A Kenward-Roger Approximation and Parametric Bootstrap Methods for Tests in Linear Mixed Models - The<i>R</i>Package<b>pbkrtest</b>

Halekoh, Ulrich; Højsgaard, Søren

doi:10.18637/jss.v059.i09

Cited by 1,104 publications

(756 citation statements)

References 12 publications

(10 reference statements)

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“…To determine the significance of each term in these models, LRtest significance (likelihood ratio test) was determined by parametric bootstrapping (PBtest) to compare the full model with the simpler model using the pbkrtest package (Halekoh and Højsgaard 2014). Model fit was evaluated based on the conditional R 2 (i.e., variance explained by both fixed and random effects) using the MuMIn package (Nakagawa andSchielzeth 2013, Barton 2016).…”

Section: Accepted Ar Ticlementioning

confidence: 99%

Forest tree neighborhoods are structured more by negative conspecific density dependence than by interactions among closely related species

et al. 2017

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Interactions among neighbors influence the structure of communities of sessile organisms. Closely related species tend to share habitat and resource requirements and to interact with the same mutualists and natural enemies so that the strength of interspecific interactions tends to decrease with evolutionary divergence time. Nevertheless, the degree to which such phylogenetically related ecological interactions structure plant communities remains unclear. Using data from five large mapped forest plots combined with a DNA barcode mega‐phylogeny, we employed an individual‐based approach to assess the collective effects of focal tree size on neighborhood phylogenetic relatedness. Abundance‐weighted average divergence time for all neighbors (ADT_all) and for heterospecific neighbors only (ADT_hetero) were calculated for each individual of canopy tree species. Within local neighborhoods, we found phylogenetic composition changed with focal tree size. Specifically, significant increases in ADT_all with focal tree size were evident at all sites. In contrast, there was no significant change in ADT_hetero with tree size in four of the five sites for both sapling‐sized and all neighbors, even at the smallest neighbourhood scale (0–5 m), suggesting a limited role for phylogeny‐dependent interactions. However, there were inverse relationships between focal tree size and the proportion of heterospecific neighbors belonging to closely related species at some sites, providing evidence for negative phylogenetic density dependence. Overall, our results indicate that negative interaction with conspecifics had a much greater impact on neighborhood assemblages than interactions among closely related species and could contribute to community structure and diversity maintenance in different forest communities.

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Section: Accepted Ar Ticlementioning

confidence: 99%

Forest tree neighborhoods are structured more by negative conspecific density dependence than by interactions among closely related species

et al. 2017

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“…The step 2 model eliminates the random effect of G on N U as it contributes little variance. The step 3 model eliminates the interaction term N U Â logðnÞ with tð98:6Þ ¼ À0:486, p ¼ 0:63 using the Kenward-Roger (KR) approximation for degrees of freedom (Halekoh and Højsgaard 2014). Graphical inspection of model residuals in a Q-Q plot indicate a nearly normal distribution.…”

Section: Uncoupled Task Analysismentioning

confidence: 99%

Collaboration and complexity: an experiment on the effect of multi-actor coupled design

Grogan

Weck

2016

Res Eng Design

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Design of complex systems requires collaborative teams to overcome limitations of individuals; however, teamwork contributes new sources of complexity related to information exchange among members. This paper formulates a human subjects experiment to quantify the relative contribution of technical and social sources of complexity to design effort using a surrogate task based on a parameter design problem. Ten groups of 3 subjects each perform 42 design tasks with variable problem size and coupling (technical complexity) and team size (social complexity) to measure completion time (design effort). Results of a two-level regression model replicate past work to show completion time grows geometrically with problem size for highly coupled tasks. New findings show the effect of team size is independent from problem size for both coupled and uncoupled tasks considered in this study. Collaboration contributes a large fraction of total effort, and it increases with team size: about 50-60 % of time and 70-80 % of cost for pairs and 60-80 % of time and 90 % of cost for triads. Conclusions identify a role for improved design methods and tools to anticipate and overcome the high cost of collaboration.

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“…Kenward-Roger approximation with the package "pbkrtest" (Halekoh & Højsgaard, 2014) was used to compute the degrees of freedom to derive information about the significance of the predictors. Results of the LME models are summarized in Tables 4 (fixed effects) and 5 (random effects).…”

Section: Training and Transfer Gainsmentioning

confidence: 99%

Does working memory training have to be adaptive?

Bastian

Eschen

2015

Psychological Research

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This study tested the common assumption that, to be most effective, working memory (WM) training should be adaptive (i.e., task difficulty is adjusted to individual performance). Indirect evidence for this assumption stems from studies comparing adaptive training to a condition in which tasks are practiced on the easiest level of difficulty only [cf. Klingberg (Trends Cogn Sci 14:317-324, 2010)], thereby, however, confounding adaptivity and exposure to varying task difficulty. For a more direct test of this hypothesis, we randomly assigned 130 young adults to one of the three WM training procedures (adaptive, randomized, or self-selected change in training task difficulty) or to an active control group. Despite large performance increases in the trained WM tasks, we observed neither transfer to untrained structurally dissimilar WM tasks nor far transfer to reasoning. Surprisingly, neither training nor transfer effects were modulated by training procedure, indicating that exposure to varying levels of task difficulty is sufficient for inducing training gains. Can fluid cognitive abilities such as working memory (WM) and reasoning be improved through computer-based WM training? This is a highly controversial question, with prior empirical studies (for reviews, see Morrison & Chein, 2011;von Bastian & Oberauer, 2014) and meta-analyses (Au et al., in press;Karbach & Verhaeghen, 2014;Lampit, Hallock, & Valenzuela, 2014;Melby-Lervåg & Hulme, 2013) providing contradictory findings. Although multiple previous studies revealed promising effects (e.g., Jaeggi, Buschkuehl, Jonides, & Perrig, 2008;Jaeggi, Buschkuehl, Shah, & Jonides, 2014;Jaeggi et al., 2010; Klingberg et al., 2005;Schweizer, Hampshire, & Dalgleish, 2011;Stepankova et al., 2014;, a growing number of other WM training interventions failed to induce such broad transfer (e.g., Chein & Morrison, 2010;Chooi & Thompson, 2012;Colom et al., 2013;Harrison et al., 2013;Redick et al., 2013;Salminen, Strobach, & Schubert, 2012; Sprenger et al., 2013;Thompson et al., 2013;von Bastian, Langer, Jäncke, & Oberauer, 2013). The factors contributing to the success of WM training interventions in terms of improving WM and reasoning are still unclear (see von Bastian & Oberauer, 2014), and large variations (and, in some occasions, serious flaws) in the methodologies and training regimens used complicate comparisons across studies (cf. Shipstead, Redick, & Engle, 2012), and thus the identification of such factors. Therefore, before we can conclude whether and under which circumstances WM training can induce transfer, carefully controlled, systematic investigations of factors potentially contributing to training effectiveness are needed.In theory, cognitive plasticity occurs if there is a "prolonged mismatch between functional organismic supplies and environmental demands" (Lövden, Bäckman, Lindenberger, Schaefer, & Schmiedek, 2010, p. 659). According to Lövden and colleagues (2010), this mismatch occurs if the environmental demands exceed the routine demands the cognitiv...

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A Kenward-Roger Approximation and Parametric Bootstrap Methods for Tests in Linear Mixed Models - TheRPackagepbkrtest

Cited by 1,104 publications

References 12 publications

Forest tree neighborhoods are structured more by negative conspecific density dependence than by interactions among closely related species

Forest tree neighborhoods are structured more by negative conspecific density dependence than by interactions among closely related species

Collaboration and complexity: an experiment on the effect of multi-actor coupled design

Does working memory training have to be adaptive?

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