cheddar (version 0.1-639)

ApplyByClass: Apply by class

Description

Apply functions to a group of values given by a node property.

Usage

ApplyByClass(community, property, class, fn, ...)
SumMByClass(community, class, na.rm=FALSE)
SumNByClass(community, class, na.rm=FALSE)
SumBiomassByClass(community, class, na.rm=FALSE)

Value

A vector or list of values, named by unique values of class.

Arguments

community

an object of class Community.

property

the property to which fn is applied.

class

the property over which fn is applied. Defaults to 'category' if the community has a node property with that name.

fn

a function.

na.rm

logical - if TRUE then NA values are removed.

...

Other parameters to fn.

Author

Lawrence Hudson

Details

ApplyByClass applies fn to property by class. property and class should both be names that meet the criteria of the properties argument of NPS.

SumMByClass, SumNByClass and SumBiomassByClass are convenient wrapper around ApplyByClass.

See Also

Community, NPS

Examples

data(TL84)

# Sum body mass by category
ApplyByClass(TL84, 'M', 'category', sum)

# A more convenient way to sum body mass by category
SumMByClass(TL84)

# Sum body mass by kingdom. The 'Unclassified flagellates' node does not have a 
# kingdom, so we get a value labelled ''.
SumMByClass(TL84, 'kingdom')

# Maximum body mass by category
ApplyByClass(TL84, 'M', 'category', max)

# A list of min and max M
ApplyByClass(TL84, 'M', 'category', range)

# A list of min and max M by kingom
ApplyByClass(TL84, 'M', 'kingdom', range)

# The same values as a matrix
do.call('rbind', ApplyByClass(TL84, 'M', 'kingdom', range))

# Broadstone Stream has some nodes in every category without M so all returned 
# values are NA.
data(BroadstoneStream)
SumMByClass(BroadstoneStream)

# Get rid of the NA values
SumMByClass(BroadstoneStream, na.rm=TRUE)