phenop: Multidimensional Analysis of Phenotypic Plasticity

Overview

phenop is an R package providing novel methods for analyzing phenotypic plasticity across multiple traits and environmental variables, with special focus on insect-fungus host-pathogen systems. It implements original multidimensional plasticity indices and interaction analyses not available in other packages.

The package bridges the gap between ecological, evolutionary, and phenotypic studies by offering comprehensive tools for plasticity analysis in eco-evolutionary contexts.

Key Features

Multidimensional Plasticity Indices - Novel metrics for assessing plasticity across multiple traits

Host-Pathogen Interaction Analysis - Specialized methods for insect-fungus systems

Environmental Optimization - Find optimal conditions considering multiple traits

Reaction Norm Visualization - Advanced plotting for genotype-environment interactions

Meta-Analysis Tools - Comprehensive analysis of plasticity studies

Trade-off Analysis - Quantify trade-offs between plasticities of different traits

Data Simulation - Generate realistic data for plasticity studies

Installation From GitHub (Development Version)

Install devtools if not already installed

if (!require("devtools")) install.packages("devtools")

# Install phenop from GitHub

devtools::install_github("leonelstazione/phenop")

Local Installation (from source)

# Download the package source and install

devtools::install_local("path/to/phenop")

Quick Start

# Load the package

library(phenop)

# Generate simulated plasticity data

sim_data <- simulate_plasticity_data(

n_genotypes = 10,

n_environments = 5,

n_traits = 3

)

# Perform G×E ANOVA for plasticity analysis

anova_results <- anova_plasticity(

data = sim_data,

response = "trait_value",

genotype = "genotype",

environment = "environment"

)

# Visualize reaction norms

plot_reaction_norm(

data = sim_data,

trait = "trait1",

genotype = "genotype",

environment = "environment"

)

# Calculate multidimensional plasticity index

mpi_results <- multidim_plasticity(

data = sim_data,

traits = c("trait1", "trait2", "trait3"),

environment = "environment",

genotype = "genotype"

)

Main Functions

Core Analysis Functions

multidim_plasticity() - Calculate Multidimensional Plasticity Index (MPI)

safe_multidim_plasticity() - Robust version with error handling

anova_plasticity() - G×E ANOVA for phenotypic plasticity

plasticity_tradeoffs() - Identify trade-offs between plasticities

plasticity_meta_analysis() - Meta-analysis of plasticity studies

Host-Pathogen Analysis

host_pathogen_interaction() - Analyze phenotypic plasticity in host-pathogen systems

host_pathogen_interaction_extended() - Comprehensive analysis with extended features

Environmental Optimization

optimize_multidim_environment() - Find optimal environmental conditions

environmental_optimization() - General environmental optimization

Visualization

plot_multidim_plasticity() - Visualize multidimensional plasticity

plot_reaction_norm() - Create reaction norm plots

plot_multidim_plasticity_extended() - Advanced SAFE visualizations

Data Management

simulate_plasticity_data() - Generate realistic simulated data

Multiple datasets - pheno_parameters, pheno_spatial, pheno_time_series

Package Structure

phenop/

├── R/ # Source code

│ ├── analyze.R # Statistical analysis functions

│ ├── multidim_plasticity.R # Multidimensional plasticity indices

│ ├── host_pathogen_interaction.R # Host-pathogen analysis

│ ├── visualize.R # Visualization functions

│ └── ... (25+ additional files)

├── data/ # Package datasets

│ ├── pheno_parameters.rda # Phenological parameters dataset

│ ├── pheno_spatial.rda # Spatial phenology data

│ └── pheno_time_series.rda # Time series data

├── tests/ # Test suite

│ └── testthat/ # Unit tests

├── vignettes/ # Tutorials and examples

│ ├── phenop_vignette.Rmd # Main tutorial

│ └── phenop_vignette_complete.Rmd # Complete demonstration

└── man/ # Documentation

Example Analysis

Complete Workflow Example

library(phenop)

library(ggplot2)

# Load example data

data("pheno_parameters")

# Analyze plasticity across environments

plasticity_results <- multidim_plasticity(

data = pheno_parameters,

traits = c("sos", "eos", "los", "ndvi_max"),

environment = "year",

genotype = "site"

)

# Visualize results

plot_multidim_plasticity(plasticity_results)

# Perform meta-analysis of plasticity

meta_results <- plasticity_meta_analysis(

data = plasticity_results,

effect_size = "plasticity_index",

study_id = "site"

)

# Analyze trade-offs

tradeoff_results <- plasticity_tradeoffs(

data = plasticity_results,

traits = c("sos", "eos", "los")

)

Host-Pathogen System Analysis

# Analyze insect-fungus interactions

host_pathogen_results <- host_pathogen_interaction(

data = fungi_insect_data,

host_trait = "host_size",

pathogen_trait = "infection_rate",

environment = "temperature"

)

# Extended analysis with multiple traits

extended_results <- host_pathogen_interaction_extended(

data = fungi_insect_data,

host_traits = c("host_size", "immune_response"),

pathogen_traits = c("infection_rate", "sporulation"),

environmental_gradient = "temperature"

)

Datasets Included

pheno_parameters

Size: ~1000 observations, 44 variables

Description: Comprehensive dataset of phenological parameters across multiple sites and species

Variables: Includes SOS, EOS, LOS, NDVI metrics, GPP, environmental variables, soil properties

Use: General plasticity analysis, environmental correlations

pheno_spatial

Size: 150 spatial features, 24 variables

Description: Spatial dataset with geographical and ecological context

Variables: Coordinates, elevation, climate, land cover, disturbance history

Use: Spatial analysis, landscape-scale plasticity studies

pheno_time_series

Size: Time series data with 29 variables

Description: Temporal observations of phenological metrics

Variables: Daily/seasonal measurements, vegetation indices, climate data

Use: Temporal trends, seasonality analysis, time-series plasticity

fungi_insect_data

Size: Simulated dataset for host-pathogen interactions

Description: Phenotypic plasticity in fungus-insect host-pathogen systems

Variables: Host traits, pathogen traits, environmental conditions

Use: Host-pathogen coevolution, infection dynamics

Technical Details

Dependencies

Imports:

dplyr (>= 1.0.0), ggplot2 (>= 3.4.0), lme4 (>= 1.1.0),

mgcv (>= 1.8.0), viridis (>= 0.6.0), patchwork (>= 1.1.0),

ggridges (>= 0.5.0), maps (>= 3.4.0), performance (>= 0.10.0),

FactoMineR (>= 2.4.0), cluster (>= 2.1.0), MASS (>= 7.3.0),

magrittr (>= 2.0.3), plotly (>= 4.10.0), sf, tidyr, stats, methods

System Requirements

R version >= 4.0.0

100MB disk space (primarily for example datasets)

Standard R installation capabilities

Performance

Optimized for datasets with up to 10^5 observations

Parallel processing capabilities for large analyses

Memory-efficient implementations for multidimensional calculations

Documentation Vignettes

# Access built-in tutorials

vignette("phenop_vignette", package = "phenop")

vignette("phenop_vignette_complete", package = "phenop")

Help System

Access function documentation

?multidim_plasticity

?plot_reaction_norm

?pheno_parameters

# List all exported functions

ls("package:phenop")

Testing The package includes comprehensive tests covering:

Functionality verification

Input validation

Output structure checks

Edge case handling

Performance benchmarks

Run tests with:

devtools::test("phenop")

Contributing We welcome contributions! Please follow these steps:

Fork the repository on GitHub

Clone your fork locally

Create a branch for your feature (git checkout -b feature/amazing-feature)

Commit your changes (git commit -m 'Add amazing feature')

Push to the branch (git push origin feature/amazing-feature)

Open a Pull Request

Contribution Guidelines

Follow the tidyverse style guide

Add tests for new functionality

Update documentation accordingly

Ensure compatibility with existing functions

Citation

If you use phenop in your research, please cite:

@software{phenop_package,

title = {phenop: Multidimensional Analysis of Phenotypic Plasticity},

author = {Leonel Stazione},

year = {2026},

url = {https://github.com/leonelstazione/phenop},

note = {R package version 0.1.0}

}

License This package is licensed under the MIT License. See the LICENSE file for details.

Bug Reports and Issues Please report bugs, issues, or feature requests on the GitHub Issues page.

Contact Author: Leonel Stazione Email: leonelstazione@hotmail.com GitHub: leonelstazione

Acknowledgments

This package was developed as part of research on phenotypic plasticity in insect-fungus systems. Special thanks to contributors and testers.