Hierarchical generalized additive models in ecology: an introduction with mgcv

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

doi:10.7717/peerj.6876

Cited by 677 publications

(733 citation statements)

References 44 publications

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“…Seasonal patterns in mean monthly depth data, and diel patterns in the hourly depth data, from the twenty individuals were assessed using a GAMM with individual (animal ID) included as random effects. An AR1 correlation structure was utilised with the corCAR1 function in the 'nlme' package [82] to account for autocorrelation in the seasonal and diel depth data [83].…”

Section: Discussionmentioning

confidence: 99%

Sex-based differences in movement and space use of the blacktip reef shark, Carcharhinus melanopterus

et al. 2020

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Information on the spatial ecology of reef sharks is critical to understanding life-history patterns, yet gaps remain in our knowledge of how these species move and occupy space. Previous studies have focused on offshore reefs and atolls with little information available on the movement and space use of sharks utilising reef habitats closer to shore. Cross-shelf differences in physical and biological properties of reefs can alter regional ecosystem processes resulting in different movement patterns for resident sharks. Passive acoustic telemetry was used to examine residency, space use and depth use of 40 blacktip reef sharks, Carcharhinus melanopterus, on an inshore reef in Queensland, Australia, and assess temporal or biological influences. All sharks showed strong site-attachment to inshore reefs with residency highest among adult females. Sharks exhibited a sex-based, seasonal pattern in space use where males moved more, occupied more space and explored new areas during the reproductive season, while females utilised the same amount of space throughout the year, but shifted the location of the space used. A positive relationship was also observed between space use and size. There was evidence of seasonal site fidelity and long-distance movement with the coordinated, annual migration of two adult males to the study site during the mating season. Depth use was segregated with some small sharks occupying shallower depths than adults throughout the day and year, most likely as refuge from predation. Results highlight the importance of inshore reef habitats to blacktip reef sharks and provide evidence of connectivity with offshore reefs, at least for adult males. OPEN ACCESSCitation: Schlaff AM, Heupel MR, Udyawer V, Simpfendorfer CA (2020) Sex-based differences in movement and space use of the blacktip reef shark, Carcharhinus melanopterus. PLoS ONE 15 (4): e0231142. https://doi.org/10.

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Section: Discussionmentioning

confidence: 99%

Sex-based differences in movement and space use of the blacktip reef shark, Carcharhinus melanopterus

et al. 2020

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“…Initial exploratory examination of pupillary dilation after stimulation was done using generalized additive models (GAMs), fitting smooth functions (spline-based) to pupil size against time, with stimulus intensity, stimulus type (mechanical or chemical) and sex as predictor variables. This was done using the MGCV package in R [44,45]. Non-linear mixed effect models were fit to pupil size against time functions, using the SAEMIX package in R [44], and non-linear regression was done in SPSS for Windows, Version 16.0 (Chicago, SPSS Inc.).…”

Section: Analysesmentioning

confidence: 99%

Pupil response to noxious corneal stimulation

Alabi

Simpson

2020

PLoS ONE

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Ocular somatosensory-autonomic reflexes play critical roles in maintaining homeostasis of the eye. The purpose of this study was to investigate the pupil response to nociceptive corneal stimuli. Methods A Waterloo-Belmonte pneumatic esthesiometer was used to determine detection thresholds and randomly deliver mechanical and chemical stimuli from levels of detection threshold to twice the threshold in 50% steps to the central cornea of 15 healthy subjects. For each stimulus, imaging of the stimulated/unstimulated eye was performed using two modified/calibrated Logitech c920 digital cameras for 4 seconds each, pre/post stimulus capture. The data were processed with a custom segmentation algorithm to help identify the pupils and pupil diameter was measured using ImageJ software. Pupil dilation response differences between the ipsi-and contralateral eye was analyzed using dependent t-tests. The effect of stimulus intensity, modality and sex of subjects were analyzed using repeated measures. Results In mechanical and chemical stimulation experiments, there was no difference in pupil responses between the stimulated eye and the unstimulated eye, (all dependent T-test p > 0.05). On average, pupil diameter increased from baseline as the corneal stimulus intensity increased. This happened regardless of whether mechanical or chemical stimulation occurred (ANOVA p < 0.05). At 200% threshold, pupil diameter was greater than at all stimulus intensities (Tukey HSD, all p < 0.05). Based on stimulus intensity, females had greater pupil diameters than males at levels of 150% threshold and 200% threshold (ANOVA p < 0.05, all Tukey HSD p < 0.05). Conclusion This study serves as a basis for the characterization of the local stimulus-response neural circuitry relating nociceptive stimuli to autonomic responses and in combination with our work on completely separate autonomic circuits of bulbar conjunctival vessel dilation and

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“…Our goals were (1) to identify major gain and loss motifs, (2) to determine whether there was significant site-to-site variation in weight pattern, and (3) to determine whether there was sufficient similarity across sites to justify a global weight model. Accordingly, we constructed three nested hierarchical GAMs, following Pedersen et al (2019) .…”

Section: Weight Monitoring and Pattern Characterizationmentioning

confidence: 99%

Characterizing the floral resources of a North American metropolis using a honey bee foraging assay

Sponsler

Shump²,

Richardson

et al. 2019

Preprint

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AbstractRoughly a third of described insect species visit flowers, making the flower-insect interface one of the chief pillars of global biodiversity. Studying flower-insect relationships at the scale of communities and landscapes has been hindered, however, by the methodological challenges of quantifying landscape-scale floral resources. This challenge is especially acute in urban landscapes, where traditional floral surveying techniques are ill-suited to the unique constraints of built environments. To surmount these challenges, we devised a “honey bee foraging assay” approach to floral resource surveying, wherein continuous colony weight tracking and DNA metabarcoding of pollen samples are used to capture both the overall availability and taxonomic composition of floral resources. We deploy this methodology in the complex urban ecosystem of Philadelphia, PA, U.S. Our results reveal distinct seasonality of floral resource availability, with pulses of high availability in May, June, and September, and a period of prolonged scarcity in August. Pollen genus richness mirrored this pattern, with peak richness in May and June. The taxonomic composition of pollen samples varied seasonally, reflecting underlying floral phenology, with especially strong turnover between May and June samples and between August and September samples delineating well-defined spring, summer, and fall floral resource communities. Trait analysis also revealed marked seasonal structure, with spring samples characterized by trees and shrubs, summer samples including a stronger presence of herbaceous “weeds”, and fall samples dominated by woody vines. Native flora predominated in spring, giving way to a preponderance of exotic flora in summer and fall. Our study provides a detailed portrait of floral resources in a complex urban environment. At a basic level, this yields insight into the assembly of novel urban floral resource communities, showcasing, for example, the emergence of a woody-vine-dominated fall flora. At an applied level, our data can inform urban land management, such as the design of ecologically functional ornamental plantings, while also providing practical guidance to beekeepers seeking to adapt their management activities to floral resource seasonality. Methodologically, our study demonstrates the potential of the honey bee foraging assay as an efficient and standardizable technique for landscape-scale floral resource surveying.

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Hierarchical generalized additive models in ecology: an introduction with mgcv

Cited by 677 publications

References 44 publications

Sex-based differences in movement and space use of the blacktip reef shark, Carcharhinus melanopterus

Sex-based differences in movement and space use of the blacktip reef shark, Carcharhinus melanopterus

Pupil response to noxious corneal stimulation

Characterizing the floral resources of a North American metropolis using a honey bee foraging assay

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