Related papers: Inference for changes in biodiversity

Compositional data arise in many areas of research in the natural and biomedical sciences. One prominent example is in the study of the human gut microbiome, where one can measure the relative abundance of many distinct microorganisms in a…

Multicellular systems play a key role in bioprocess and biomedical engineering. Cell ensembles encountered in these setups show phenotypic variability like size and biochemical composition. As this variability may result in undesired…

The state-of-the-art methods for estimating high-dimensional covariance matrices all shrink the eigenvalues of the sample covariance matrix towards a data-insensitive shrinkage target. The underlying shrinkage transformation is either…

Weighting procedures are used in observational causal inference to adjust for covariate imbalance within the sample. Common practice for inference is to estimate robust standard errors from a weighted regression of outcome on treatment.…

Many natural patterns, such as the distributions of blood particles in a blood sample, proteins on cell surfaces, biological populations in their habitat, galaxies in the universe, the sequence of human genes, and the fitness in…

Recently, the Shannon entropy, which was introduced originally as a measure of information amount, has been widely used as a useful index of various diversities such as biodiversity and geodiversity. In this work we have evaluated the…

Differential abundance analysis is a key component of microbiome studies. Although dozens of methods exist there is currently no consensus on the preferred methods. While the correctness of results in differential abundance analysis is an…

Diversity is a concept relevant to numerous domains of research varying from ecology, to information theory, and to economics, to cite a few. It is a notion that is steadily gaining attention in the information retrieval, network analysis,…

Ecosystems are formed by networks of species and their interactions. Traditional models of such interactions assume a constant interaction strength between a given pair of species. However, there is often significant trait variation among…

Shrunk sample covariance matrix is a factor model of a special form combining some (typically, style) risk factor(s) and principal components with a (block-)diagonal factor covariance matrix. As such, shrinkage, which essentially inherits…

Multivariate meta-analysis is gaining prominence in evidence synthesis research because it enables simultaneous synthesis of multiple correlated outcome data, and random-effects models have generally been used for addressing between-studies…

Identification of features is a critical task in microbiome studies that is complicated by the fact that microbial data are high dimensional and heterogeneous. Masked by the complexity of the data, the problem of separating signals from…

In human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This paper considers the problem of analyzing two repeated measurements of…

We derive an analytical approximation for making quantitative predictions for ecological communities as a function of the mean intensity of the inter-specific competition and the species richness. This method, with only a fraction of the…

This paper considers the problem of inference after ranking. In our setting, we are interested in any population whose rank according to some random quantity, such as an estimated treatment effect, a measure of value-added, or benefit (net…

Studies often estimate associations between an outcome and multiple variates. For example, studies of diagnostic test accuracy estimate sensitivity and specificity, and studies of predictive and prognostic factors typically estimate…

Frailty models are essential tools in survival analysis for addressing unobserved heterogeneity and random effects in the data. These models incorporate a random effect, the frailty, which is assumed to impact the hazard rate…

Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…

Global species richness is a key biodiversity metric. Despite recent efforts to estimate global species richness, the resulting estimates have been highly uncertain and often logically inconsistent. Estimates lower down either the taxonomic…

Soil microbial communities are known to be robust against perturbations such as nutrition inputs, which appears as an obstacle for the soil improvement. On the other hand, its adaptable aspect has been also reported. Here we propose simple…