R package for animal behaviour classification from accelerometer data - rabc

Yu, Hui; Klaassen, Marcel

doi:10.22541/au.160594403.36425983/v1

Cited by 5 publications

(6 citation statements)

References 18 publications

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“…iterations and 5000-step burn-in using the R package R2Jags (Yu & Yajima, 2012), using the data augmentation method of Royle et al (2007) (Royle et al, 2007). We confirmed the model's fit…”

Section: Population Sizesupporting

confidence: 61%

Long‐term data reveal fitness costs of anthropogenic prey depletion for a subordinate competitor, the African wild dog (Lycaon pictus)

Reyes de Merkle,

Creel,

Becker

et al. 2024

Ecology and Evolution

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Within carnivore guilds, dominant competitors (e.g., lions, Panthera leo) are limited primarily by the density of prey, while subordinate competitors (e.g., African wild dogs, Lycaon pictus) have been limited by the density of dominant competitors. Historically, the fitness and population density of subordinate competitors have not been tightly linked to prey density. However, populations of large herbivores have declined substantially across sub‐Saharan Africa due to human impacts, and where prey depletion is severe, fitness costs for competitive subordinates may begin to outweigh the benefits of competitive release. Using long‐term intensive monitoring of African wild dogs in Zambia's Luangwa Valley Ecosystem (LVE), we tested the effects of prey depletion on survival and reproduction. We hypothesized that African wild dog fitness would be lower in prey‐depleted areas, despite lower lion densities. Our study area included four contiguous regions that varied in protection level, prey density, and lion density. We fit Bayesian Cormack–Jolly–Seber and closed‐capture models to estimate effects on survival and population density, and generalized linear models to estimate effects on reproductive success. We found that the LVE is a stronghold for African wild dogs, with an estimated median density of 4.0 individuals/100 km2. Despite this high density, survival and reproduction differed among regions, and both components of fitness were substantially reduced in the region with the lowest prey density. Anthropogenic prey depletion is becoming an important limiting factor for African wild dogs. If prey depletion (or any other form of habitat degradation) becomes severe enough that its fitness costs outweigh the benefits of competitive release, such changes can fundamentally alter the balance between limiting factors for competitively subordinate species.

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“…iterations and 5000-step burn-in using the R package R2Jags (Yu & Yajima, 2012), using the data augmentation method of Royle et al (2007) (Royle et al, 2007). We confirmed the model's fit…”

Section: Population Sizesupporting

confidence: 61%

Long‐term data reveal fitness costs of anthropogenic prey depletion for a subordinate competitor, the African wild dog (Lycaon pictus)

Reyes de Merkle,

Creel,

Becker

et al. 2024

Ecology and Evolution

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“…A website Venn diagrams tool ( Bardou et al, 2014 ) 3 was used to identify the commonly upregulated or downregulated DEGs in the immune and stromal groups. Heatmaps and clustering were generated using the R package “ggplot2” ( Wickham, 2016 ), “ggtree” ( Yu, 2020b ), and “aplot” ( Yu, 2020a ).…”

Section: Methodsmentioning

confidence: 99%

Identification of Prognostic Stromal-Immune Score–Based Genes in Hepatocellular Carcinoma Microenvironment

Liu

et al. 2021

Front. Genet.

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A growing amount of evidence has suggested the clinical importance of stromal and immune cells in the liver cancer microenvironment. However, reliable prognostic signatures based on assessments of stromal and immune components have not been well-established. This study aimed to identify stromal-immune score–based potential prognostic biomarkers for hepatocellular carcinoma. Stromal and immune scores were estimated from transcriptomic profiles of a liver cancer cohort from The Cancer Genome Atlas using the ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumors using Expression data) algorithm. Least absolute shrinkage and selection operator (LASSO) algorithm was applied to select prognostic genes. Favorable overall survivals and progression-free interval were found in patients with high stromal score and immune score, and 828 differentially expressed genes were identified. Functional enrichment analysis and protein–protein interaction networks further showed that these genes mainly participated in immune response, extracellular matrix, and cell adhesion. MMP9 (matrix metallopeptidase 9) was identified as a prognostic tumor microenvironment–associated gene by using LASSO and TIMER (Tumor IMmune Estimation Resource) algorithms and was found to be positively correlated with immunosuppressive molecules and drug response.

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“…Based on the NMDS analysis, we assigned strains to effector clusters, which were plotted on a worldwide map with the packages 'ggplot2' and 'scatterpie' 110,111 . The map was created in R with the packages 'cowplot', 'ggrepel', 'ggspatial', 'libwgeom', 'sf', 'rgeos', 'memisc', 'oz', 'maptools' and 'rnaturalearth' with the function 'ne_countries' 109,[112][113][114][115][116][117][118][119] .…”

Section: Core Gene Phylogenymentioning

confidence: 99%

Intercontinental dissemination and diversification ofXanthomonas perforansin tomato production

Timilsina,

Iruegas-Bocardo,

Jibrin

et al. 2024

Preprint

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Tomato is a high value crop that requires quality seed each season. Tomato production often relies on international breeding and production chains with a global network to deliver seeds to growers. Xanthomonas perforans, one of the causal agents of bacterial spot of tomato, is seedborne and has rapidly emerged and displaced other bacterial spot xanthomonads in tomato production regions around the world. The objectives of this work were to determine if different tomato production regions contain genetically distinct X. perforans populations, examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, estimate the timing of X. perforans population expansion relative to its first report in 1991, and evaluate variation in type III effectors, which are critical pathogenicity and virulence factors. Our results showed extensive genetic diversity in the pathogen and highly similar strains in distant tomato production regions, which is consistent with global dissemination. Furthermore, we found genetically similar strains in tomato seed production and fruit production regions, as would be expected if the pathogen was being moved through tomato production chains from a common origin. We found waves of diversification of populations in the United States, where our sampling was more extensive, before and since its first detection, consistent with emergence of new X. perforans genotypes from diverse source populations. Variation in gene content, including effector genes, within and between core genome lineages suggests the potential for rapid changes to the accessory genome upon dissemination. Evolution of the X. perforans pangenome, including the acquisition and loss of type III secreted effectors, will continue to challenge sustainable management of tomato bacterial spot.

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R package for animal behaviour classification from accelerometer data - rabc

Cited by 5 publications

References 18 publications

Long‐term data reveal fitness costs of anthropogenic prey depletion for a subordinate competitor, the African wild dog (Lycaon pictus)

Long‐term data reveal fitness costs of anthropogenic prey depletion for a subordinate competitor, the African wild dog (Lycaon pictus)

Identification of Prognostic Stromal-Immune Score–Based Genes in Hepatocellular Carcinoma Microenvironment

Intercontinental dissemination and diversification ofXanthomonas perforansin tomato production

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