A causal view on compositional data

Many scientific datasets are compositional in nature. Important examples include species abundances in ecology, rock compositions in geology, topic compositions in large-scale text corpora, and sequencing count data in molecular biology. Here, we provide a causal view on compositional data in an instrumental variable setting where the composition acts as the cause. First, we crisply articulate potential pitfalls for practitioners regarding the interpretation of compositional causes from the viewpoint of interventions and warn against attributing causal meaning to common summary statistics such as diversity indices. We then advocate for and develop multivariate methods using statistical data transformations and regression techniques that take the special structure of the compositional sample space into account. In a comparative analysis on synthetic and real data we show the advantages and limitations of our proposal. We posit that our framework provides a useful starting point and guidance for valid and informative cause-effect estimation in the context of compositional data.