rarify: Rarify

Description Usage Arguments Details Value Examples

View source: R/rarify.R

Description

This function allows you to generate a fixed subsample.

Usage

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rarify(inbug, sample.ID, abund, subsiz)

Arguments

inbug

data frame of SampleID, Count, and TaxaCode

sample.ID

data frame field with sample ID

abund

data frame field with number of individuals

subsiz

target subsample size

Details

rarify function: R function to rarify (subsample) a macroinvertebrate sample down to a fixed count; by John Van Sickle, USEPA. email: [email protected] ; Version 1.0, 06/10/05;

See rarify.help.txt for function documentation; See rarify.examples.r.txt for examples of usage; Modifications to generate reproducible subsamples. Set the seed for the random number generator to a fixed number. [email protected] (2016)

Value

Returns the original data frame with an additional column for count

Examples

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# Location of files.
path <- getwd()
setwd(path)

library("MMIcalcNV")

# read in test data
#bugnew.raw <- read.csv(file="bugsamples.csv")
bugnew.raw <- NV.bugs
head(bugnew.raw)
#aggregate samples by bug code and sample
bugnew.raw <- bugnew.raw[,c("Samp_Rep","Individuals","TaxaID_Stage")]
bugnew.raw.ag <- aggregate(Individuals~TaxaID_Stage+Samp_Rep,data=bugnew.raw,sum)
#resample to 300 counts
bugnew.300cnt <- rarify(inbug=bugnew.raw.ag, sample.ID="Samp_Rep", abund="Individuals", subsiz=300)
# remove taxa with a count of zero
bugnew.300cnt <- bugnew.300cnt[bugnew.300cnt$Count>0,]

leppott/MMIcalcNV documentation built on May 21, 2017, 12:34 p.m.