Beta Regression in<i>R</i>

Cribari‐Neto, Francisco; Zeileis, Achim

doi:10.18637/jss.v034.i02

Cited by 1,696 publications

(1,054 citation statements)

References 30 publications

(44 reference statements)

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“…Because the response variable, percentage of introgression, is a real-valued variable bounded to the interval 0−100%, we used beta regression (Ferrari & Cribari-Neto 2004, Cribari-Neto & Zeileis 2010 with a logit link function. We considered all possible model combinations resulting from our 4 explanatory variables, resulting in 16 candidate models.…”

Section: Discussionmentioning

confidence: 99%

Genetic introgression of farmed salmon in native populations: quantifying the relative influence of population size and frequency of escapees

Heino¹,

Svåsand²,

Wennevik³

et al. 2015

Aquacult. Environ. Interact.

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Farmed escapees may threaten the genetic integrity of native salmon populations through interbreeding. However, introgression requires survival until maturation, successful reproduction and successful early development. These traits are often compromised in domesticated animals selected for high performance in captivity. This makes it difficult to predict introgression levels in native populations. A recent study estimated genetic introgression of farmed escaped Atlantic salmon Salmo salar in 20 Norwegian rivers and found highly population-specific levels of introgression. The underlying causes of these patterns, however, remain unknown. Here, using a modeling approach on empirical and demographic data, we demonstrated that a combination of the observed relative frequency of escaped farmed salmon and the average annual angling catch weights for rivers, provides a significantly better predictor for cumulative introgression of farmed salmon in wild populations than the frequency of farmed salmon alone. Our results suggest that the demography of the native population is a significant factor influencing the relative success of farmed salmon in the wild.

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Section: Discussionmentioning

confidence: 99%

Genetic introgression of farmed salmon in native populations: quantifying the relative influence of population size and frequency of escapees

Heino¹,

Svåsand²,

Wennevik³

et al. 2015

Aquacult. Environ. Interact.

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“…Density, biomass, and edge erosion stress measurements from The Netherlands were square root, third root, and log transformed, respectively, to satisfy the assumption of normality for ANOVAs. Beta regression analysis was applied to survivorship data in both sites, where ANOVA assumptions of normality could not be met (65).…”

Section: Methodsmentioning

confidence: 99%

Facilitation shifts paradigms and can amplify coastal restoration efforts

Silliman

Schrack

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Restoration has been elevated as an important strategy to reverse the decline of coastal wetlands worldwide. Current practice in restoration science emphasizes minimizing competition between outplanted propagules to maximize planting success. This paradigm persists despite the fact that foundational theory in ecology demonstrates that positive species interactions are key to organism success under high physical stress, such as recolonization of bare substrate. As evidence of how entrenched this restoration paradigm is, our survey of 25 restoration organizations in 14 states in the United States revealed that >95% of these agencies assume minimizing negative interactions (i.e., competition) between outplants will maximize propagule growth. Restoration experiments in both Western and Eastern Atlantic salt marshes demonstrate, however, that a simple change in planting configuration (placing propagules next to, rather than at a distance from, each other) results in harnessing facilitation and increased yields by 107% on average. Thus, small adjustments in restoration design may catalyze untapped positive species interactions, resulting in significantly higher restoration success with no added cost. As positive interactions between organisms commonly occur in coastal ecosystems (especially in more physically stressful areas like uncolonized substrate) and conservation resources are limited, transformation of the coastal restoration paradigm to incorporate facilitation theory may enhance conservation efforts, shoreline defense, and provisioning of ecosystem services such as fisheries production.shoreline defense | facilitation | coastal wetlands | wetland restoration D egradation of coastal ecosystems is occurring worldwide (1).Human-generated threats such as overharvesting, eutrophication, climate change, habitat destruction, and pollution have threatened these valuable ecosystems at local, regional and global scales (2-6). As these threats have intensified and combined, substantial declines in overall habitat coverage have occurred in almost all major coastal ecosystems, including those generated by key habitat-forming foundation species. For example, oyster reefs have declined by at least ∼85% (7), coral reefs by ∼19% (8), seagrasses by ∼29% (9), North American salt marshes by ∼42% (10), and mangroves by ∼35% (1). Because these ecosystems generate some of the richest biodiversity hotspots on Earth (11, 12), and provide critical services for human populations, including storm protection (13), fisheries production (2, 14, 15), and carbon storage (16, 17), conservation resources totaling over 1 billion US dollars have been spent globally in an attempt to halt and reverse the decline of foundation species in the coastal realm (18,19).A number of strategies have been used to conserve coastal ecosystems, including threat reduction, marine protected areas, buffer establishment, and international treaties. Habitat restoration, although in existence for many decades, has only recently been elevated as a global strategy for ...

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“…To assess the significance of changes in necrotic leaf area, we modeled our response variable-the percentage of necrotic leaf area-using beta regression with a logit link function, an extension of generalized linear modeling (Ferrari and Cribari-Neto 2004), implemented in R in the 'betareg' package (Cribari-Neto and Zeileis 2010). This analysis method is robust to heteroscedasticity and unbalanced designs.…”

Section: Statistical Analysesmentioning

confidence: 99%

Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf pathogen, Drepanopeziza populi

et al. 2013

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Abstract. Fungal leaf endophytes-nonpathogenic microfungi that live within plant leaves-are ubiquitous in land plants. Leaf endophytes and host plant genotypes may interact to determine plant disease severity. In a greenhouse inoculation experiment, we found that leaf endophyte species and Populus angustifolia genotypes both affected disease outcomes in plants inoculated with the necrotrophic leaf pathogen Drepanopeziza populi. Contrary to many studies showing endophytes conferring defense, all plant genotypes inoculated with the endophyte Penicillium sp. prior to inoculation with the pathogen D. populi were characterized by greater pathogen symptom severity than plants inoculated with the pathogen only. We quantified defense gene expression via qRT-PCR, but found no evidence that increased pathogen damage was related to differential expression of the assayed genes. A second endophyte, Truncatella angustata, which was previously found to reduce symptom severity of the biotrophic pathogen Melampsora in Populus trichocarpa, did not affect symptom severity of the necrotrophic pathogen D. populi or defense gene expression. Overall, our study highlights the variable effects of endophytes on pathogen symptom severity, and illustrates that plant genotypic variation can remain important for disease outcomes even in the presence of endophytes altering disease. Additional work is needed to elucidate the mechanism by which fungal leaf endophytes alter disease in their host plants.

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Beta Regression inR

Cited by 1,696 publications

References 30 publications

Genetic introgression of farmed salmon in native populations: quantifying the relative influence of population size and frequency of escapees

Genetic introgression of farmed salmon in native populations: quantifying the relative influence of population size and frequency of escapees

Facilitation shifts paradigms and can amplify coastal restoration efforts

Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf pathogen, Drepanopeziza populi

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