wfinsinger / rrarefy.record

R function that resamples randomly and without replacement counts, and calculates rarefied richness (N0), diversity (N1, N2) and evenness (N2/N0) (after Hill (1973) and Birks et al. (2016))

This R function resamples randomly and without replacement counts (for instance pollen counts), and calculates rarefied richness (N0), diversity (N1, N2) and evenness (N2/N0) (after Hill (1973) and Birks et al. (2016)).

For additional details, please refer to Finsinger et al. (2017), or contact me directly.

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The R function requires a data.frame and input parameters:

One data.frame formatted as:

• Column 1: sample depths
• Column 2: sample ages
• Columns 3-n: counts for n taxa

Input parameters:

• counts.file = name of the data.frame.
• site.name = site name
• zones = zone boundaries. By default zones=NULL
• n.random = number of samples taken randomly and without replacement. By default n.random=1000

To run the analysis simply:

Load the R script into the R Environment:

source("rrarefy.record.r")

Load the data file into the R Environment:

my.data <- read.csv("my_data.csv")

Run the rrarefy.record analysis:

my.data.rar <- rrarefy.record(my_data, site.name="My Site")

Output:

The function creates an output to the Environment.

An output figure can be plotted using the dedicated plotting function:

plot(my.data.rar)

Dependencies

The function uses the rrarefy() function from the 'vegan' package (Oksanen et al. 2016) to draw random samples without replacement.

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References:

Birks, H.J.B., Felde, V.A., Bjune, A.E., Grytnes, J.-A., Seppä, H., Giesecke, T., 2016. Does pollen-assemblage richness reflect floristic richness? A review of recent developments and future challenges. Review of Palaeobotany and Palynology 228, 1–25. http://dx.doi.org/10.1016/j.revpalbo.2015.12.011

Finsinger, W., Morales-Molino, C., Gałka, M., Valsecchi, V., Bojovic, S., Tinner, W., 2017. Holocene vegetation and fire dynamics at Crveni Potok, a small mire in the Dinaric Alps (Tara National Park, Serbia). Quaternary Science Reviews 167, 63–77. http://dx.doi.org/10.1016/j.quascirev.2017.04.032

Hill, M.O., 1973. Diversity and Evenness: A Unifying Notation and Its Consequences. Ecology 54, 427–432. http://onlinelibrary.wiley.com/doi/10.2307/1934352/abstract

Oksanen, J., Blanchet, G.B., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., Minchin, P.R., O’Hara, R.B., Simpson, G.L., Solymos, P., Stevens, M.H.H., Szoecs, E., Wagner, H., 2017. vegan: Community Ecology Package. R package version 2.4-1. https://CRAN.R-project.org/package=vegan