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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# aquaman
<!-- badges: start -->
[](https://github.com/aquaMetrics/aquaman/actions/workflows/R-CMD-check.yaml)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://app.codecov.io/gh/aquaMetrics/aquaman?branch=main)
<!-- badges: end -->
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:
```r
install.packages("devtools")
devtools::install_github("aquaMetrics/aquaman")
```
## Model IQI
This example shows you how to calculate mixing zone from demo IQI input data:
```{r example}
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**
```{r}
# Run the IQI model based on demo taxanomic data
iqi_scores <- iqi(demo_taxa)
head(iqi_scores, 5)
```
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.
```r
# 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
```