utils: Utility functions.

Description Usage Arguments Details Value Author(s) References

Description

Utility functions to perform simple computations, transformations, formatting etc.

Usage

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make.dummy(fact)

dummy2factor(x)

Hill.N2(df, margin=2)

site.summ(y, max.cut=c(2, 5, 10, 20))

sp.summ(y, n.cut=c(5, 10, 20))

write.list.Excel(x, fName)

Arguments

fact

a factor to convert to a matrix of dummy variables.

x

a matrix or data frame of dummy variables to convert to a factor, or a list to save as an Excel file.

df

a data frame of species abundance data.

margin

margin to calculate over: 1 = by rows, 2 = by columns.

fName

file name for Excel file.

y

data frame or matrix of species by sites data.

n.cut

cut levels of abundance for species summary (see below).

max.cut

cut levels of occurence for species sumamry.

Details

Function make.dummy converts a factor into a matrix of dummy (1/0) variables. dummy2factor converts a matrix or data frame of dummy variables into a factor.

Function Hill.N2 returns Hill's N2 values for species or samples for a given species by sites dataset (Hill 1973).

Function write.list.Excel saves the data frames in a list object as a series of names worksheets in Excel format. Not that this function is only available on Windows. See package WriteXLS for a Linux / MacOS X alternative.

Value

make.dummy returns a matrix of dummay variables. dummy2factor returns a factor.

Hill.N2 returns a numeric vector of N2 values.

sp.summ returns a matrix with columns for the number of occurences, Hill's N2 and maximum abundance of each species, and the number of occurences at abundance greater than the cut levels given in n.cut.

sam.summ returns a matrix with columns for the number of taxa, Hill's N2, maximum value and site total of each site (sample), and the number of taxa in each site with abundance greater than the cut levels given in max.cut.

Author(s)

Steve Juggins

References

Hill, M.O. (1973) Diversity and evenness: a unifying notation and its consequences. Ecology, 54, 427-432.



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