Conditional covariance penalties for mixed models

Säfken, Benjamin; Kneib, Thomas

doi:10.1111/sjos.12437

Cited by 6 publications

(4 citation statements)

References 31 publications

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“…The cohort level analyses were conducted with R (version 3.5.0; https://www.r-project.org/) and rvtests . R package “cAIC4” was used to calculate cAIC …”

Section: Methodsmentioning

confidence: 99%

Genomewide association study of Parkinson's disease clinical biomarkers in 12 longitudinal patients' cohorts

et al. 2019

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Background Several reports have identified different patterns of Parkinson's disease progression in individuals carrying missense variants in GBA or LRRK2 genes. The overall contribution of genetic factors to the severity and progression of Parkinson's disease, however, has not been well studied. Objectives To test the association between genetic variants and the clinical features of Parkinson's disease on a genomewide scale. Methods We accumulated individual data from 12 longitudinal cohorts in a total of 4093 patients with 22,307 observations for a median of 3.81 years. Genomewide associations were evaluated for 25 cross‐sectional and longitudinal phenotypes. Specific variants of interest, including 90 recently identified disease‐risk variants, were also investigated post hoc for candidate associations with these phenotypes. Results Two variants were genomewide significant. Rs382940(T>A), within the intron of SLC44A1, was associated with reaching Hoehn and Yahr stage 3 or higher faster (hazard ratio 2.04 [1.58–2.62]; P value = 3.46E‐8). Rs61863020(G>A), an intergenic variant and expression quantitative trait loci for α‐2A adrenergic receptor, was associated with a lower prevalence of insomnia at baseline (odds ratio 0.63 [0.52–0.75]; P value = 4.74E‐8). In the targeted analysis, we found 9 associations between known Parkinson's risk variants and more severe motor/cognitive symptoms. Also, we replicated previous reports of GBA coding variants (rs2230288: p.E365K; rs75548401: p.T408M) being associated with greater motor and cognitive decline over time, and an APOE E4 tagging variant (rs429358) being associated with greater cognitive deficits in patients. Conclusions We identified novel genetic factors associated with heterogeneity of Parkinson's disease. The results can be used for validation or hypothesis tests regarding Parkinson's disease. © 2019 International Parkinson and Movement Disorder Society

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“…The cohort level analyses were conducted with R (version 3.5.0; https://www.r-project.org/) and rvtests . R package “cAIC4” was used to calculate cAIC …”

Section: Methodsmentioning

confidence: 99%

Genomewide association study of Parkinson's disease clinical biomarkers in 12 longitudinal patients' cohorts

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Most models tested returned highly significant values ( p < 0.001) due to large sample sizes. Thus, we used conditional Aikaike Information Criterion (cAIC), which is appropriate for linear mixed effects model selection (Greven & Kneib, 2010; Saefken et al, 2014) using the cAIC4 package (Säfken et al, 2018) in R 3.6.0. Due to maximum likelihood estimation, traditional R 2 calculations cannot be estimated with mixed‐effects.…”

Section: Methodsmentioning

confidence: 99%

River network travel time is correlated with dissolved organic matter composition in rivers of the contiguous United States

Hosen

Allen

Amatuli

et al. 2021

Hydrological Processes

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Most terrestrial allochthonous organic matter enters river networks through headwater streams during high flow events. In headwaters, allochthonous inputs are substantial and variable, but become less important in streams and rivers with larger watersheds. As allochthonous dissolved organic matter (DOM) moves downstream, the proportion of less aromatic organic matter with autochthonous characteristics increases. How environmental factors converge to control this transformation of DOM at a continental scale is less certain. We hypothesized that the amount of time water has spent travelling through surface waters of inland systems (streams, rivers, lakes, and reservoirs) is correlated to DOM composition. To test this hypothesis, we used established river network scaling relationships to predict relative river network flow-weighted travel time (FWTT) of water for 60 stream and river sites across the contiguous United States (3090 discrete samples over 10 water years). We estimated lentic contribution to travel times with upstream in-network lake and reservoir volume. DOM composition was quantified using ultraviolet and visible absorption and fluorescence spectroscopy. A combination of FWTT and lake and reservoir volume was the best overall predictor of DOM composition among models that also incorporated discharge, specific discharge, watershed area, and upstream channel length. DOM spectral slope ratio (R 2 = 0.77) and Freshness Index (R 2 = 0.78) increased and specific ultraviolet absorbance at 254 nm (R 2 = 0.68) and Humification Index (R 2 = 0.44) decreased across sites as a function of FWTT and upstream lake volume. This indicates autochthonous-like DOM becomes continually more dominant in waters with greater FWTT. We assert that river FWTT can be used as a metric of the continuum of DOM composition from headwaters to rivers. The nature of the changes to DOM composition detected suggest this continuum is driven by a combination of photo-oxidation, biological processes, hydrologically varying terrestrial subsidies, and aged groundwater inputs.

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“…We assessed model accuracy by calculating the area under the receiver operating characteristic curve (AUC) with the ROCR package (Sing, Sander, Beerenwinkel, & Lengauer, 2005). Because we were primarily concerned with modelling fixed effects and used the same random effect structure for all of our models, we used the marginal Akaike information criteria (mAIC) to select our best model, where the lowest mAIC value indicated the model with the best fit (Säfken, Rügamer, Kneib, & Greven, 2018).…”

Section: Methodsmentioning

confidence: 99%

Killing time in cover crops? Artificial perches promote field use by raptors

Zagorski

2020

Annals of Applied Biology

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Cover crops are an increasingly common conservation practice in intensive row‐crop agriculture of the Midwestern United States and can improve wildlife habitat. However, they also benefit agricultural pest species such as voles (Microtus), which have damaged cover‐cropped soybean fields in Indiana. We tested the feasibility of attracting raptors, which are natural predators of voles, to cover‐cropped fields by supplying artificial perches from which to hunt. We assessed raptor use of artificial perches in cover‐cropped fields during the winters of 2018 and 2019. Perches were erected at three different distances from the field edge: 50, 125 and 200 m. We modelled perch use of our three most common species, great horned owl, red‐tailed hawk and American kestrel, with a logistic generalised linear mixed model. Raptors used 82% of the perches, and perch use was greatest at 200 m. However, even at peak use, our best model predicted a low probability of overall perch use for all three species. Artificial perches can attract raptors into large row‐crop fields. Sturdier perch design, extended perch availability and greater vole populations could increase use of perches. Although raptor perch use by itself is unlikely to control vole populations in cover‐cropped fields, artificial perches could form a valuable component of an integrated pest management system.

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Conditional covariance penalties for mixed models

Cited by 6 publications

References 31 publications

Genomewide association study of Parkinson's disease clinical biomarkers in 12 longitudinal patients' cohorts

Genomewide association study of Parkinson's disease clinical biomarkers in 12 longitudinal patients' cohorts

River network travel time is correlated with dissolved organic matter composition in rivers of the contiguous United States

Killing time in cover crops? Artificial perches promote field use by raptors

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