statmod: Probability Calculations for the Inverse Gaussian Distribution

Giner, Göknur; Smyth, Gordon K.

doi:10.32614/rj-2016-024

Cited by 106 publications

(72 citation statements)

References 17 publications

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“…Subsequently, we estimated the mean-variance relationship and calculated weights for each observation. To account for the correlation between technical replicates of the same clone when performing the differential analysis, we fit a mixed linear model, using the function "duplicateCorrelation" from the statmod R package (45) to block on clone. The differential analysis was then performed using the limma R package.…”

Section: Methodsmentioning

confidence: 99%

Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome

Carosso¹,

Boukas²,

Augustin³

et al. 2019

JCI Insight

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Section: Methodsmentioning

confidence: 99%

Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome

Carosso¹,

Boukas²,

Augustin³

et al. 2019

JCI Insight

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“…The significance of each explanatory term was tested using a Wald test (Luke, 2017) and looking at confidence intervals on the estimates. Homoscedasticity, independence and normality of residues were checked for each model (package statmod; Giner & Smyth, 2016). The absence of spatial autocorrelation in the residuals of the final models has been assessed based on Moran's I values and associated P values for each model using the ncf package (Bjornstad, 2018).…”

Section: Analysis Of Geographical and Climatic Rangesmentioning

confidence: 99%

Range limits in sympatric cryptic species: a case study in Tetramorium pavement ants (Hymenoptera: Formicidae) across a biogeographical boundary

Cordonnier

Bellec

Dumet

et al. 2018

Insect Conserv Diversity

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In the context of climate changes, factors that determine the distribution patterns of European species of the ubiquitous ant genus Tetramorium were investigated. The study took place along a steep North‐South climatic gradient across the boundary between the European Continental and Mediterranean biogeographical regions spanning 460 km along the Rhône valley, France. Ants from 1690 Tetramorium colonies were collected in 19 sampling zones. Species were identified using an integrative approach based on a two‐step process combining nuclear DNA (14 microsatellite markers), morphological examination and mitochondrial DNA cytochrome oxidase I sequencing. The impact of climate on species distribution patterns was tested using bioclimatic variables. Species discrimination was successful, despite a complex situation with cryptic species, inter‐specific hybridisation and uneven sampling across species. Our results showed a strong effect of latitude, temperature and rainfall on the distribution of three of four species. Tetramorium semilaeve was found only south of the boundary, in warmer and dryer sites; Tetramorium caespitum extended north and 70 km south of the boundary and favoured colder sites with strong seasonal variation. Tetramorium immigrans was absent from the northernmost sampling zones and favoured warmer and wetter sites. Tetramorium moravicum was mostly found close to the boundary, but without significant climatic preferences. The fundamental role of climate as a factor limiting the ranges of these species at a major biogeographical boundary is confirmed. Monitoring range limits of these strongly climate‐dependant species may offer exciting insights on the impact of climate changes on species distributions.

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“…In our models we also consider more standard interactions between log(p), log(GDP) and S(T ) > 0. To assess if model assumptions were adequately met we computed and plotted the randomized quantile residuals (RQRs), implemented in the statmod package (Giner and Smyth, 2016). RQRs are based on the idea of inverting the estimated distribution function for each observation to obtain standard normal residuals if model assumptions are met and the model fits adequately.…”

Section: Model Validationmentioning

confidence: 99%

Temperature impacts the transmission of malaria parasites byAnopheles gambiaeandAnopheles stephensimosquitoes

Villena

Ryan

Murdock

et al. 2020

Preprint

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Transmission of malaria and other vector-borne diseases (VBDs) is greatly influenced by environmental factors, especially temperature, due to the ectothermic nature of insect and arthropod vectors. However, the response of transmission to temperature and other drivers is complex, as thermal traits of ectotherms are typically non-linear, and they interact to determine transmission constraints. In this study, we assess and compare the effect of temperature on the transmission of two malaria parasites, Plasmodium falciparum and Plasmodium vivax, by two malaria vector species, Anopheles gambiae and Anopheles stephensi. We model the non-linear responses of temperature dependent mosquito and parasite traits (mosquito development rate, bite rate, fecundity, egg to adult survival, vector competence, mortality rate, and parasite development rate) and incorporate these traits into a suitability metric based on a model for the basic reproductive number across temperatures. Our model predicts that the optimum temperature for transmission suitability is similar for the four mosquito-parasite combinations assessed in this study. The main differences are found at the thermal limits. More specifically, we found significant differences in the upper thermal limit between parasites spread by the same mosquito (An. stephensi) and between mosquitoes carrying P. falciparum. In contrast, at the lower thermal limit the significant differences were primarily between the mosquito species that both carried the same pathogen (e.g., An. stephensi and An. gambiae both with P. falciparum). Using prevalence data from Africa and Asia, we show that the transmission suitability metric S(T) calculated from our mechanistic model is an important predictor of malaria prevalence. We mapped risk to illustrate the areas in Africa and Asia that are suitable for malaria transmission year-round based temperature. The wider thermal range of transmission by An. stephensi for both malaria parasites allows for a greater geographic potential for malaria spread. This study could be useful in planing preventive strategies for areas where malaria outbreaks might occur.

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statmod: Probability Calculations for the Inverse Gaussian Distribution

Cited by 106 publications

References 17 publications

Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome

Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome

Range limits in sympatric cryptic species: a case study in Tetramorium pavement ants (Hymenoptera: Formicidae) across a biogeographical boundary

Temperature impacts the transmission of malaria parasites byAnopheles gambiaeandAnopheles stephensimosquitoes

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