Related papers: A multistate dynamic site occupancy model for spat…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
The presence of one or more species at some spatial locations but not others is a central matter in ecology. This phenomenon is related to ecological pattern formation. Nonlocal interactions can be considered as one of the mechanisms…
The parameters of a discrete stationary Markov model are transition probabilities between states. Traditionally, data consist in sequences of observed states for a given number of individuals over the whole observation period. In such a…
In the companion paper of this set (Capitan and Cuesta, 2010) we have developed a full analytical treatment of the model of species assembly introduced in Capitan et al. (2009). This model is based on the construction of an assembly graph…
Failing to account for ecological processes such as dispersal and connectivity when modeling distributions can lead to biased inference about environmental drivers and reduced predictive performance. Spatial dynamic occupancy models are…
1. Temporal trends in species distributions are necessary for monitoring changes in biodiversity, which aids policymakers and conservationists in making informed decisions. Dynamic species distribution models are often fitted to ecological…
This study proposes a novel approach based on the Ising model for analyzing socio-economic emerging patterns between municipalities by investigating the observed configuration of a network of selected territorial units which are classified…
Spatiotemporal processes have the potential to be one of the most influential factors governing how fisheries targeting sedentary species respond to harvesting. Despite this, management strategy evaluation often fails to account for space…
In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on…
Advances in field techniques have lead to an increase in spatially-referenced capture-recapture data to estimate a species' population size as well as other demographic parameters and patterns of space usage. Statistical models for these…
We describe a computational framework for modeling and statistical inference on high-dimensional stochastic dynamic systems. Our primary motivation is the investigation of metapopulation dynamics arising from a collection of spatially…
Determining spatial distributions of species and communities are key objectives of ecology and conservation. Joint species distribution models use multi-species detection-nondetection data to estimate species and community distributions.…
Clustered multistate process data are commonly encountered in multicenter observational studies and clinical trials. A clinically important estimand with such data is the marginal probability of being in a particular transient state as a…
For many taxonomic groups, online biodiversity portals used by naturalists and citizen scientists constitute the primary source of distributional information. Over the last decade, site-occupancy models have been advanced as a promising…
Physically motivated stochastic dynamics are often used to sample from high-dimensional distributions. However such dynamics often get stuck in specific regions of their state space and mix very slowly to the desired stationary state. This…
Statistical multispecies models of multiarea marine ecosystems use a variety of data sources to estimate parameters using composite or weighted likelihood functions with associated weighting issues and questions on how to obtain variance…
We propose a deep generative Markov State Model (DeepGenMSM) learning framework for inference of metastable dynamical systems and prediction of trajectories. After unsupervised training on time series data, the model contains (i) a…
Many state of the art methods for the thermodynamic and kinetic characterization of large and complex biomolecular systems by simulation rely on ensemble approaches, where data from large numbers of relatively short trajectories are…
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into…
To effectively monitor biodiversity in streams and rivers, we need to quantify species distribution accurately. Occupancy models are useful for distinguishing between the non-detection of a species and its actual absence. While these models…