Future-proofing code: Principles of coding for plant ecophysiology with {photosynthesis} as a case study

SummaryPlant physiological ecology 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 most 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 outline principles and standards for coding in plant ecophysiology to develop: 1) standardized nomenclature, 2) consistency in style, 3) increased modularity/extensibility for easier editing and understanding; 4) code scalability for application to large datasets, 5) documented contingencies for code maintenance; 6) documentation to facilitate user understanding; and 7) extensive tutorials for biologists new to coding to rapidly become proficient with software.We illustrate these principles using a new R package, {photosynthesis}, designed to provide a set of analytical tools for plant ecophysiology.Our goal with these principles is to future-proof coding efforts to ensure new advances and analytical tools can be rapidly incorporated into the field, while ensuring software maintenance across scientific generations.

La fisiología ecológica de plantas en México

Research on plant physiological ecology provides tools to understand the basic functional factors determining plant abundance and distribution, and how interacting environmental resources control plant growth. This knowledge is important for the proper natural resources management. In Mexico, ecophysiology has an incipient development but some valuable contributions have been produced.

El papel del microclima en la fisiología ecológica vegetal

The development of more efficient and accurate instruments to measure the microclimatic components have allowed the researches to get environmental information of great value for research on plant physiological ecology. In this paper some examples of applications in the study of water economy and other plant processes are presented. Examples from an area of natural vegetation are given.

Plant physiological ecology and the global changes

The global changes are marked by alteration on the normal patterns of important biochemical and biophysical processes of the Earth. However, the real effects as well as the feedbacks of the global changes over vegetation are still unclear. Part of this uncertainty can be attributed to the inattention of stakeholders and scientists towards vegetation and its complex interrelations with the environment, which drive plant physiological processes in different space-time scales. Notwithstanding, some key subjects of the global changes could be better elucidated with a more plant physiological ecology approach. We discuss some issues related to this topic, going through some limitations of approaching vegetation as a static component of the biosphere as the other sub-systems of the Earth-system change. With this perspective, this review is an initial reflection towards the assessment of the role and place of vegetation structure and function in the global changes context. We reviewed the Earth-system and global changes terminology; attempted to illustrate key plant physiological ecology researches themes in the global changes context; consider approaching plants as complex systems in order to adequately quantify systems characteristics as sensibility, homeostasis, and vulnerability. Moreover, we propose insights that would allow vegetation studies and scaling procedures in the context of the Earth-system. We hope this review will assist researchers on their strategy to identify, understand and anticipate the potential effects of global changes over the most vulnerable vegetation processes from the leaf to the global levels.

The importance of evolutionary history in studies of plant physiological ecology: examples from cerrados and forests of central Brazil

Studies that compare physiology, anatomy, and ecology across species have offered some of the best insight into adaptation and evolutionary constraints in plants. As a result, the comparative approach has become increasingly used in studies of plant physiological ecology. The high species diversity of Brazilian biomes provides many excellent opportunities for comparative plant ecophysiology, and could be better exploited for understanding the evolution of plant form and function. In this paper we emphasize the importance of considering phylogenetic information for the design and analysis of comparative studies, relying on examples from comparisons of woody plants from cerrado and gallery (riparian) forests. The use of congeneric species pairs, each containing one cerrado species and one forest species of the same genus, greatly improves statistical power while assuring phylogenetic independence, an essential condition for inference in comparative studies. For example, in a study of seedlings of nine cerrado species and nine forest species, when we ignore phylogenetic relationships, it is not be possible to conclude that cerrado and forest species differ with regard to leaf area ratio (LAR), specific leaf area (SLA), or seedling height. If, however, we use the generic groupings to account for phylogenetic effects, then we find that seedlings of savanna species have lower LAR, SLA, and seedling height. Much of the phylogenetic inertia observed for these traits appears related to the fact that these traits are all strongly correlated with seed mass, which has been previously shown to be strongly conserved phylogenetically. These examples emphasize the importance of phylogenetic information in comparative studies.