ViSiElse: An innovative R-package to visualize raw behavioral data over time

Garnier, Élodie; Fouret, Nastasia; Descoins, Médéric

doi:10.7287/peerj.preprints.27665v3

Cited by 13 publications

(14 citation statements)

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“…Since we included same year density as a control variable, we kept these models as is, despite high VIFs. Plots were generated using ggplot2 (Wickham, 2009), ggeffects (Lüdecke, 2018), and viridis (Garnier, 2018). All analysis and plotting were conducted in R v. 3.6.3 (R Development Core Team 2020).…”

Section: Methodsmentioning

confidence: 99%

Influence of delayed density and ultraviolet radiation on caterpillar baculovirus infection and mortality

Pepi¹,

Pan²,

Karban³

2021

Preprint

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Infectious disease is an important potential driver of population cycles, but this must occur through delayed density-dependent infection and resulting fitness effects. Delayed density-dependent infection by baculoviruses can be caused by environmental persistence of viral occlusion bodies, which can be influenced by environmental factors. In particular, ultraviolet radiation is potentially important in reducing the environmental persistence of viruses by inactivating viral occlusion bodies. Delayed density-dependent viral infection has rarely been observed empirically at the population level although theory predicts that it is necessary for these pathogens to drive population cycles. Similarly, field studies have not examined the potential effects of ultraviolet radiation on viral infection rates in natural animal populations. We tested if viral infection is delayed density-dependent with the potential to drive cyclic dynamics and if ultraviolet radiation influences viral infection. We censused 18 moth populations across nearly 9 degrees of latitude over two years and quantified the effects of direct and delayed density and ultraviolet radiation on granulovirus infection rate, infection severity, and survival to adulthood. Caterpillars were collected from each population in the field and reared in the laboratory. We found that infection rate, infection severity, and survival to adulthood exhibited delayed density-dependence. Ultraviolet radiation in the previous summer decreased infection severity, and increased survival probability of the virus. Structural equation modelling found that the effect of lagged density on moth survival was mediated through infection rate and infection severity, and was 2.5 fold stronger than the effect of ultraviolet radiation on survival through infection severity.

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Section: Methodsmentioning

confidence: 99%

Influence of delayed density and ultraviolet radiation on caterpillar baculovirus infection and mortality

Pepi¹,

Pan²,

Karban³

2021

Preprint

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“…Finally, we ordered blocks according to flowering sequence and we created one heat map (packages ‘ ggplot2 ’ and ‘ viridis ’, Wickham 2016, Garnier 2018) for each urban class with tiles coloured as a function of site density (i.e. the number of sites included at any time t i in a given block).…”

Section: Methodsmentioning

confidence: 99%

Urbanization drives an early spring for plants but not for pollinators

Fisogni

Hautekèete

Piquot

et al. 2020

Oikos

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Urbanization is one of the major threats to wild plants and pollinators, and its global increase demands a better understanding of the mechanism driving its negative impact. Urban warming and altered local environmental conditions have the potential to affect the timing of flowering and of pollinator activity. While previous evidence has shown that plant phenology tends to advance in urban areas, little is known about its effects on pollinator phenology. In this study we simultaneously assessed the response of the timing of flowering of native plants and of the flight period of wild pollinators to increased urbanization. We collected data from 12 sites along an urbanization gradient in northern France, a region under strong anthropogenic pressure. Overall, we recorded more than 70 plant species, and we sampled more than 4300 wild bees and hoverflies belonging to 154 species. Plant flowering showed a strong response to urbanization at the community level with a striking advancement of the flowering peak in sites at high urbanization. On the contrary, pollinator communities did not show any clear shift of their flight phenology along the gradient, neither regarding abundance nor diversity. Our results indicate that phenologies of plant and pollinator communities can respond differently along the same urbanization gradient. These asymmetric responses can drive modifications in the structure of plant–pollinator networks, and potentially negatively affect the fitness of both mutualistic partners.

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“…We also used R packages ape 55 , data.table 56 , dplyr 57 , ggplot2 58 , gridExtra 59 , mapdata 60 , plyr 61 , png 62 , RcolorBrewer 63 , rgdal 64 , raster 65 and viridis 66 .…”

Section: Methodsmentioning

confidence: 99%

Responses of global waterbird populations to climate change vary with latitude

Amano

Székely

Wauchope

et al. 2019

Preprint

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2While climate change continues to present a major threat to global biodiversity and 2 3 ecosystems, most research on climate change impacts do not have the resolution to detect 2 4 changes in species abundance and are often limited to temperate ecosystems. This limits our 2 5understanding of global responses in species abundance-a determinant of ecosystem 2 6 function and services-to climate change including in the highly-biodiverse tropics. We 2 7 address this knowledge gap by quantifying abundance responses to climate change in 2 8 waterbirds, an indicator taxon of wetland biodiversity, at 6,822 sites between -55° and 64°. 9Using 1,303,651 count records since 1990 of 390 species, we show that with temperature 3 0 increase, the abundance of species and populations decreased at lower latitudes, particularly 3 1 in the tropics, but increased at higher latitudes. These contrasting responses to temperature 3 2 increase according to latitude indicate potential global-scale poleward shifts of species 3 3 abundance under climate change, providing empirical support for predictions by earlier 3 4 studies. The negative responses to temperature increase in tropical species and populations 3 5are of conservation concern, as they are often also threatened by other anthropogenic factors. 6Our results suggest that existing biases in studies towards temperate regions could 3 7 underestimate the impact of climate change on waterbirds and other species.3 8 3 9 4 1 urgent need to understand how species respond to changing climates globally. A wide range 4 2 of species have already shown responses to climate change, such as changes in geographical 4 3 3 range 1 , phenology 2 and abundance 3 . However, the rate and direction of these responses vary 4 4 greatly among species and locations 1,2,4 . As climate-driven changes in biodiversity are 4 5 expected to affect ecosystem functioning, human well-being, and the dynamics of climate 4 6 change itself 5 , understanding how species' responses to climate change may vary globally 4 7 could provide crucial evidence for a more effective allocation of limited resources on a 4 8 priority basis for the conservation of species and ecosystems threatened the most by climate 4 9 change, and for assessing how climate-driven changes in biodiversity may affect human 5 0 societies. 5 1Existing gaps in the geographical coverage of available evidence seriously limit our 5 2 understanding of species' responses to climate change and its variations across the globe 6 . 3Earlier global reviews of species' responses to climate change have rarely incorporated 5 4 species and studies in the tropics, due to the lack of relevant information 7 . Such geographical 5 5 biases are even more prominent in studies investigating responses in species abundance 8,9 , 5 6 which is a major determinant of species extinction risk 10 , ecosystem function and services 11 . 7Research on abundance responses to climate change to date has largely been conducted in 5 8 Europe, North America and the Arctic 3,12-14 , with a rec...

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ViSiElse: An innovative R-package to visualize raw behavioral data over time

Cited by 13 publications

References 0 publications

Influence of delayed density and ultraviolet radiation on caterpillar baculovirus infection and mortality

Influence of delayed density and ultraviolet radiation on caterpillar baculovirus infection and mortality

Urbanization drives an early spring for plants but not for pollinators

Responses of global waterbird populations to climate change vary with latitude

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