ArticleAoB PLANTS2021
Principles of resilient coding for plant ecophysiologists.
Article in AoB PLANTS, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Parameterizing steady-state C3 photosynthesis models using photosynthesis response curves: which models to use and which parameter estimates to trust?Journal of experimental botany · 2026Article
- Leaf COThe New phytologist · 2026Article
- Developing carbon assimilation methods in duckweed for insights into photosynthesis and growth mechanisms.Plant physiology · 2026Article
- Co-occurring congeners coordinate drought and shade tolerance traits along gradients of canopy openness.Oecologia · 2026Article
- pam: An R Package for Fast and Efficient Processing of Pulse-Amplitude Modulation Data.Ecology and evolution · 2026Article
- Fern Gametophytes Exhibit Distinct Patterns of Niche Expansion and Convergence in Ecophysiological Functioning.Ecology and evolution · 2026Article
- Decoupled Climatic Drivers of Tree and Ground-Layer Carbon Uptake in Mountain Ecosystems Around the World.Global change biology · 2026Article
- PhotoGEA: An R Package for Closer Fitting of Photosynthetic Gas Exchange Data With Non-Gaussian Confidence Interval Estimation.Plant, cell & environment · 2025Article
- Limit and enhancing potential of canopy photosynthesis for greenhouse tomato: a model analysis in different climatic environments.Plant phenomics (Washington, D.C.) · 2025Article
- PhoTorch: a robust and generalized biochemical photosynthesis model fitting package based on PyTorch.Photosynthesis research · 2025Article
- GasanalyzeR: advancing reproducible research using a new R package for photosynthesis data workflows.AoB PLANTS · 2024Article
- Stomatal behaviour and water relations in ferns and lycophytes across habits and habitats.AoB PLANTS · 2024Article
- Plant physiological indicators for optimizing conservation outcomes.Conservation physiology · 2023Article
- Field-grown ictB tobacco transformants show no difference in photosynthetic efficiency for biomass relative to the wild type.Journal of experimental botany · 2022Article
- Flexible drought deciduousness in a neotropical understory herb.American journal of botany · 2022Article
- Activation of COFrontiers in plant science · 2022Article
- Principles of resilient coding for plant ecophysiologists.AoB PLANTS · 2021Article
- Wheat Functional Traits and Photosynthetic Responses to Dynamic Shading in Agrivoltaic Systems.Physiologia plantarumArticle
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Plant ecophysiology is founded on a rich body of physical and chemical theory, but it is challenging to connect theory with data in unambiguous, analytically rigorous and reproducible ways. Custom scripts written in computer programming languages (coding) enable plant ecophysiologists to model plant processes and fit models to data reproducibly using advanced statistical techniques. Since many ecophysiologists lack formal programming education, we have yet to adopt a unified set of coding principles and standards that could make coding easier to learn, use and modify. We identify eight principles to help in plant ecophysiologists without much programming experience to write resilient code: (i) standardized nomenclature, (ii) consistency in style, (iii) increased modularity/extensibility for easier editing and understanding, (iv) code scalability for application to large data sets, (v) documented contingencies for code maintenance, (vi) documentation to facilitate user understanding; (vii) extensive tutorials and (viii) unit testing and benchmarking. We illustrate these principles using a new R package, {photosynthesis}, which provides a set of analytical and simulation tools for plant ecophysiology. Our goal with these principles is to advance scientific discovery in plant ecophysiology by making it easier to use code for simulation and data analysis, reproduce results and rapidly incorporate new biological understanding and analytical tools.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.