cladCount: cladCount

In shiggo/jezioro: Tools for Paleolimnological Analyses at the Paleoecological Environmental Assessment and Research Laboratory

Description

cladCount determines the maximum number of individuals represented in raw counts of cladoceran subfossils

Usage

cladCount(d, percCutoff=2, sampleCutoff=2, outputType="indiv")

Arguments

d	matrix or data frame containing the input data
percCutoff	(defaults to 2): minimum relative abundance (i.e. %) required for a taxon to be included in the the reduced subset ('gt' - abbreviation of 'greater than')
sampleCutoff	(defaults to 2): minimum number of samples a taxon must be present in with at least a relative abundance of percCutoff for inclusion in the reduced subset ('gt')
outputType	(defaults to 'indiv'): the format of the output, either individuals ('indiv'), relative abundance ('perc'), or the reduced subset ('gt')

Details

The input data should be in the form of a matrix or data frame with at least 3 columns:

• Column 1: taxon name

• Column 2: subfossil name

• Column 3+: count of each taxon/subfossil remain type

NOTE: Special characters in the column headings may interfere with import of the input file. The script uses string matching to identify body parts, anything other than the following list in the body part column (i.e. spelling errors) will be ignored.

• Body part (number of subfossils per individual)

• Headshield (1)

• Carapace (2)

• PA Claw (2)

• Postabdomen (1)

• Mandible (2)

• Caudal Furca (2)

• Exopodite Segment (2)

• Basal Exp Segment (2)

• Exp Segment 2 (2)

• Exp Segment 3 (2)

• Antennule (2)

• Tail Stem (1)

Value

cladCount will return one of:

• indiv: table listing the minimum number of individuals of each taxa represented in each interval

• perc: table listing the relative abundance of each taxa within each interval

• gt: relative abundances of those taxa meeting the sampleCutoff and percCutoff criteria

Author(s)

Adam Jeziorski, Andrew Labaj

References

Korhola A, Rautio M (2001) 2. Cladocera and other branchiopod crustaceans. In: Smol JP, Birks HJB, Last WM (eds.) Tracking Environmental Change Using Lake Sediments. Volume 4: Zoological Indicators. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 4-41 t' increases by 1 for each new taxa

Examples

#load example cladoceran count data
data(cladCountInput)
cladCount(cladCountInput)

#Return the values for only taxa with greater than 4 percent abundance in at least 2 samples
cladCount(cladCountInput, percCutoff=4, sampleCutoff=2)

shiggo/jezioro documentation built on Sept. 7, 2020, 7:34 p.m.