TaxCI-package: Tools for checking the integrity of DNA-barcode data

In eberlejonas/TaxCI: Calculate the Consistency Index and the Retention Index for taxonomic data

Description

The package contains tools for checking the quality of barcoding data prior to submission. It is intended for highlighting for instance contaminations or misidentifications in very large trees in two steps:
1. By reconstructing the Consistency Index (Kluge and Farris 1969) along phylogenetic trees. (Usable with taxonomic data on different levels.)
2. By evaluating individual composition of barcoding-clusters. (On species level.)

Details

Package:	TaxCI
Type:	Package
Version:	0.5-0
Date:	2018-11-22
License:	GPL-3

Main function: tci, BCCluster

Author(s)

Jonas Eberle [e-mail]

References

Kluge, A.G, Farris, J.S. (1969). Quantitative phyletics and the evolution of anurans. Syst. Zool. 18: 1-32.

Examples

library(TaxCI)

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# load some data
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data(Carabidae)
head(Carabidae$metadata)


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# analyses
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# taxonomic consistency analysis
ci <- tci(Carabidae$tree, Carabidae$metadata, level="binomial")

# cluster analysis
cl <- BCCluster(Carabidae$alignment, Carabidae$metadata, sp.col="binomial")

# prepare data for plotting
p1 <- plotParamTCI(Carabidae$tree, Carabidae$metadata, ci)
p2 <- plotParamBCC(Carabidae$tree, Carabidae$metadata, cl, p1)


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# multipageplot to pdf
# use oma for page bleed margin [inch]
# and mai for controlling overlap of pages [inch]
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npages <- ceiling(length(Carabidae$tree$tip.label) / 130)
pdf("Carabidae.pdf", width=8.3, height=11.7, pointsize=3.5)
par(oma=c(1,1,1,3)+5, mai=c(0,0,0,0)+.03, xaxs="i", yaxs="i", xpd=TRUE)
TaxCIplot(Carabidae$tree, Carabidae$metadata, p1, p2,
       box.placement="auto", npages=npages,
       cex=.7, lwd=.6, edge.width=.6, legend=TRUE,
       info="R-package 'TaxCI'\nExample script 'Carabidae'\npdf output")
dev.off()


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# write output table
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makeTable(p1, p2, "score", "score_table.tsv")
#

result <- TaxCIsummary(Carabidae$tree, Carabidae$metadata, sp.col="binomial", BCCluster.result=cl, plotParamTCI.result=p1, plotParamBCC.result=p2, analysis="example")

###
# you can do another set of analyses and compare the results with:
# cbind(result, result2)
###

eberlejonas/TaxCI documentation built on July 20, 2021, 9:46 a.m.