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Maximum likelihood or restricted maximum likelihood (REML) estimates of the
parameters in linear mixed-effects models can be determined using the lmer
function in the lme4 package for R. As for most model-fitting functions in R,
the model is described in an lmer call by a formula, in this case including
both fixed- and random-effects terms. The for...
Context in source publication
Context 1
... The profile pairs plot (Figure 4; splom) gives an approximation of the two-dimensional profiles of pairs of parameters, interpolated from the univariate profiles as described in Bates and Watts (1988, Chapter 6). The profile pairs plot shows two-dimensional 50%, 80%, 90%, 95% and 99% marginal confidence regions based on the likelihood ratio, as well as the profile traces, which indicate the conditional estimates of each parameter for fixed values of the other parameters. ...
Citations
... We ran all analyses in the R language environment (R Core Team, 2021) with libraries "MuMIn" v.1.43.17 (Bartoń, 2020), "lme4" v. 1.1.27.1 (Bates et al., 2015). ...
Urbanization reduces insectivorous bird specific richness and functional diversity. • Tree diversity within city increases bird insectivory. • Modeling intra-urban heterogeneity is essential to understand trophic interactions. A B S T R A C T Urbanization is one of the main drivers of biotic homogenization in bird communities worldwide. Yet, only a few studies have addressed its functional consequences on the top-down control birds exert on insect herbivores. We hypothesized that their inconsistent results reflect the overlooked heterogeneity of the urban habitat for birds, and in particular the distribution and diversity of urban trees. We monitored tree diversity, bird diversity, avian predation attempts on artificial prey, and the effect of bird exclusion on insect herbivory in 97 trees distributed among 24 urban experimental plots in the city of Montreal, Canada. We characterized urbanization levels through a combination of variables related to tree density, impervious surfaces, anthropic noise, and human population density. Bird diversity decreased with increasing urbanization, whereas the frequency of generalist synurbic species increased. We found no significant relationship between predation and urbanization or between predation and bird diversity. However, tree diversity was positively correlated with predation attempts on artificial prey, irrespective of bird diversity. We revealed a mismatch between the effects of urbanization on bird diversity and on the regulation service and unraveled the functional importance of tree diversity in shaping the avian predation function in urban ecosystems. Our study advocates for the consideration of intra-urban heterogeneity in the investigation of trophic cascades within cities.
... The effect of PD, N timing strategy, and their interaction on corn yield and cumulative growing season N 2 O emissions were tested with linear mixed models, using year as a random factor. The statistical tests were performed with the lme4 package in R (Bates et al., 2015). The assumption of normality and homogeneity of variance of model residuals was evaluated using residual plots. ...
Context: The impact of nitrogen fertilizer (N) application timing on nitrous oxide (N2O) emissions is inconsistent in the literature. This inconsistency is attributed to year-to-year weather variations, which affect soil conditions around N application time. Planting dates (PD) also vary year-to-year based on weather, and PD can influence N timing decisions. Objective: The study aims to evaluate: i) the long-term effects of different N application timings on N2O emissions and, ii) how variations in PD influence the relative performance of different N timing strategies. Methods: We used the DeNitirifcation-DeComposition (DNDC) model, calibrated with field measurements from Elora, Ontario, Canada, to simulate 39 growing seasons using historical weather data. Three N timing strategies were tested: spring application one day before planting, in-season application at the V6 growth stage, and a split-N strategy with N applied at both times. PDs were either dynamically adjusted each year based on rainfall or fixed to one of three typical corn (Zea mays L.) planting dates in Ontario: April 25, May 5, and May 15. Results: For the first objective, the long-term simulation found that average N2O emissions were greatest when N was applied at V6 (3.2 kg N ha−1) compared to when N was applied pre-plant (2.3 kg N ha−1) or split-applied (2.0 kg N ha−1). This was caused by slightly greater rainfall around V6 than planting. For the second objective, the relative performance of different N-timing strategies was affected by PD. Earlier PDs resulted in lower N₂O emissions compared to later PDs, primarily due to lower soil temperatures around the time of N fertilizer application. Earlier PDs also led to the largest differences in N2O emissions among the N timing strategies, with PD delays leading to smaller differences among N timing strategies. Conclusions: Large single N applications, particularly those applied in-season, resulted in greater N2O emissions than split and at-planting N applications in a long-term simulation. Early PDs consistently reduced N2O emissions by creating less favourable conditions for N2O production. Moreover, the relative performance of N timing strategies was mediated by PD. Implications: This study highlights the interconnected nature of cropping systems, where one management practice, PD, can influence a seemingly unrelated outcome, N2O emissions. Long-term climatic, social, economic, and technological changes that influence PD will also influence N2O emissions from spring and summer-applied N fertilizer.
... The data from the wet and dry seasons were analysed independently. Linear mixedeffect models were used to analyse the effect of functional group on the response variables using the lme4 package (Bates et al., 2015), together with lmerTest to show significance (Kuznetsova et al., 2017). Temp., VPD, PAR, leaf gs, leaf Tr, soil water content and cocoa yield (mature pods per tree) were considered as the response variable with the functional groups as fixed effect while the shade trees (tree nested to farm) were considered as random effect. ...
Agroforestry has the potential to enhance climate change adaptation. While benefits from agroforestry systems consisting of cash crops and shade trees are usually attributed to the (shade) trees, the trees can also have negative impacts due to resource competition with crops. Our hypothesis is that leaf phenology and height of shade trees determine their seasonal effect on crops. We test this hypothesis by categorizing shade tree species into functional groups based on leaf phenology, shade tree canopy height and shade tree light (wet and dry season) interception as well as the effects. To this end, leaf phenology and the effects on microclimate (tem-perature, air humidity, intercepted photoactive radiation (PAR)), soil water, stomatal conductance and cocoa yield were monitored monthly during wet and dry seasons over a two-year period on smallholder cocoa plantations in the northern cocoa belt of Ghana. Seven leaf phenological groups were identified. In the wet season, highest buffering effect of microclimate was recorded under the trees brevi-deciduous before dry season. During dry season, high PAR and lowest reduction in soil moisture were observed under the trees in the group of completely deciduous during dry season. The evergreen groups also showed less reduction in soil water than the brevi-deciduous groups. In the wet season, shade tree effects on cocoa tree yields in their sub canopy compared to the respective control of outer canopy with full sun ranged from positive (+10 %) to negative (-15 %) for the deciduous groups, while yield reductions for the evergreen groups ranged from − 20 % to − 33 %. While there were negative yield impacts for all phenological groups in the dry season, the trees in completely deciduous during dry season group recorded least penalties (-12 %) and the trees with evergreen upper canopy the highest (-35 %). The function of shade trees in enhancing climate resilience is therefore strongly dependent on their leaf phenological characteristics. Our study demonstrates how the key trait leaf phenology can be applied to successful design of climate-resilient agroforestry systems.
... Linear mixed-effects models were fitted with R package "lme4" (Bates et al., 2015) to test for significant differences in the resilience indices between species. Full models include all species and variables for direct comparison of the resilience indices between species. ...
... As inspection of the raw data (see Supplemental Figure 4) did not suggest better alignment with nonlinear models, we opted to apply linear analysis to make our results directly comparable to previous publications (for systematic review see Beutler et al., 2022).To examine the influence of dissociative symptoms on HR, we calculated a linear mixed-effects model (LMM) using restricted maximum likelihood (REML) and listwise data exclusion with the lmer function of the lme4 package (Bates et al., 2015) and the results report package (Makowski et al., 2023), implemented in R (v.4.2.2; R Core Team, 2022). Within this model, we included the covariates age, body mass index (BMI), and smoking as informed by Bodin et al. (2017), Molfino et al. (2009), andShaffer andGinsberg (2017). ...
... We used the lme4 package (Bates et al., 2015) in R, version 4.2.1 (R Core Team, 2022) to build multilevel linear models predicting each IER strategy by empathy components and relationship closeness. We used multilevel models due to the hierarchical structure in our data (measurement occasions (t: 1-21 EMA surveys) nested within persons (j: 1-135 participants) with level 1 as the situation-level and level 2 as the person-level. ...
Background:
Empathic behavior is crucial in promoting positive social outcomes and
strengthening interpersonal bonds. Research on how empathy modulates responses to others’ emotions remains scarce yet is fundamental for elucidating mechanisms of impaired social functioning in psychopathology and its treatment.
Methods:
Two ecological momentary assessment studies (Ns = 125 and 204) investigated participants’ empathy ratings and usage of interpersonal emotion regulation strategies in 5,537 social interactions. We measured empathy, a multi-faceted construct, as dissected into its components of mentalizing and experience sharing in Study 1, while Study 2 additionally investigated empathic concern and personal distress.
Results:
Findings revealed that empathizers engage in significantly increased other-focused regulation, especially when feeling empathic concern. We also found differences in the strengths of the links between empathy and responses to others’ emotions: When we mentalize, share others’ emotions, or feel concerned, we choose more relationship- oriented strategies, including validation and soothing and less cognitive reappraisal and avoidance to regulate others’ emotions. In contrast, when personally distressed by others’ emotions, we select more cognitive reappraisal and avoidance and less relationship-oriented strategies.
Limitations:
Both studies relied on regulator reports.
Conclusions:
Empathy facets distinctly shape our responses to others’ emotions and can drive us to be increasingly emotionally responsive and relationship-oriented. Understanding these dynamics can enhance empathic interpersonal emotion regulation, a potentially valuable tool in treating affective disorders.
... The analyses on problem-size effect difference depending on the solving strategy (finger or mental) were conducted using mixed-effect models with the lmer function of the ''lme4" package (Bates et al., 2015) (see Appendix B in the supplementary material for details on the analyses conducted). ...
Determining how children solve arithmetic problems when they stop using their fingers is a real challenge. To take it up, the evolution of problem-size effects for tie and non-tie problems was observed when 6-year-olds (N = 65) shift from finger counting to mental strategies. These observations revealed that the problem-size effect remained the same for non-tie problems, whereas it drastically decreased for tie problems. Moreover, the solving strategy for tie problems switched directly from the representation of both operands on fingers to retrieval without transition through the representation of only one operand on fingers. This direct switch could be made possible by the relative ease to commit symmetrical representations to memory (in the case of tie problems) rather than non-symmetrical ones (in the case of non-tie problems). This would explain why, early during development, small tie problems are solved quickly and present null or negligible size effects. All in all, our results and interpretations provide an answer to the long-standing question as to why tie problems have a special cognitive status. Our results also nuance the classical description of the developmental pattern reported in all textbook chapters devoted to numerical cognition according to which a finger strategy where only one operand is represented on fingers constitutes a developmental stage between the representation of two operands on fingers and retrieval. We demonstrate here that it is true only for non-tie problems.
... Due to the singularity fitting and non-convergence problems caused by the complex random effect structure, we further removed the correlations between the random intercept and the random slope first, and then removed the random slope with the smallest variance until there were no singularity fitting or non-convergence warnings. The LME regression was conducted in R (R Core Team, 2021) using the lme4 package (Bates et al., 2015), with p-values estimated by the Satterthwaite approximation method implemented in the lmerTest package (Kuznetsova et al., 2017). To obtain the main effects and the interaction effect, we first used deviation coding for tonal relatedness (0.5: related; − 0.5: unrelated) and syllabic relatedness (0.5: related; − 0.5: unrelated). ...
Lexical tone is an important phonological property in tonal languages, but its encoding process in speech production remains unclear. We conducted two electroencephalographic (EEG) experiments to investigate the time course of tonal encoding relative to that of syllabic encoding in Mandarin Chinese disyllabic and monosyllabic word production respectively. We employed a phonologically primed picture naming task and orthogonally manipulated the tonal and syllabic overlap between the prime and the target word. In both experiments, the ERP data revealed that the main effect of tonal relatedness began to emerge alone in an early time window before that of syllabic relatedness, indicating an early independent retrieval process for lexical tone. Moreover, we observed a significant interaction between tonal and syllabic relatedness in later ERP time window(s) and onset latencies, indicating a later tone-to-syllable integration process. These results support the two-stage model of tonal encoding in Mandarin word production and offer implications for current speech production models.
... One participant lacked data on ratings and was thus excluded, leaving a sample of 37 participants to be included in the analyses. Analyses of the participants' choices were carried out by fitting Generalized Linear Mixed Models (GLMMs) using the lme4 package 36 . Here, the dependent variable was participant choice, coded according to optimality, based on which choice option was assigned the lowest probability of being followed by a shock (Optimal choice = 1, Suboptimal choice = 0). ...
Observational learning enables us to make decisions by watching others’ behaviors. The quality of such learning depends on the abilities of those we observe, but also on our beliefs about those abilities. We have previously demonstrated that observers learned better from demonstrators described as high vs. low in ability, regardless of their actual performance. The current study aimed to conceptually replicate these findings, and explore the neural mechanisms involved. Forty-five participants performed an observational learning task while undergoing functional magnetic resonance imaging (fMRI). We hypothesized that participants would perform better when demonstrators were described as having high vs. low ability. Unexpectedly, participants performed equally well regardless of described demonstrator ability. The behavioral effects of biased observational learning seem to be driven by mentalizing processes together with general learning and decision-making processes.
... For each eye-tracking measure, we ran (generalized) linear mixed-effects models using the lme4 package (Bates et al., 2015) in R statistical software (R Core Team, 2016, version 4.2.1). For generating Cohen's d values for all significant effects in the models, we used the function lme.dscores in the R package EMAtools (Kleiman, 2017). ...
The proactive gain control hypothesis suggests that the global language context regulates lexical access to the bilinguals' languages during reading. Specifically, with increasing exposure to non-target language cues, bilinguals adjust the lexical activation to allow non-target language access from the earliest word recognition stages. Using the invisible boundary paradigm, we examined the flow of lexical activation in 50 proficient Russian-English bilinguals reading in their native Russian while the language context shifted from a monolingual to a bilingual environment. We gradually introduced non-target language cues (the language of experimenter and fillers) while also manipulating the type of word previews (identical, code-switches, unrelated code-switches, pseudowords). The results revealed the facilitatory reading effects of code-switches but only in the later lexical processing stages and these effects were independent of the global language context manipulation. The results are discussed from the perspective of limitations imposed by script differences on bilingual language control flexibility. Highlights • We examined time course of lexical access to L2 English in reading in L1 Russian • Bilinguals read Russian sentences with parafoveally presented English code-switches • We gradually introduced English language cues to create a bilingual environment • No effect of the global language context found on early or late eye-movement measures • Results don't fully support proactive gain control hypothesis but align with Multilink
