asvoccur

R tools for ASV occurrence data in SBDI.

News

• March 2025: Switched counts table to sparse matrices to handle large datasets from the Insect Biome Atlas project, as previous implementation using data.table caused RAM exhaustion. Sparse matrices are currently applied only to counts, but further use for other objects (asvs, events, emof) may follow. This change is available in the develop branch.

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)

GitHub installations (local builds) may occasionally fail. If so:

remove.packages("asvoccur")
# restart R / RStudio
install_github("biodiversitydata-se/asvoccur@develop", force = TRUE)

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