Extracting, Computing and Exploring the Parameters of Statistical Models using R

Makowski D., Ben-Shachar M., Lüdecke D.

The Bayesian framework for statistics is quickly gaining in popularity among scientists, for reasons such as reliability and accuracy (particularly in noisy data and small samples), the possibility of incorporating prior knowledge into the analysis, and the intuitive interpretation of results (Andrews & Baguley, 2013; Etz & Vandekerckhove, 2016; Kruschke, 2010; Kruschke, Aguinis, & Joo, 2012; Wagenmakers et al., 2017). Adopting the Bayesian framework is more of a shift in the paradigm than a change in the methodology; all the common statistical procedures (t-tests, correlations, ANOVAs, regressions, etc.) can also be achieved within the Bayesian framework. One of the core difference is that in the frequentist view, the effects are fixed (but unknown) and data are random. On the other hand, instead of having single estimates of the “true effect”, the Bayesian inference process computes the probability of different effects given the observed data, resulting in a distribution of possible values for the parameters, called the posterior distribution. The bayestestR package provides tools to describe these posterior distributions.

Lüdecke D., Waggoner P., Makowski D.

Lakens D., Scheel A.M., Isager P.M.

Psychologists must be able to test both for the presence of an effect and for the absence of an effect. In addition to testing against zero, researchers can use the two one-sided tests (TOST) procedure to test for equivalence and reject the presence of a smallest effect size of interest (SESOI). The TOST procedure can be used to determine if an observed effect is surprisingly small, given that a true effect at least as extreme as the SESOI exists. We explain a range of approaches to determine the SESOI in psychological science and provide detailed examples of how equivalence tests should be performed and reported. Equivalence tests are an important extension of the statistical tools psychologists currently use and enable researchers to falsify predictions about the presence, and declare the absence, of meaningful effects.

Zeileis A.

Putkonen A., Jiang Y., Zeng J., Tammilehto O., Jokinen J.P., Oulasvirta A.

Zickfeld J.H., Gonzalez A.S., Mitkidis P.

Charles C., Khelidj N., Mottet L., Tu B.N., Adatte T., Bomou B., Faria M., Monbaron L., Reubi O., de Vere N., Grand S., Losapio G.

Belen S., Patt N., Kupjetz M., Ueland P.M., McCann A., Gonzenbach R., Bansi J., Zimmer P.

Yadav H., Iwachido Y., Phartyal S.S., Sasaki T.

Abstract Urbanisation influences various aspects of species interactions, including animal-mediated endozoochorous seed dispersal – an essential mechanism that facilitates plant dispersal and establishment in urban environments. However, in-depth and systematic assessments of how urbanisation shape endozoochory interactions remain limited. To address this knowledge gap, we reviewed studies on endozoochory in urban ecosystems and examined the effects of urbanisation on endozoochorous seed dispersal. We also assessed whether urban endozoochorous networks exhibit high evenness and nestedness. Additionally, we analyzed trends in the abundance of the resulting plant functional diversity in urban ecosystems. Our review identified 34 studies on endozoochory in urban ecosystems across 17 countries, documenting 429 interactions involving 69 animal and 212 plant species. Most studies (26) focused on a single animal species as a seed disperser, while only two examined urbanisation rates. Furthermore, only 15 studies conducted germination tests on dispersed seeds, indicating limited attention to post-dispersal seed fate. We found substantial interaction evenness in urban endozoochory, alongside a reduction in the functional diversity of dispersed native plants compared to all dispersed plants, including non-native species. Among animal dispersers, only bats exhibited a positive response to urbanisation in terms of the number of plant species dispersed. Additionally, fleshy and dark-coloured fruits that often contain large seeds were positively correlated with urbanisation, suggesting that these traits may facilitate the dispersal of large-sized seeds in urban areas. Our findings highlight urbanisation as a key driver of endozoochorous interactions, emphasizing the need for future research to deepen our understanding of urban endozoochory and to enhance biodiversity conservation efforts.

Gorrod E., White L., Slavich E., Woodward R., McAllister D., Travers S.K., Spooner P., Lawrie K.

Thickening of woody vegetation has degraded numerous ecosystems globally. In forests, woody thickening often follows gap‐creating disturbance that removes mature trees and promotes the dense recruitment of woody resprouts or seedlings. Restoration thinning seeks to reduce tree densities in thickened forests to hasten recovery of stand structure for habitat and other conservation outcomes. However, as restoration thinning involves gap‐creating disturbance, it may stimulate further recruitment. We investigated recruitment responses to restoration thinning in thickened river red gum (Eucalyptus camaldulensis Dehnh.) forests on the Murray River floodplain in semiarid south‐eastern Australia by implementing mechanical thinning at various intensities. The average distance between retained trees (up to 15 m) was intended to be insufficient to stimulate further recruitment, and herbicide was applied to cut stumps to reduce resprouting. We recorded seedling abundance annually for 5 years and resprout abundance after 5 years. Resprouting occurred at all levels of thinning intensity. On average, almost one third of the trees affected by thinning resprouted with over three resprout stems per resprouting tree. Thinning that reduced tree densities to below about 400 per hectare also increased seedling abundance by up to 7500 additional seedlings per hectare in some plots in the fifth year of the study when establishment conditions were favorable. These results demonstrate that effective recruitment controls must be identified prior to implementing restoration thinning programs. Without effective recruitment controls, restoration thinning may stimulate more stems than were removed by thinning, and therefore be an ineffective conservation intervention.

Schmieding M.L., Kopka M., Bolanaki M., Napierala H., Altendorf M.B., Kuschick D., Piper S.K., Scatturin L., Schmidt K., Schorr C., Thissen A., Wäscher C., Heintze C., Möckel M., Balzer F., et. al.

Background Symptom checker apps (SCAs) are layperson-facing tools that advise on whether and where to seek care, or possible diagnoses. Previous research has primarily focused on evaluating the accuracy, safety, and usability of their recommendations. However, studies examining SCAs’ impact on clinical care, including the patient-physician interaction and satisfaction with care, remain scarce. Objective This study aims to evaluate the effects of an SCA on satisfaction with the patient-physician interaction in acute care settings. Additionally, we examined its influence on patients’ anxiety and trust in the treating physician. Methods This parallel-group, randomized controlled trial was conducted at 2 emergency departments of an academic medical center and an emergency practice in Berlin, Germany. Low-acuity patients seeking care at these sites were randomly assigned to either self-assess their health complaints using a widely available commercial SCA (Ada Health) before their first encounter with the treating physician or receive usual care. The primary endpoint was patients’ satisfaction with the patient-physician interaction, measured by the Patient Satisfaction Questionnaire (PSQ). The secondary outcomes were patients’ satisfaction with care, their anxiety levels, and physicians’ satisfaction with the patient-physician interaction. We used linear mixed models to assess the statistical significance of primary and secondary outcomes. Exploratory descriptive analyses examined patients’ and physicians’ perceptions of the SCA’s utility and the frequency of patients questioning their physician’s authority. Results Between April 11, 2022, and January 25, 2023, we approached 665 patients. A total of 363 patients were included in the intention-to-treat analysis of the primary outcome (intervention: n=173, control: n=190). PSQ scores in the intervention group were similar to those in the control group (mean 78.5, SD 20.0 vs mean 80.8, SD 19.6; estimated difference –2.4, 95% CI –6.3 to 1.1, P=.24). Secondary outcomes, including patients’ and physicians’ satisfaction with care and patient anxiety, showed no significant group differences (all P>.05). Patients in the intervention group were more likely to report that the SCA had a beneficial (66/164, 40.2%) rather than a detrimental (3/164, 1.8%) impact on the patient-physician interaction, with most reporting no effect (95/164, 57.9%). Similar patterns were observed regarding the SCA’s perceived effect on care. In both groups, physicians rarely reported that their authority had been questioned by a patient (intervention: 2/188, 1.1%; control: 4/184, 2.2%). While physicians more often found the SCA helpful rather than unhelpful, the majority indicated it was neither helpful nor unhelpful for the encounter. Conclusions We found no evidence that the SCA improved satisfaction with the patient-physician interaction or care in an acute care setting. By contrast, both patients and their treating physicians predominantly described the SCA’s impact as beneficial. Our study did not identify negative effects of SCA use commonly reported in the literature, such as increased anxiety or diminished trust in health care professionals. Trial Registration German Clinical Trial Register DRKS00028598; https://drks.de/search/en/trial/DRKS00028598/entails International Registered Report Identifier (IRRID) RR2-10.1186/s13063-022-06688-w

Burns J., Li A.R., Rohr K.E., Thomas M.L., McCarthy M.J., Meruelo A.D.

Glerean N., Talman K., Glerean E., Hupli M., Haavisto E.

Higgins W.C., Savalei V., Polito V., Ross R.M.

The Reading the Mind in the Eyes Test (RMET) is widely used in clinical and non-clinical research. However, the structural properties of RMET scores have yet to be rigorously examined. We analyzed the structural properties of RMET scores in nine existing datasets comprising non-clinical samples ranging from 558 to 9,267 (median = 1,112) participants each. We used confirmatory factor analysis to assess two theoretically derived factor models, exploratory factor analysis to identify possible alternative factor models, and reliability estimates to assess internal consistency. Neither of the theoretically derived models was a good fit for any of the nine datasets, and we were unable to identify any better fitting multidimensional models. Internal consistency metrics were acceptable in six of the nine datasets, but these metrics are difficult to interpret given the uncertain factor structures. Our findings contribute to a growing body of evidence questioning the reliability and validity of RMET scores.

Losapio G., Mottet L., Khelidj N., Tu B.N., Cerabolini B.E., Grand S., de Vere N., Guisan A.

AbstractThe retreat of glaciers due to climate change is reshaping mountain landscapes and biodiversity. While previous research has documented vegetation succession after glacier retreat, our understanding of functional diversity dynamics is still limited. In this case study, we address the effects of glacier retreat on plant functional diversity by integrating plant traits with ecological indicator values across a 140-year chronosequence in a subalpine glacier landscape. We reveal that functional richness and functional dispersion decrease with glacier retreat, while functional evenness and functional divergence increase, suggesting a shift towards more specialized and competitive communities. Our findings highlight the critical role of ecological factors related to soil moisture, soil nutrients, and light availability in shaping plant community dynamics. The integrative approach of this case study provides novel insights into the potential response of alpine plant communities to climate change, offering a deeper understanding of how to predict and anticipate the effects of glacier extinction on biodiversity in rapidly changing environments.

Nomura N., Kasai A.

Abstract Resource competition is a key factor in shaping community structure. In herbivorous insects, living space occupation is likely to lead to exclusion due to resource competition with coercion of consuming poor resources. Given that eggs are immobile, their placement is critical for larval survival and development, especially in terms of optimal resource consumption, making oviposition site selection a crucial factor for females. Therefore, competition for oviposition sites may lead to exclusion if resources are scarce. This study examined the competitive relationships among three leaf beetle species (Coleoptera: Chrysomelidae): Aspidimorpha difformis (Motschulsky), Aspidimorpha transparipennis (Motschulsky) and Laccoptera nepalensis Boheman. Competitive dynamics were assessed using field surveys, experiments and simulations. Results revealed that habitats for both Aspidimorpha species were less than half the size of L. nepalensis habitats. Additionally, both Aspidimorpha species avoided oviposition on leaves with the oothecae of other species, with A. difformis showing a reduction of up to 70% in ootheca number. Simulation results indicated that only A. difformis, which experienced oviposition site reductions due to other species, faced certain extinction under conditions mimicking natural habitats. Our findings suggest that A. difformis experiences unilateral exclusion due to resource competition for oviposition sites, as observed in the field. Thus, based on our findings, even free‐living herbivorous insects can be excluded due to interference competition during their immobile stage, such as eggs.

de‐Carvalho M., Diniz P., Pires Júnior O.R., Macedo R.H., Nardoto G.B.

Carotenoid‐based plumage color is crucial in avian mate selection, often serving as an indicator of individual quality. To determine whether carotenoid‐derived color can be a sign of individual condition and if there is a relationship between an individual's condition and color production, it is necessary to identify how carotenoids are acquired by individuals and subsequently used by the organism. Our objective was to determine how carotenoid pigments are used in the stripe‐tailed yellow finch Sicalis citrina, a species wherein females exhibit a light yellowish ventral color while males are bright yellow. By using carbon and nitrogen stable isotope analyses we were able to determine if these carotenoid‐derived colors are a signal of individual condition in terms of physiological stress and body condition. Females with low δ13C values (≈ −18‰) indicating the consumption of C3 and C4 seeds, exhibited colors shifted toward longer wavelengths and better body condition, and those with such color shifts also had higher carotenoid concentrations. In contrast, brighter females had higher δ15N values, indicating greater consumption of arthropods. Males with more saturated ventral patches had higher carotenoid concentrations, while those with colors shifted toward shorter wavelengths or lower H/L ratios, i.e. less stress, exhibited high δ15N values, suggesting that they supplement their diet with arthropods (δ15N ≈ 5‰). Our results show that the carotenoids dynamics in stripe‐tailed yellow finches differ between sexes and highlight how food sources impact condition, stress, and ornamentation. Our study indicates that sexual dimorphism extends beyond plumage color to deeper physiological and ecological differences.

Weisman K., Luhrmann T.M.

AbstractPhenomenal experiences of immaterial spiritual beings—hearing the voice of God, seeing the spirit of an ancestor—are a valuable and largely untapped resource for the field of cognitive science. Such experiences, we argue, are experiences of the mind, tied to mental models and cognitive‐epistemic attitudes about the mind, and thus provide a striking example of how, with the right combination of mental models and cognitive‐epistemic attitudes, one's own thoughts and inner sensations can be experienced as coming from somewhere or someone else. In this paper, we present results from a large‐scale study of U.S. adults (N = 1779) that provides new support for our theory that spiritual experiences are facilitated by a dynamic interaction between mental models and cognitive‐epistemic attitudes: A person is more likely to hear God speak if they have the epistemic flexibility and cultural support to shift, temporarily, away from a mundane model of mind into a more “porous” way of thinking and being. This, in turn, lays the foundation for a meditation on how mental models and cognitive‐epistemic attitudes might also interact to facilitate other phenomena of interest to cognitive science, such as fiction writing and scientific discovery.

Stocco G., Cipolat-Gotet C., Summer A., Tiezzi F., Blotta S., Negro A., Castiglioni B., Biffani S.