asvoccur

R tools for ASV occurrence data in SBDI.

Overview

The asvoccur R package, currently under development, provides tools for unpacking and processing ASV occurrence data and metadata downloaded from the Swedish ASV portal. It enables users to convert condensed DwC archives into ASV table format for easier downstream analysis in R, by using functions that load, merge, and aggregate ASV counts across taxonomic ranks.

Install

install.packages('devtools')
library(devtools)
install_github("biodiversitydata-se/asvoccur")
# or:
# install_github("biodiversitydata-se/asvoccur@develop")
library(asvoccur)

Run

data_path <- '/path-to/dataset-folder'
loaded <- load_data(data_path)
merged <- merge_data(loaded)
summed <- sum_by_clade(merged$counts, merged$asvs)
summed_df <- convert_to_df(summed)

Get help

?asvoccur::load_data
?asvoccur::merge_data
?asvoccur::sum_by_clade
?asvoccur::convert_to_df