arctic-biogeographical-analysis-pipeline's Introduction

R scripts for the Analysis of Arctic Community Similarity using DNA Barcoding Data

Prerequisite Files

Please see files in the Chironomid Datasets and Arctic Shapefile folders.

For convenience, the links to the files have been provided here as well.

To run either of the biogeography analysis pipelines with the Chironomid datasets, please ensure you have the following files in your current working R directory:

Public BOLD data from October/2017 download:

Greenland

dfNearctic_Oct17.csv (Nearctic must be unzipped first with 7zip software)

Palearctic

Alternatively current BOLD data can be used via a direct download from the BOLD API by running the commands:

dfNearctic <- read_tsv("http://www.boldsystems.org/index.php/API_Public/combined?taxon=Chironomidae&geo=Alaska|Canada&format=tsv")
dfGreenland <- read_tsv("http://www.boldsystems.org/index.php/API_Public/combined?taxon=Chironomidae&geo=Greenland&format=tsv")
dfPalearctic <- read_tsv("http://www.boldsystems.org/index.php/API_Public/combinedtaxon=Chironomidae&geo=Norway|
                          Denmark|Iceland|Sweden|Finland&format=tsv")

For using the datasets provided by Torbjørn Ekrem and Elisabeth Stur (datasets are now publicly available on BOLD):

Taxonomic Data

Sequence Data

Curated Greenland Species Data

Multiple sequence alignments for single-linkage clustering with a 4, 4.5 or 5% cutoff threshold:

Full Dataset Alignment

Subarctic Filtered Alignment

To run the Subarctic Shapefile Filtered Pipeline please ensure the following shapefiles are also included in the current working R directory:

Installation

Please ensure the following packages are installed in R/RStudio:

install.packages("foreach")
install.packages("ape")
install.packages("readr")
source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")
biocLite("muscle")
biocLite("DECIPHER")
install.packages("plotly")
install.packages ("ggplot2") 
install.packages("raster")
install.packages("rgdal")
install.packages("rgeos")
install.packages("vegan")
install.packages("tidyr")
install.packages("dplyr")
install.packages("data.table")
install.packages("vegan")

Authors of Pipeline

Matthew Orton

Dr. Sally Adamowicz

Acknowledgments

Dr. Torbjørn Ekrem and Dr. Elisabeth Stur for kindly providing their Chironomid datasets.

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arctic-biogeographical-analysis-pipeline's Issues

Notes on Pipeline

Hi Sally, you will see I just added the pipeline, I still dont have filtering by shapefile but I did manage to incorporate the private data into the accumulation curve so there is a section of code for that now.

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