crosstab {ecodist}

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])