README.md

In IGNEX/IgnexCompare:

IgnexCompare

Tools to compare pollen sequences (work in progress)

SEQUENCE SLOTTING

```R

Installing and loading a required package

install.packages("devtools") library(devtools)

Installing and loading the package IgnexTaxonomy

install_github("IGNEX/IgnexCompare") library(IgnexCompare)

Recreating example of the book "Numerical methods in Quaternary pollen analysis" (Birks and Gordon, 1985)

seqB=SequenceB[c(7,16,25,29,32,36,39), ] seqA=SequenceA[c(6,11,22,24,29,31,38,39,43,45), ]

PREPARING INPUT DATA

sequences=PrepareSequences(sequence.A=seqA, sequence.B=seqB, sequence.A.name="Abernethy Forest 1970" , sequence.B.name="Abernethy Forest 1974", if.empty.cases="zero", transformation="proportion") names(sequences) sequences$metadata sequences$sequence.A sequences$sequence.B

computing distance matrix

sequences=DistanceMatrix(sequences=sequences, method="manhattan") sequences$distance.matrix

WITH NO DIAGONALS

COMPUTING SLOTTING AND p-value THROUGH DISTANCE MATRIX RANDOMIZATION

sequences.nodiagonal=SequenceSlotting(sequences=sequences, compute.p.value=TRUE, method="manhattan", diagonal=FALSE) sequences.nodiagonal$psi sequences.nodiagonal$p.value

plotting the distance matrix and the best alignment among sequences

PlotSequenceSlotting(sequences.nodiagonal)

WITH DIAGONALS

COMPUTING SLOTTING AND p-value THROUGH DISTANCE MATRIX RANDOMIZATION

sequences.diagonal=SequenceSlotting(sequences=sequences, compute.p.value=TRUE, method="manhattan", diagonal=TRUE) sequences.diagonal$psi sequences.diagonal$p.value

plotting the distance matrix and the best alignment among sequences

PlotSequenceSlotting(sequences.diagonal)

IGNEX/IgnexCompare documentation built on May 8, 2019, 10:53 a.m.