aquaman

The goal of aquaman R package is to calculate ecology metrics needed to assess the mixing zone area, fulfilling these specific steps:

• Assign bacteria taxa from DNA reads using dada2 package.
• Model IQI metric from assigned bacteria families.

This package is in an experimental phase. This package will provide inputs to the halia package which then calculates the area of the mixing zone.

Installation

You can install the development version of aquaman like so:

install.packages("devtools")
devtools::install_github("aquaMetrics/aquaman")

Model IQI

This example shows you how to calculate mixing zone from demo IQI input data:

library(aquaman)

Using assigned family-level bacteria taxa as predictors, calculate benthic invert IQI as an outcome.

WORK IN PROGRESS - DO NOT USE IN PRODUCTION

# Run the IQI model based on demo taxanomic data
iqi_scores <- iqi(demo_taxa)
#> Warning in iqi(demo_taxa): WORK IN PROGRESS - DO NOT USE IN PRODUCTION
head(iqi_scores, 5)
#>    site 1    site 2    site 3    site 4    site 5 
#> 0.7436820 0.6092373 0.6048445 0.7551401 0.7568501

IQI prediction model created by Tom Wilding (SAMS) based on training data from SEPA And MOWI.

Assign Taxa

WORK IN PROGRESS - DO NOT USE IN PRODUCTION

Assign bacteria families based on S-16 DNA reads. This may in time provide the input to iqi() function. Currently, a Qiime 2 command line script achieves this part of the process.

Note, you will be prompted to download a reference taxonomic file on first use. This will be stored locally.

# Provide a path to the demo data within the package:
taxa <- assign_taxa(demo_path())
# ...this could take some time...
head(taxa, 5)
#>        sample_id                 Family reads
#> 1   MHS-ARD-0-E2           Mitochondria     8
#> 2   MHS-ARD-0-E2           Mitochondria    47
#> 3   MHS-ARD-0-E2           Mitochondria   384
#> 4   MHS-ARD-0-E2        Anaerolineaceae     7
#> 5   MHS-ARD-0-E2                   <NA>    10