Temperature effects on optimality-based phytoplankton growth model

Overview This repository contains R scripts for analyzing and visualizing outputs from an optimality-based phytoplankton growth model under different temperature and nutrient regimes to describe the importance of temperature dependence of physiological parameters. The workflow focuses on comparing multiple model configurations (species-specific temperature dependent - SS, non-species-specific temperature dependent - nSS, and species-specific non-temperature dependent - noTemp) against observational datasets (data.rds; Moorthi et al., 2016) and their visualization. The primary outputs include: * Time series comparisons (model vs observations)* Biomass and stoichiometric ratios (C:N, C:P)* Model envelopes (uncertainty/range visualization)* Error estimatation (J) and comparison among model configurations Core Scripts cmo_dyn.R:Core model definitions, Differential equations / biological processes,Parameter definitions,Utility functions used across scripts Phytoplankton_Model.R:Main execution script,Runs simulations,Post-processes outputs (derived variables)Computes statistics (means, cost function J, Wilcoxon signed-rank test)Compares model output with observational data plot_AS.R: Functions for plotting model outputs and comparisons Optimization.RImplements CMA-ES algorithm for parameter estimationCalls model repeatedly with different parameter setsMinimizes cost function J (defined in cmo_dyn.R) Parameters_coef.RUses optimized parametersFits/derives temperature-dependent coefficientsLikely applies regression or curve fitting SA_notemp.RQuantifies how ±10% perturbations in parameters affect model performanceIdentifies the most influential physiological parameters Dependencies The following R packages are required: library(ggplot2)library(viridis)library(cowplot)library(ggpubr)library(plyr)library(patchwork)library(dplyr)library(tidyr)library(units)require(deSolve)library(parallel)library(doParallel)library(foreach) Model Configurations The analysis compares three model variants: * SS — species-specific temperature dependent model* nSS — non-species-specific temperature dependent model* noTemp — species-specific model without temperature dependence Contact / Usage This code is intended for scientific analysis of phytoplankton–nutrient dynamics.Adaptation may be required for different datasets or model structures.For any question, please contact: [e-mail] ---