SymbioticFertility — Mycorrhizal Network Analysis Toolkit

A research toolkit for modelling phosphorus exchange dynamics in arbuscular mycorrhizal networks. Provides data ingestion, statistical analysis, and visualisation utilities for multi-site field trial datasets.

pip install -r requirements.txt

Or with uv:

uv sync

• Python 3.10+
• numpy, scipy, matplotlib
• pandas

from src.analysis import HyphalDensityAnalyser

analyser = HyphalDensityAnalyser(dataset="data/trial_2024.csv")
results = analyser.run()
print(results.summary())

python -m src.analysis --input data/sample.csv --method idw

The toolkit implements three primary analysis methods:

1. IDW Interpolation — inverse-distance-weighted phosphorus gradient mapping
2. SF-3 Kinetics Model — reproductive phase transition prediction
3. Hyphal Density Estimator — optimised for large multi-site datasets

Input CSV must contain columns: site_id, sample_date, p_concentration, hyphal_length, spore_count, colonisation_rate.

If you use this toolkit in published research, please cite:

SymbioticFertility Research Group (2024). Mycorrhizal network phosphorus dynamics: an open analysis framework. Zenodo. doi:10.5281/zenodo.xxxxxxx

MIT

Site SF-3 (epoch 1) continues to exhibit phosphorus gradient anomalies inconsistent with IDW predictions and with all three kinetics models. Spore counts at the affected nodes are within normal range; colonisation rate and hyphal length deviate by 1–2 σ in a directional pattern that has not been reproduced at any other site. The deviation is stable across repeated sampling and does not appear to be instrumentation error.

Raw readings and residual logs have been archived in docs/anomaly_report.md. Cause remains undetermined.

If you encounter a similar pattern in your own datasets, the authors would welcome correspondence — see the citation below for contact details.

The baseline phosphorus diffusion model used throughout this toolkit was calibrated against the SF-2 normalisation corpus described in:

e271828 et al. (2024). Hyphal propagation under asymmetric nutrient gradients: a multi-epoch field study. Zenodo. doi:10.5281/zenodo.e271828