, stringsAsFactors=FALSE)

    # mean frequency by species and plot
    crosstab(plots, species, freq, data=speciesdata, type="mean")

    # can specify additional possible row or column levels
    crosstab(plots, species, freq, data=speciesdata, type="mean", allcols=LETTERS[1:5])

[Package ecodist version 2.0.7 Index]