Randomization, Bootstrap and Monte Carlo Methods in Biology

Manly, Bryan F. J.; Alberto, Jorge

doi:10.1201/9780429329203

Cited by 167 publications

(200 citation statements)

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“…The permutation scheme can be adapted in different ways to obtain approximate exchangeability. Freedman and Lane () proposed to permute the estimated residuals from the model under the null hypothesis (also referred to as the reduced model); ter Braak () proposed to permute residuals of the full model; other authors (Manly, ; Oja, ) propose to permute other quantities, such as the covariates' values, or the responses. Anderson and Robinson () compared Freedman and Lane's methodology and other approaches by a simulation study, concluding that the Freedman and Lane permutation scheme gives the best empirical results in terms of the power and the size of the test.…”

Section: Introductionsupporting

confidence: 94%

A permutation approach to the analysis of spatiotemporal geochemical data in the presence of heteroscedasticity

et al. 2019

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This paper proposes a novel nonparametric approach to model and reveal differences in the geochemical properties of the soil, when these are described by space-time measurements collected in a spatial region naturally divided into two parts. The investigation is motivated by a real study on a space-time geochemical data set, consisting of measurements of potassium chloride pH, water pH, and percentage of organic carbon collected during the growing season in the agricultural and forest areas of a site near Brno (Czech Republic). These data are here modeled as spatially distributed functions of time. A permutation approach is introduced to test for the effect of covariates in a spatial functional regression model with heteroscedastic residuals. In this context, the proposed method accounts for the heterogeneous spatial structure of the data by grounding on a permutation scheme for estimated residuals of the functional model. Here, a weighted least squares model is fitted to the observations, leading to asymptotically exchangeable and, thus, permutable residuals. An extensive simulation study shows that the proposed testing procedure outperforms the competitor approaches that neglect the spatial structure, both in terms of power and size. The results of modeling and testing on the case study are shown and discussed.KEYWORDS edge effect on soil, functional data, functional regression, geostatistics, nonparametric inference Environmetrics. 2019;e2611.wileyonlinelibrary.com/journal/env

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Section: Introductionsupporting

confidence: 94%

A permutation approach to the analysis of spatiotemporal geochemical data in the presence of heteroscedasticity

et al. 2019

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“…We tested whether the patterns described above were due to chance with a randomization analysis (Manly ). First, we calculated the sum of the squared residuals from fitting the polynomial cubic model to the

\overset{w_{i}}{true}

vs. (

italicDS - \overset{w_{i}}{true}

) data (e.g., Fig.…”

Section: Resultsmentioning

confidence: 99%

Response of small sharks to nonlinear internal waves

Pineda

Rouse

Starczak

et al. 2019

Limnology & Oceanography

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Plankton and nekton may respond passively or actively to large-amplitude, nonlinear internal waves (NLIW), with periods and wavelengths on the order of minutes and hundreds of meters, and the NLIW can cause direct or indirect changes in distribution. NLIW are ubiquitous in the coastal ocean, but understanding the influence of NLIW on organism response and distribution is challenging, because of NLIW unpredictability, short temporal and spatial scales, and the difficulty in resolving the biological response. Measurements of currents, temperature, and shark acoustic traces in Massachusetts Bay were used to evaluate the short-term response of individuals as well as the mean effects on the distribution of an aggregation of small sharks, Squalus acanthias. In two NLIW events, we detected 527 and 3240 shark traces. Individuals moved up and down in response to the currents associated with the sinking and rising of the thermocline. However, mean distribution deepened during one of the events, suggesting that organisms did not merely move in concert with the thermocline oscillation, but that sharks instead might have responded actively. Measurements of vertical currents and shark's depth change during one of the NLIW events indicate that with downward currents (sinking of the thermocline), the sharks tend to react passively. However, in response to the fastest upward currents, sharks appeared to swim down, supporting an active response in the rising phase of the wave. NLIW and other high-frequency processes can have a profound influence on the distribution of pelagic organisms, yet their ecological consequences remain largely unaccounted for.

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“…The mean growth rate and survival percentages for each size category were calculated in the three experiments. Because neither the linear extension rates nor the weight increment data showed homoscedasticity (Levene's test; p < 0.05) or normality of the residuals (Shapiro–Wilks test; p < 0.05), comparisons of growth rates between size classes and between experiments were performed with a randomized one‐way analysis of variance (ANOVA) (10,000 randomizations) using the Manly approach () for unequal variances.…”

Section: Methodsmentioning

confidence: 99%

Coral reef restoration in the Eastern Tropical Pacific: feasibility of the coral nursery approach

Ishida‐Castañeda

Pizarro

López‐Victoria

et al. 2019

Restoration Ecology

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Due to the worldwide degradation of coral reefs, the active restoration of these ecosystems has received considerable attention in recent decades. This study investigated (1) the feasibility of using coral nurseries for restoration projects, (2) the minimum size required for a Pocillopora damicornis (Pocilloporidae) coral fragment to survive and grow in a nursery, and (3) the optimal transplant size of a fragment when transplanted to a degraded reef at Gorgona Island (Colombian Pacific). For this investigation, 230 fragments were transplanted directly to El Remanso reef, and another 150 fragments were maintained in in situ nurseries. Every 2 months, the length, weight, and survival of the fragments were recorded. After growing for 134 days in the nurseries, the 52 surviving fragments were transplanted to El Remanso reef, and after 5 months, the same variables were measured. Among the nursery-reared fragments, the largest (4 to <8 cm) had the highest survival and growth rates, whereas among the directly transplanted fragments, the smallest fragments (<2 cm) had the highest survival and growth rates. However, the nursery-reared fragments acquired greater structural complexity (arborescent morphology), and they were all alive 156 days after transplantation and presented a maximum linear growth rate of over 2 cm, which was higher than that of the directly transplanted fragments. Apparently, the arborescent morphology acquired during the nursery period provides advantages to the colonies that favor greater success when transplanted. Therefore, nursery-reared fragments of P. damicornis between 2 and 4 cm are the most appropriate for use in restoration projects.

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Randomization, Bootstrap and Monte Carlo Methods in Biology

Cited by 167 publications

References 0 publications

A permutation approach to the analysis of spatiotemporal geochemical data in the presence of heteroscedasticity

A permutation approach to the analysis of spatiotemporal geochemical data in the presence of heteroscedasticity

Response of small sharks to nonlinear internal waves

Coral reef restoration in the Eastern Tropical Pacific: feasibility of the coral nursery approach

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