Analysis Of Ecological Data Research Articles

Editorial: Coastal environmental and ecological data analysis

Editorial: Coastal environmental and ecological data analysis

Application of “rdacca.hp” R package in ecological data analysis: case and progress

Application of “rdacca.hp” R package in ecological data analysis: case and progress

The EAT-Lancet Commission Planetary Health Diet Compared with Institute of Health Metrics and Evaluation Global Burden of Disease Ecological Data Analysis

The EAT-Lancet Commission Planetary Health Diet Compared with Institute of Health Metrics and Evaluation Global Burden of Disease Ecological Data Analysis

Follow the Geographic Information: The Challenges of Spatial Analysis in Digital Methods

In the digital environment, defined as a space with no anchors (Menduni 2014), the spatial dimension may have a significant role, mostly in relation to the Internet or digital studies. Social Media Geographic Information (Campagna et al. 2016), even if limited, can be highly useful to overcome some limitations of social media analysis and user generated content. With the objective to report the potential and limits of this approach, in this article a case study will be presented on the individual perception related to COVID-19 in Italy. Starting from the analysis of ecological data and the social media data, we reproduce three measures by exploring three different elements that could be anchored to a geographical dimension: the storytelling of COVID (COVID-Issues), the spread of infection (COVID-Spread), and the distribution of measures (COVID-Measures) to understand the regional trends of the second wave of the pandemic emergence that represent the timespan of this contribution. Keywords: geo-social media, twitter, ecological analysis, case study, API

EcoCountHelper: an R package and analytical pipeline for the analysis of ecological count data using GLMMs, and a case study of bats in Grand Teton National Park.

Here we detail the use of an R package, 'EcoCountHelper', and an associated analytical pipeline aimed at making generalized linear mixed-effects model (GLMM)-based analysis of ecological count data more accessible. We recommend a GLMM-based analysis workflow that allows the user to (1) employ selection of distributional forms (Poisson vs negative binomial) and zero-inflation (ZIP and ZINB, respectively) using AIC and variance-mean plots, (2) examine models for goodness-of-fit using simulated residual diagnostics, (3) interpret model results via easy to understand outputs of changes in predicted responses, and (4) compare the magnitude of predictor variable effects via effects plots. Our package uses a series of easy-to-use functions that can accept both wide- and long-form multi-taxa count data without the need for programming experience. To demonstrate the utility of this approach, we use our package to model acoustic bat activity data relative to multiple landscape characteristics in a protected area (Grand Teton National Park), which is threatened by encroaching disease-white nose syndrome. Global threats to bat conservation such as disease and deforestation have prompted extensive research to better understand bat ecology. Notwithstanding these efforts, managers operating on lands crucial to the persistence of bat populations are often equipped with too little information regarding local bat activity to make informed land-management decisions. In our case study in the Tetons, we found that an increased prevalence of porous buildings increases activity levels of Eptesicus fuscus and Myotis volans; Myotis lucifugus activity decreases as distance to water increases; and Myotis volans activity increases with the amount of forested area. By using GLMMs in tandem with 'EcoCountHelper', managers without advanced programmatic or statistical expertise can assess the effects of landscape characteristics on wildlife in a statistically-robust framework.

Insight into the Burden of Malignant Respiratory Tumors and their Relationship with Smoking Rates and Lead Contamination in Mexico.

We aimed to report the results from the Global Burden of Disease Study 2019 related to respiratory malignant tumors (tracheal, bronchial, and lung) in Mexico. We also evaluated the relationship between the burden of these neoplasms and the proportion of daily smokers and total lead emissions in 2019. A cross-sectional analysis of ecological data was performed. The burden of these tumors was 152,189 disability-adjusted life-years (DALYs), and years of life lost (YLL) contributed to 99% of them. The highest DALYs rates (per 100,000) were observed in the states of Sinaloa, Chihuahua, Baja California Sur, Sonora, and Nayarit. We documented a linear relationship between the DALYs rates and the prevalence of daily smokers (β = 8.50, 95% CI 1.58-15.38) and the total lead emissions (tons/year: β = 4.04, 95% CI 0.07-8.01). If later replicated, our study would provide insight into the major relevance of regulating tobacco use and the activities associated with the production of lead dust and other hazardous contaminants.

Responses of synanthropic vegetation to composting facility

Composting facilities are habitats where biological materials are bio-oxidized. Biological waste represents a source of plant species diaspores and may promote changes in the species composition of the surrounding. The studied composting facility is situated in the Bohemian-Moravian Highlands, Czech Republic. Four sites, the composting pile and three habitats nearby were chosen of different use and disturbance conditions. Phytosociological plots were recorded in each of the habitat and the results were processed using multivariate analyses of ecological data. The information about plant species indication values was also analysed: (i) the relationship between soil disturbance and plant species occurrence, (ii) seed dormancy, (iii) seed bank, and (iv) vector of seed dispersion. During the research, 119 plant taxa were found in total. Conditions of the composting process (frequent disturbances, excessive available nutrients, enough water, and supply of new diaspores) represent a challenge for plant species. The presence of plant diaspores in the biowaste is a reason why the fundamental principle of appropriate composting process has to be adhered to. Another important task is to give attention to the methods determining the share of living diaspores in the final compost, which is still missing in practice. Compost might become a vehicle for spreading weeds. The capacity of vegetation to survive and multiply on the premises of composting facilities increases the importance of vegetation monitoring and control of the adjacent areas. The usual occurrence of rural brownfields near composting facilities increases the risk of diaspores being transmitted into biowaste or compost, thus increasing the share of undesirable viable diaspores. Composting facilities generate specific synanthropic conditions for the vegetation. Therefore, the composting facility projects should take into consideration the surrounding areas and vegetation management. It is recommended that the project should include semi-natural vegetation, which can create efficient barriers to the spreading of undesirable ruderal plant species. The novelty of this study is the confirmation that composting facilities and compost become a new factor affecting vegetation, which has been disregarded so far. The link between composting facilities and vegetation has to be included in the legislation related to parameters of compost quality. Moreover, the issue of weeds, their reproductive organs and their spread should be considered in the guidelines for the design, location, construction, and operation of composting facilities.

Analysis of presence-only data via exact Bayes, with model and effects identification

This paper provides an exact modeling approach for the analysis of presence-only ecological data. Our proposal is also based on frequently used inhomogeneous Poisson processes but does not rely on model approximations, unlike other approaches. Exactness is achieved via a data augmentation scheme. One of the augmented processes can be interpreted as the unobserved occurrences of the relevant species, and its posterior distribution can be used to make predictions of the species over the region of study beyond the observer bias. The data augmentation also leads to a natural Gibbs sampler to make Bayesian inference through MCMC. The proposal shows better performance than the currently standard method based on Poisson process with intensity function depending log-linearly on the covariates. Additionally, an identification problem that arises in the traditional model does not seem to affect our proposal in the analyses of real ecological data.

A Taxonomic Revision of the Amazonian Genus Dicorynia (Fabaceae: Dialioideae)

Dicorynia stands out among the 17 genera of the diverse legume subfamily Dialioideae as an example of extreme floral reduction and specialization. It has asymmetric flowers presenting a heteromorphic calyx, trimerous corolla, and pair of highly dimorphic stamens, with one or both anthers polysporangiate. The two species of Dicorynia are Amazonian trees, one of which is highly valued for its timber. Despite the economic importance of the genus and an abundance of new collections, no comprehensive taxonomic study of Dicorynia has been completed since the publication of Koeppen’s monograph almost six decades ago, in which two species were recognized, one of which divided into six varieties. The present work employs integrative analysis of geographical, ecological, and extensive specimen-based morphological data to test previous delimitations of species and varieties. A new classification is adopted in an updated and comprehensive taxonomic revision of Dicorynia. We maintain two morphologically distinct and geographically separated species, D. guianensis and D. paraensis. The former is restricted to portions of the Guiana Shield north of the Amazon basin. At the same time, the latter is broadly distributed in the Amazon basin, but mainly north of the Amazon River. We recognize several taxonomically significant entities within the latter species, which, because they display limited morphological overlap and substantial geographical sympatry, we treat as varieties. However, we reduce the number of varieties from six to four. The taxonomic treatment contains new descriptions and illustrations, distribution maps, including two new areas of occurrence, conservation status assessments for all treated taxa, and identification keys to distinguish them. Nomenclatural, biogeographical, and ecological comments, including two new lectotypifications, are provided.

Malaria epidemics detection and associated climatic factors in the Hauts Bassins Health Region of Burkina Faso

Background: Malaria is endemic in the Hauts Bassins Health Region, making it necessary to detect epidemics. Though malaria is a climatic sensitive disease, the association between malaria occurrence and climate is not well known in the Hauts Bassins Health Region. The study sought to detect malaria epidemics and assess the correlation of malaria cases with climate. Methods: A secondary analysis of ecological data from the National Health Information System (NHIS) and the General Directorate of Meteorology of Burkina Faso was conducted. Mean, quartiles and cumulative sum methods were performed to set epidemic thresholds. Correlation between malaria and climatic factors in the health region was assessed using Spearman's test. A Mann-Whitney test determined the association of malaria transmission seasons with climatic variables, at 5%. Kruskal-Wallis test evaluated the relationship between malaria and the years of the occurrence, at a 5% significance level. Results: From 2013 to 2016, 2,521,789 malaria cases were reported in the region, with a mean incidence of 269 cases per 10,000 people. The annual incidence increased from 2,048 cases per 10,000 people in 2013 to 5,277 cases per 10,000 people in 2016. Regardless of the method used, cases were high in 2016, with few exceptions. There was a weak negative correlation between malaria and minimum (r=-0,292; p-value=0.044) and maximum (r=-0,391; p-value=0.006) temperatures. The relationship between relative humidity and malaria was positive and weak (r=0,304; p-value=0.036). Lowest temperatures and highest relative humidity simultaneously drove malaria within-year variability during the high transmission season. Conclusion: Malaria incidence increased unexpectedly in 2016. Malaria endemicity hides a within-year and year-to-year variability, partially driven by the temperature, relative humidity and rainfall.

Coefficients of association between nominal and fully ranked ordinal variables with applications to ecological network analysis

A central issue of ecological data analysis is the pairwise comparison of variables describing biological entities and the environment. Difficulties arise with calculations if the measurement scales of the variables differ. In particular, no method is available for measuring the association between a nominal and a fully ranked ordinal variable. Here two coefficients are suggested by reducing this problem to the evaluation of pattern in string representations. The first one is a topological measure that counts the number of other types of elements occurring between pairs of elements of a given state along the entire length of the string, thus providing a global coefficient of aggregation/segregation. The second coefficient is based on counting the number of different elements within substrings generated from the complete string with the moving window technique. Thus, it is a local measure. There is no compact and general formula for calculating these measures, and heuristics are involved for finding the possible minimum and maximum values by algorithmic approximation and Markov Chain Monte Carlo simulation. An R function is provided for computations. The methods are applied to the comparison of nominal variables (biological traits) categorizing marine food web nodes with fully ranked variables describing major graph theory properties of the same nodes in the network. The most descriptive traits (mobility, major functional group) significantly associated with network metrics (weighted indices) were identified from a variety of combinations across three marine ecosystems. These coefficients thus provide an objective, statistically-sound method for identifying ecologically meaningful traits.

Unlocking the potential of deep learning for marine ecology: overview, applications, and outlook

AbstractThe deep learning (DL) revolution is touching all scientific disciplines and corners of our lives as a means of harnessing the power of big data. Marine ecology is no exception. New methods provide analysis of data from sensors, cameras, and acoustic recorders, even in real time, in ways that are reproducible and rapid. Off-the-shelf algorithms find, count, and classify species from digital images or video and detect cryptic patterns in noisy data. These endeavours require collaboration across ecological and data science disciplines, which can be challenging to initiate. To promote the use of DL towards ecosystem-based management of the sea, this paper aims to bridge the gap between marine ecologists and computer scientists. We provide insight into popular DL approaches for ecological data analysis, focusing on supervised learning techniques with deep neural networks, and illustrate challenges and opportunities through established and emerging applications of DL to marine ecology. We present case studies on plankton, fish, marine mammals, pollution, and nutrient cycling that involve object detection, classification, tracking, and segmentation of visualized data. We conclude with a broad outlook of the field’s opportunities and challenges, including potential technological advances and issues with managing complex data sets.

Naltrexone moderates the association of alcohol use and affect among adolescent drinkers in daily life.

Naltrexone is an efficacious medication for the treatment of alcohol use disorder in adults. As an opioid receptor antagonist, naltrexone blocks activation of the endogenous opioid system, which is involved in the affectively reinforcing properties of substance use. Few studies, however, have examined the moderating effect of naltrexone on the association between affect and alcohol use. Additionally, most existing research on naltrexone has been with adults in the human laboratory. We conducted a secondary analysis of ecological momentary assessment data from a randomized, double-blinded, placebo-controlled cross-over study that compared naltrexone (50mg/daily) and placebo in 26 adolescents (15 to 19years old) who exhibited problematic drinking patterns. Multilevel models tested whether naltrexone moderated associations of alcohol use with both positive and negative affect (PA, NA). Results indicated that, during naltrexone treatment, greater estimated blood alcohol concentration (eBAC) levels were associated with greater NA further into drinking episodes. In turn, greater NA after the first drink of an episode was associated with reduced subsequent eBAC values during naltrexone treatment. Low PA was also associated with lower subsequent eBAC levels in the naltrexone condition after the first drink. These findings support the idea that naltrexone can disrupt the association between affect and alcohol use, effects that emerge later in drinking episodes. Greater attention to the effects of naltrexone on affect and reinforcement may help to tailor psychotherapy to maximize the benefits of naltrexone. However, in the present study, as most drink reports were in the first 2h of the drinking episode and participants reported affect only at the first three end-drink reports of a drinking episode (limiting the number of drinks reported), we had reduced power to detect effects in the continuation phase. Thus, replication of the findings is needed using a design that assesses the impact of naltrexone across the entire episode.

The EAT-Lancet Commission Planetary Health Diet Compared with Institute of Health Metrics and Evaluation Global Burden of Disease Ecological Dietary Data Analysis—Gbd Dietary Risk Factors Correlated with Noncommunicable Disease Early Deaths

The EAT-Lancet Commission Planetary Health Diet Compared with Institute of Health Metrics and Evaluation Global Burden of Disease Ecological Dietary Data Analysis—Gbd Dietary Risk Factors Correlated with Noncommunicable Disease Early Deaths

Global Burden of Disease Ecological Data Analysis of Noncommunicable Disease Early Deaths in the World's Highest Animal Food Consuming 1 Billion People to Derive a Multiple Regression Risk Factor Formula with Coefficients Equated to Population Attributable Risk Percents

Global Burden of Disease Ecological Data Analysis of Noncommunicable Disease Early Deaths in the World's Highest Animal Food Consuming 1 Billion People to Derive a Multiple Regression Risk Factor Formula with Coefficients Equated to Population Attributable Risk Percents

Global Burden of Disease Ecological Data Analysis of Noncommunicable Disease Early Deaths in the World's Highest Animal Food Consuming 1 Billion People to Derive a Multiple Regression Risk Factor Formula with Coefficients Equated to Population Attributable Risk Percents

Global Burden of Disease Ecological Data Analysis of Noncommunicable Disease Early Deaths in the World's Highest Animal Food Consuming 1 Billion People to Derive a Multiple Regression Risk Factor Formula with Coefficients Equated to Population Attributable Risk Percents

Effect of the FDA Black Box Suicidality Warnings for Antidepressants on Suicide Rates in the USA.

Background: Some authors claimed that the US Food and Drug Administration (FDA) black box warning on treatment-emergent suicidality with antidepressants in adolescents (issued 2004) and young adults (issued 2006) led to an increase of suicides, based on the analyses of ecological data with debatable assumptions about putative changes in suicide rates. Aims: To explore if putative changes in suicide rates in adolescents and young adults at the time of the FDA warnings is a detectable signal in the data or compatible with random fluctuations. Method: We applied different changepoint analyses for adolescent and young adult suicide rates from 1981 to 2019 in the USA. Results: Changepoint analysis did not support a detrimental effect of the FDA black box warnings. The downward trend of suicides reversed several years after the warning in adolescents (2007-2009) and many years before in young adults (1999-2001). Limitations: Our analyses cannot rule out detrimental effects of the FDA warnings. However, even if there was such an effect, it was likely small and indistinguishable from random fluctuations in the available suicide data. Conclusion: There is no detectable change of trend in adolescent or young adult suicide rates in line with a detrimental effect of the FDA black box warnings on treatment-emergent suicidality.

Understanding contexts of smoking and vaping among dual users: analysis of ecological momentary assessment data.

To understand dual users' cigarette and e-cigarette use patterns, including the contexts in which they vape versus smoke and to understand how environmental and internal contexts and smoking patterns differ between dual users and exclusive smokers. Longitudinal observational trial. Research center in Wisconsin, USA. Adult dual users (n = 162) and adults who exclusively smoked (n = 143), with no plans to quit smoking or vaping in the next 30 days. Participants carried smartphones for 2 weeks at baseline to record each use event for the two products and report on the context of their product use. The percentage of mornings where participants vaped first versus smoked were used to compute e-cigarette dependence. Hierarchical linear regression models with random slopes and intercepts examined the within- and between-subject effects of context on the likelihood of vaping (versus smoking); significant fixed effects were tested for moderation by e-cigarette dependence. Dual users reported significantly more puffs/cigarette [mean = 13.1, standard deviation (SD) = 10.2] than puffs/vape event (mean = 11.7, SD = 11.5; P = 0.01). E-cigarette dependence moderated the influence of social cues (t-ratio = 2.4, P = 0.02) and smoking restrictions (t-ratio = 3.1, P = 0.003) on the likelihood of vaping versus smoking [odds ratio (OR) = 2.30, P = 0.02]. Context was more related to which product was used in those of low versus higher e-cigarette dependence. Reports of strong cravings to smoke and positive expectancies for cigarettes were associated with a reduced likelihood of vaping, whereas strong cravings to vape and positive vaping expectancies were related to increased likelihood of vaping. Among dual users of cigarettes and e-cigarettes with no motivation to quit, vaping appears to be related to internal cues and more highly linked with social contexts and smoking restrictions (i.e. under stronger external stimulus control) among those with low to moderate e-cigarette dependence compared with high e-cigarette dependence. These findings illustrate the importance of contextual factors in tobacco product use among dual users with the influence of context being reduced at high levels of e-cigarette dependence.

Spatial and spatio-temporal distribution of women living with HIV mortality in Porto Alegre, Brazil, from 2007 to 2017.

ABSTRACTOBJETIVE:To present some factors related to the mortality rates of WLHIV in the city of Porto Alegre-RS.METHODS:This is a spatial and spatio-temporal analysis of ecological data about all women monitored by the health care services for the vertical transmission (VT) of HIV, between 2007 and 2017, residing in the city that died during the period. The units of analysis were the 17 sanitary districts of the city. The dependent variable was the mortality rate. The independent territorial variables were the indicators of vulnerability to poverty, women householder proportion, lack of infrastructure, HDI, and GINI index. Still, the individual data collected were: age, race/color, level of education, and period since the HIV diagnosis. The analyses used SPSS 20.0, and QGIS 218.15.RESULTS:Regions with higher vulnerability to poverty and precarious local infrastructure registered higher WLHIV mortality rates, especially black/”pardo” women in fertile age with low education. The regions with most women householders presented a risk of mortality seven times higher. The population with vulnerability to poverty presented the same result.CONCLUSIONS:Regions with critical indicators of vulnerability presented higher mortality rates of WLHIV, which demonstrates social inequalities’ impact for these women.

The improvement of molluscs population: as a parameter of success of local scale mangrove conservation on the south coast of Lombok

Mangroves are known by local people as mangrove plants that contribute to the sustainability of the diversity of marine biota species, such as molluscs. At the study site, mangrove conservation activities have been carried out by the community and are thought to influence the development of molluscs populations significantly. The study aims to assess the results of local-scale mangrove conservation with the development of molluscs populations. The research method uses observation methods with transect methods for ecological data. Ecological data analysis uses the index of evenness, richness, and diversity. The analysis found 27 species of molluscs consisting of 21 species of gastropods and 6 species of bivalves. The highest evenness and diversity was found at 2.4 in Gerupuk, while the highest wealth index was 16.8 in Poton Bakau. Furthermore, the molluscs species found consists of two classes, namely bivalves and gastropods. The main factor in determining species richness, is more determined by the condition of the substrate. In this case, the presence of mangroves is very important in creating the substrate conditions needed by the diversity of mollusc species. Therefore, mangrove conservation is very important for the protection and preservation and diversity of molluscs species. Information on the ecological potential of mangroves on fauna diversity, especially molluscs, can be a major source of ecosystem-based marine resource management, such as at the study site.