rarify: Rarify

In leppott/MMI_NV: MMI calculation NV, Calculate Predicted Metrics

Description

This function allows you to generate a fixed subsample.

Usage

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: [e-mail] ; 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. [e-mail] (2016)

Value

Returns the original data frame with an additional column for count

Examples

# 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/MMI_NV documentation built on May 21, 2019, 5:10 a.m.