Data Processing for Aquatic Ecology

Facilitate the analysis of data related to aquatic ecology, specifically the establishment of carbon budget. Currently, the package allows the below analysis. (i) the calculation of greenhouse gas flux based on data obtained from trace gas analyzer using the method described in Lin et al. (2024). (ii) the calculation of Dissolved Oxygen (DO) metabolism based on data obtained from dissolved oxygen data logger using the method described in Staehr et al. (2010). Yong et al. (2024) . Staehr et al. (2010) .

Overview

aelab is an R package for aquatic ecology data analysis. It provides tools for:

1. GHG flux calculation — process raw data from LI-COR and LGR gas analyzers, calculate chamber flux, convert units, compute Minimum Detectable Flux (MDF), and aggregate to CO₂-equivalents.
2. Net ecosystem metabolism (NEM) — calculate gross primary production (GPP), ecosystem respiration (ER), and net ecosystem production (NEP) from high-frequency dissolved oxygen data.
3. Statistical analysis — descriptive statistics, outlier detection, normality testing, data transformation, one-way ANOVA (Tukey HSD), and Kruskal-Wallis (Dunn post-hoc) with compact letter display.
4. Visualization — ggplot2-based plot wrappers (point, line, box, bar) with a consistent theme and custom colour palettes.

Installation

The aelab package can be installed from:

1. GitHub (development version):

# install.packages("devtools")
devtools::install_github("Zhao-Jun-Yong/aelab")

1. CRAN (stable version):

install.packages("aelab")

Features

For a full walkthrough with worked examples and code output, see the package vignette:

vignette("aelab")