scholarly journals Changes in the analysis of temporal community dynamics data: a 29-year literature review

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11250 ◽  
Author(s):  
Hannah L. Buckley ◽  
Nicola J. Day ◽  
Gavin Lear ◽  
Bradley S. Case
Keyword(s):  
Time Series ◽  
Experimental Design ◽  
Best Practice ◽  
Community Dynamics ◽  
Temporal Dynamics ◽  
Habitat Type ◽  
Community Analysis ◽  
Median Number ◽  
Biological Communities ◽  
Short Time

Background Understanding how biological communities change over time is of increasing importance as Earth moves into the Anthropocene. A wide variety of methods are used for multivariate community analysis and are variously applied to research that aims to characterise temporal dynamics in community composition. Understanding these methods and how they are applied is useful for determining best practice in community ecology. Methodology We reviewed the ecological literature from 1990 to 2018 that used multivariate methods to address questions of temporal community dynamics. For each paper that fulfilled our search criteria, we recorded the types of multivariate analysis used to characterise temporal community dynamics in addition to the research aim, habitat type, location, taxon and the experimental design. Results Most studies had relatively few temporal replicates; the median number was seven time points. Nearly 70% of studies applied more than one analysis method; descriptive methods such as bar graphs and ordination were the most commonly applied methods. Surprisingly, the types of analyses used were only related to the number of temporal replicates, but not to research aim or any other aspects of experimental design such as taxon, or habitat or year of study. Conclusions This review reveals that most studies interested in understanding community dynamics use relatively short time series meaning that several, more sophisticated, temporal analyses are not widely applicable. However, newer methods using multivariate dissimilarities are growing in popularity and many can be applied to time series of any length.

scholarly journals Measuring change in biological communities: multivariate analysis approaches for temporal datasets with low sample size

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11096
Author(s):  
Hannah L. Buckley ◽  
Nicola J. Day ◽  
Bradley S. Case ◽  
Gavin Lear
Keyword(s):  
Time Series ◽  
Sample Size ◽  
Statistical Power ◽  
Structural Changes ◽  
Linear Models ◽  
Environmental Changes ◽  
Short Time Series ◽  
Biological Communities ◽  
Extinction Events ◽  
Short Time

Effective and robust ways to describe, quantify, analyse, and test for change in the structure of biological communities over time are essential if ecological research is to contribute substantively towards understanding and managing responses to ongoing environmental changes. Structural changes reflect population dynamics, changes in biomass and relative abundances of taxa, and colonisation and extinction events observed in samples collected through time. Most previous studies of temporal changes in the multivariate datasets that characterise biological communities are based on short time series that are not amenable to data-hungry methods such as multivariate generalised linear models. Here, we present a roadmap for the analysis of temporal change in short-time-series, multivariate, ecological datasets. We discuss appropriate methods and important considerations for using them such as sample size, assumptions, and statistical power. We illustrate these methods with four case-studies analysed using the R data analysis environment.

Daily Dynamics of an Ant Community in a Mountaintop Ecosystem

2020 ◽  
Vol 49 (2) ◽  
pp. 383-390 ◽  
Author(s):  
Eloá Gonçalves Calazans ◽  
Fernanda Vieira da Costa ◽  
Maykon Passos Cristiano ◽  
Danon Clemes Cardoso
Keyword(s):  
Community Dynamics ◽  
Temporal Dynamics ◽  
Abiotic Factors ◽  
Great Influence ◽  
Species Traits ◽  
Daily Temperature ◽  
Abiotic Conditions ◽  
Biological Communities ◽  
Ant Community ◽  
Soil Temperatures

Abstract Abiotic conditions have a great influence on the structure of biological communities, especially considering ectothermic organisms, such as ants. In this study, we tested whether the daily temporal dynamics of an ant community in a tropical mountainous ecosystem is driven by daily fluctuations of abiotic factors, such as temperature and humidity. We also investigated whether the strong oscillation in daily temperature leads to high heterogeneity in ant species thermal responses. We have found that air and soil temperatures positively influenced the richness and frequency of foraging ants, while air humidity caused the opposite effect. Ant activity followed daily temperature fluctuations, which resulted in subtle differences in foraging patterns featured by heat-tolerant and heat-intolerant species. Moreover, the studied ant community exhibited broad and highly overlapped thermal responses, suggesting a likely resilience under temperature oscillations. Lastly, identifying how species traits are linked to oscillations in abiotic conditions is a necessary step to predict the effects of future climatic changes on biological community dynamics and ecosystem functioning.

scholarly journals Modeling Best Practice Life Expectancy Using Gumbel Autoregressive Models

Risks ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 51
Author(s):  
Anthony Medford
Keyword(s):  
Time Series ◽  
Life Expectancy ◽  
Extreme Value Theory ◽  
Autoregressive Model ◽  
Best Practice ◽  
Gumbel Distribution ◽  
Value Theory ◽  
Model Diagnostics ◽  
Temporal Dependence ◽  
Simulation Results

Best practice life expectancy has recently been modeled using extreme value theory. In this paper we present the Gumbel autoregressive model of order one—Gumbel AR(1)—as an option for modeling best practice life expectancy. This class of model represents a neat and coherent framework for modeling time series extremes. The Gumbel distribution accounts for the extreme nature of best practice life expectancy, while the AR structure accounts for the temporal dependence in the time series. Model diagnostics and simulation results indicate that these models present a viable alternative to Gaussian AR(1) models when dealing with time series of extremes and merit further exploration.

scholarly journals Identifying bidirectional total and non-linear information flow in functional corticomuscular coupling during a dorsiflexion task: a pilot study

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Tie Liang ◽  
Qingyu Zhang ◽  
Xiaoguang Liu ◽  
Bin Dong ◽  
Xiuling Liu ◽  
...  
Keyword(s):  
Time Series ◽  
Information Flow ◽  
Gamma Band ◽  
Motor Dysfunction ◽  
Beta Band ◽  
Short Time Series ◽  
Information Interaction ◽  
Stroke Group ◽  
Short Time ◽  
Maximal Information Coefficient

Abstract Background The key challenge to constructing functional corticomuscular coupling (FCMC) is to accurately identify the direction and strength of the information flow between scalp electroencephalography (EEG) and surface electromyography (SEMG). Traditional TE and TDMI methods have difficulty in identifying the information interaction for short time series as they tend to rely on long and stable data, so we propose a time-delayed maximal information coefficient (TDMIC) method. With this method, we aim to investigate the directional specificity of bidirectional total and nonlinear information flow on FCMC, and to explore the neural mechanisms underlying motor dysfunction in stroke patients. Methods We introduced a time-delayed parameter in the maximal information coefficient to capture the direction of information interaction between two time series. We employed the linear and non-linear system model based on short data to verify the validity of our algorithm. We then used the TDMIC method to study the characteristics of total and nonlinear information flow in FCMC during a dorsiflexion task for healthy controls and stroke patients. Results The simulation results showed that the TDMIC method can better detect the direction of information interaction compared with TE and TDMI methods. For healthy controls, the beta band (14–30 Hz) had higher information flow in FCMC than the gamma band (31–45 Hz). Furthermore, the beta-band total and nonlinear information flow in the descending direction (EEG to EMG) was significantly higher than that in the ascending direction (EMG to EEG), whereas in the gamma band the ascending direction had significantly higher information flow than the descending direction. Additionally, we found that the strong bidirectional information flow mainly acted on Cz, C3, CP3, P3 and CPz. Compared to controls, both the beta-and gamma-band bidirectional total and nonlinear information flows of the stroke group were significantly weaker. There is no significant difference in the direction of beta- and gamma-band information flow in stroke group. Conclusions The proposed method could effectively identify the information interaction between short time series. According to our experiment, the beta band mainly passes downward motor control information while the gamma band features upward sensory feedback information delivery. Our observation demonstrate that the center and contralateral sensorimotor cortex play a major role in lower limb motor control. The study further demonstrates that brain damage caused by stroke disrupts the bidirectional information interaction between cortex and effector muscles in the sensorimotor system, leading to motor dysfunction.

scholarly journals Uncertainty quantification of the effects of biotic interactions on community dynamics from nonlinear time-series data

2018 ◽  
Vol 15 (147) ◽  
pp. 20180695 ◽  
Author(s):  
Simone Cenci ◽  
Serguei Saavedra
Keyword(s):  
Time Series ◽  
Community Dynamics ◽  
Time Series Data ◽  
Multivariate Time Series ◽  
Model Averaging ◽  
Biotic Interactions ◽  
Series Data ◽  
Time Intervals ◽  
Novel Approach ◽  
Data Generating Process

Biotic interactions are expected to play a major role in shaping the dynamics of ecological systems. Yet, quantifying the effects of biotic interactions has been challenging due to a lack of appropriate methods to extract accurate measurements of interaction parameters from experimental data. One of the main limitations of existing methods is that the parameters inferred from noisy, sparsely sampled, nonlinear data are seldom uniquely identifiable. That is, many different parameters can be compatible with the same dataset and can generalize to independent data equally well. Hence, it is difficult to justify conclusive assertions about the effect of biotic interactions without information about their associated uncertainty. Here, we develop an ensemble method based on model averaging to quantify the uncertainty associated with the effect of biotic interactions on community dynamics from non-equilibrium ecological time-series data. Our method is able to detect the most informative time intervals for each biotic interaction within a multivariate time series and can be easily adapted to different regression schemes. Overall, this novel approach can be used to associate a time-dependent uncertainty with the effect of biotic interactions. Moreover, because we quantify uncertainty with minimal assumptions about the data-generating process, our approach can be applied to any data for which interactions among variables strongly affect the overall dynamics of the system.

scholarly journals Extracting Features from Time Series

2018 ◽  
pp. 85-100 ◽  
Author(s):  
Christian Herff ◽  
Dean J. Krusienski
Keyword(s):  
Time Series ◽  
Feature Extraction ◽  
Clinical Data ◽  
Noise Filtering ◽  
Time Intervals ◽  
Time Points ◽  
Biomedical Systems ◽  
Patient Weight ◽  
Short Time

AbstractClinical data is often collected and processed as time series: a sequence of data indexed by successive time points. Such time series can be from sources that are sampled over short time intervals to represent continuous biophysical wave-(one word waveforms) forms such as the voltage measurements representing the electrocardiogram, to measurements that are sampled daily, weekly, yearly, etc. such as patient weight, blood triglyceride levels, etc. When analyzing clinical data or designing biomedical systems for measurements, interventions, or diagnostic aids, it is important to represent the information contained within such time series in a more compact or meaningful form (e.g., noise filtering), amenable to interpretation by a human or computer. This process is known as feature extraction. This chapter will discuss some fundamental techniques for extracting features from time series representing general forms of clinical data.

scholarly journals A reliable measure of similarity based on dependency for short time series: an application to gene expression networks

2009 ◽  
Vol 10 (1) ◽  
pp. 270 ◽  
Author(s):  
Mônica G Campiteli ◽  
Frederico M Soriani ◽  
Iran Malavazi ◽  
Osame Kinouchi ◽  
Carlos AB Pereira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Time Series ◽  
Reliable Measure ◽  
Short Time Series ◽  
Measure Of Similarity ◽  
Short Time

scholarly journals Time series analysis of trial-to-trial variability of MEG power spectrum during rest state, unattented listening and frequency-modulated tones classification

2021 ◽  
Author(s):  
Lech Kipiński ◽  
Wojciech Kordecki
Keyword(s):  
Stochastic Process ◽  
Time Series ◽  
Power Spectrum ◽  
Spectral Density ◽  
Cognitive Task ◽  
Clinical Neuroscience ◽  
Rest State ◽  
Short Time ◽  
Low Complex ◽  
Dominant Frequencies

AbstractThe nonstationarity of EEG/MEG signals is important for understanding the functioning of human brain. From the previous research we know that even very short, i.e. 250—500ms MEG signals are variance-nonstationary. The covariance of stochastic process is mathematically associated with its spectral density, therefore we investigate how the spectrum of such nonstationary signals varies in time.We analyze the data from 148-channel MEG, that represent rest state, unattented listening and frequency-modulated tones classification. We transform short-time MEG signals to the frequency domain using the FFT algorithm and for the dominant frequencies 8—12 Hz we prepare the time series representing their trial-to-trial variability. Then, we test them for level- and trend-stationarity, unit root, heteroscedasticity and gaussianity and based on their properties we propose the ARMA-modelling for their description.The analyzed time series have the weakly stationary properties independently of the functional state of brain and localization. Only their small percentage, mostly related to the cognitive task, still presents nonstationarity. The obtained mathematical models show that the spectral density of analyzed signals depends on only 2—3 previous trials.The presented method has limitations related to FFT resolution and univariate models, but it is not computationally complicated and allows to obtain a low-complex stochastic models of the EEG/MEG spectrum variability.Although the physiological short-time MEG signals are in principle nonstationary in time domain, its power spectrum at the dominant frequencies varies as weakly stationary stochastic process. Described technique has the possible applications in prediction of the EEG/MEG spectral properties in theoretical and clinical neuroscience.

Sign in / Sign up

Export Citation Format

Share Document