Hierarchical generalized additive models: an introduction with mgcv

Pedersen, Eric J.; Miller, David L.; Simpson, Gavin L.; Ross, Noam

doi:10.7287/peerj.preprints.27320v1

Cited by 17 publications

(7 citation statements)

References 27 publications

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“…Next, we tested for differences in survival responses between plant functional groups (grasses, forbs, N‐fixers) by constructing a GAMM (family: binomial, link‐function: logit) with survival as the response variable, functional group with dry or wet start as fixed factor and mesocosm nested in plot as random block. A final GAMM (family: binomial, link function: logit) was constructed to test for differences in survival between individual species, including species with dry or wet start as fixed factor and mesocosm nested in plot as random block (Pedersen et al, 2018). We then determined two factors to explain differences in individual species survival: baseline competitive success and sensitivity to stress.…”

Section: Methodsmentioning

confidence: 99%

Risk of short‐term biodiversity loss under more persistent precipitation regimes

Reynaert

Boeck

Verbruggen

et al. 2021

Global Change Biology

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Recent findings indicate that atmospheric warming increases the persistence of weather patterns in the mid‐latitudes, resulting in sequences of longer dry and wet periods compared to historic averages. The alternation of progressively longer dry and wet extremes could increasingly select for species with a broad environmental tolerance. As a consequence, biodiversity may decline. Here we explore the relationship between the persistence of summer precipitation regimes and plant diversity by subjecting experimental grassland mesocosms to a gradient of dry–wet alternation frequencies whilst keeping the total precipitation constant. The gradient varied the duration of consecutive wet and dry periods, from 1 up to 60 days with or without precipitation, over a total of 120 days. An alternation of longer dry and wet spells led to a severe loss of species richness (up to –75% relative to the current rainfall pattern in W‐Europe) and functional diversity (enhanced dominance of grasses relative to nitrogen (N)‐fixers and non‐N‐fixing forbs). Loss of N‐fixers and non‐N‐fixing forbs in severe treatments was linked to lower baseline competitive success and higher physiological sensitivity to changes in soil moisture compared to grasses. The extent of diversity losses also strongly depended on the timing of the dry and wet periods. Regimes in which long droughts (≥20 days) coincided with above‐average temperatures showed significantly more physiological plant stress over the experimental period, greater plant mortality, and impoverished communities by the end of the season. Across all regimes, the duration of the longest period below permanent wilting point was an accurate predictor of mortality across the communities, indicating that increasingly persistent precipitation regimes may reduce opportunities for drought stress alleviation. We conclude that without recruitment, which was precluded in this experiment, summer precipitation regimes with longer dry and wet spells will likely diminish plant diversity, at least in the short term.

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Section: Methodsmentioning

confidence: 99%

Risk of short‐term biodiversity loss under more persistent precipitation regimes

Reynaert

Boeck

Verbruggen

et al. 2021

Global Change Biology

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“…Since the Bythotrephes populations of each lake are below detection until mid‐summer, we needed to account for this seasonality and variable sampling times among years to estimate Bythotrephes density in each lake. We used a hierarchical generalized additive model framework where Bythotrephes count was dependent on lake‐specific seasonal (∼ s[day of the year]) and long‐term (∼ s[year]) factor‐smoothed trends that were penalized against general seasonal and long‐term smoothed trends that were shared between the neighboring, connected lakes (Pedersen et al 2019). The model was fit with Poisson‐distributed error and natural log‐transformed tow volume (ln[π × net radius 2 × tow depth]) as an offset (package “mgcv” in Wood 2015).…”

Section: Methodsmentioning

confidence: 99%

Climate and food web effects on the spring clear‐water phase in two north‐temperate eutrophic lakes

Matsuzaki

Lathrop

Carpenter

et al. 2020

Limnology & Oceanography

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Although climate change has shifted the phenological timing of plankton in lakes, few studies have explicitly addressed the relative contributions of climate change and other factors, including planktivory and nutrient availability. The spring clear-water phase is a period of marked reduction in algal biomass and increased water transparency observed in many lakes. Here, we quantified the phenological patterns in the start date, maximum date, duration, and magnitude of the clear-water phase over 38 yr in Lakes Mendota and Monona, and examined the effects of water temperature, total phosphorus, and food web structure (proportion of large-bodied Daphnia pulicaria and density of invasive Bythotrephes) and interactions between temperature and other predictors on these clear-water phase metrics. We found that climate and food web structure affected the clear-water phase, but the effects differed among the metrics. Higher water temperature led to earlier clear-water phase start dates and maximum dates in both lakes. The proportion of D. pulicaria affected all clear-water phase metrics in both lakes. When D. pulicaria proportion was higher, the clear-water phase occurred earlier, lasted longer, and the water was clearer. Moreover, high Bythotrephes density delayed clear-water phase start dates (both lakes), and decreased clear-water phase duration (Lake Mendota) in the following year. These results suggest that variation in food web structure changes the full phenological dynamics of the clear-water phase, while variation in climate condition affects clear-water phase timing only. Our findings highlight the importance of large-bodied grazers for managing water quality under climate change.

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“…Following ), in which anatomical location and diet treatment were used as fixed effects, and mouse ID used to control for repeated sampling as needed. Generalized additive models were used to assess trends in alpha diversity using time as a smoother (92). Jaccard unweighted similarity was used to calculate sample similarity based on community membership (species presence/absence), visualized with non-parametric multidimensional scaling, and tested with permutational analysis of variance (permANOVA) by using the vegan package (93).…”

Section: Bacterial Community Sequencing and Analysismentioning

confidence: 99%

Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice

Holman

Colucci

Baudewyns

et al. 2023

Preprint

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Inflammatory Bowel Diseases (IBD) are devastating conditions of the gastrointestinal tract with limited treatments, and dietary intervention may be effective, affordable, and safe for managing symptoms. Ongoing research has identified inactive compounds in broccoli sprouts, glucoraphanin, and indicated that mammalian gut microbiota play a role in metabolizing it to the anti-inflammatory sulforaphane. The biogeographic location of participating microbiota and how that affects anti-inflammatory benefits to the host is unknown. We fed specific pathogen free C57BL/6 mice either a control diet or a 10% steamed broccoli sprout diet, and gave a three-cycle regimen of 2.5% dextran sodium sulfate (DSS) in drinking water over a 40-day experiment to simulate chronic, relapsing ulcerative colitis. We monitored body weight, fecal characteristics, fecal lipocalin, and bacterial communities from the digesta and epithelium in the jejunum, cecum, and colon. Mice fed the broccoli sprout diet while receiving DSS performed better than mice fed the control diet while receiving DSS for all disease parameters, including significantly more weight gain, lower Disease Activity Index scores, and higher bacterial richness in all gut locations. Bacterial communities were assorted by gut location except in the mice receiving the control diet and DSS treatment. Importantly, our results suggested that broccoli sprout feeding completely abrogated the effects of DSS on gut microbiota, as bacterial communities were similar between mice receiving broccoli sprouts with and without DSS. Collectively, these results strongly support the protective effect of steamed broccoli sprouts against gut microbiota dysbiosis and development of colitis induced by DSS.

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Hierarchical generalized additive models: an introduction with mgcv

Cited by 17 publications

References 27 publications

Risk of short‐term biodiversity loss under more persistent precipitation regimes

Risk of short‐term biodiversity loss under more persistent precipitation regimes

Climate and food web effects on the spring clear‐water phase in two north‐temperate eutrophic lakes

Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice

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