Randomization, Bootstrap and Monte Carlo Methods in Biology

By Andrew P. Robinson. 2007

708 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/0ee4eee78e9ee538c8091c769a214ddae04bb3e1

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Citations in the corpus

Dredging for edible cockles (Cerastoderma edule) on intertidal flats: short-term consequences of fisher patch-choice decisions for target and non-target benthic fauna (2007, methodology): “Observed values were then compared with bootstrapped values (Manly 1997).”
What is hot in tree rings? The wood density of surviving Douglas-firs to the 2003 drought and heat wave (2008, methodology): “In order to construct a reference distribution for each estimator (mean stem density, diameter growth and 7 ring variables times 17 years), from which inferences over D1 and D1ij could be made, we used a Monte-Carlo randomization approach (Mainly, 1997).”
Effect size, confidence interval and statistical significance: a practical guide for biologists (2007, background): “Thus, the interested reader is referred to Davison & Hinkley (1997) and Manly (2007).”
Rerandomization to improve covariate balance in experiments (2012, neutral): “…intervals and tests, for additive treatment effects a confidence interval can be produced from a randomization distribution as the set of all values for which the observed data would not reject such a null hypothesized value [Lehmann and Romano (2005); Manly (2007), Section 3.5, Section 1.4].”
Do we protect biological originality in protected areas? A new index and an application to the Bonifacio Strait Natural Reserve (2008, methodology): “We then compared the mean observed CBO index to the null distribution in order to obtain the p-value which was the type I error (probability of rejecting the null hypothesis whereas it is true (Manly, 1998)).”
Spatial ecology of the European wildcat in a Mediterranean ecosystem: dealing with small radio‐tracking datasets in species conservation (2009, methodology): “The significance of the difference between the obtained index value and zero (randomness) was evaluated by 1000 replicates’ bootstrap resampling (Manly, 1997) and by recalculating the Jacobs index for each bootstrap sample.”
Alternative height strategies among 45 dicot rain forest species from tropical Queensland, Australia (2005, methodology): “We tested first for significant heterogeneity among slopes for the two sets, by estimating a common slope (following Warton & Weber 2002) and permuting residuals from the common slope among groups (Manly 1997).”
Home range overlap, matrilineal and biparental kinship drive female associations in bottlenose dolphins (2010, methodology): “A partial Mantel test is an extension of the two-way Mantel test, which allows for the correlation of two variables while controlling for a third (Smouse et al. 1986; Manly 2001).”
Spatial variation in species diversity and composition of flea assemblages in small mammalian hosts: geographical distance or faunal similarity? (2005, methodology): “Following Poulin (2003), the significance of each regression model was tested using a randomization approach (Manly, 1997) using the RT 2.”
Network position: a key component in the characterization of social personality types (2012, neutral): “Following the usual definition of randomization tests (Manly 2007) for a given level α, we regard the value SV(R1) of our observed matrix R1 as significant, if it is among the m×α smallest values of the sequence SV(R1), SV(R2), .”
An Empirical Bayes Approach to Combining and Comparing Estimates of the Value of a Statistical Life for Environmental Policy Analysis (2006, positive): “Bootstrapping is equivalent to random sampling with replacement and is used to model the unknown real population (Manly 1997).”
Neonicotinoid clothianidin adversely affects insect immunity and promotes replication of a viral pathogen in honey bees (2013, methodology): “A randomization test was used to test the significance of the observed time-dependent pattern of Dmel\LRR expression after immune challenge (61).”
Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist. (2011, methodology): “undisturbed environments? Specifically, we may wish to test for a difference in the sizes of individual components; is b diversity at the scale of sites, r̂2sites, significantly larger (or smaller) in disturbed than in undisturbed environments? A direct multivariate analogue to the univariate two-ta”
Permutation inference for the general linear model (2014, background): “While the validity of parametric tests relies on random sampling, permutation tests have their justi ﬁ cation on the idea of random allocation of experimental units, with no reference to any underlying population (Edgington, 1995; Manly, 2007).”
Grouping Patterns and Competition Among Female Pan troglodytes schweinfurthii at Ngogo, Kibale National Park, Uganda (2008, neutral): “To validate statistically that the observed clusters were socially meaningful, I compared the mean DAI for females within and between each cluster and then conducted a resampling procedure with 5000 iterations for each cluster (Manly 1997).”
A new method for detecting and interpreting biodiversity and ecological community thresholds (2010, methodology): “1, Step 3; Manly 1997; Toms & Lesperance 2003).”
Continental‐scale spatial phylogenetics of Australian angiosperms provides insights into ecology, evolution and conservation (2016, background): “The rank position of each observed value relative to the random realizations is used to determine its significance level (Manly, 2006).”
Repeatability for Gaussian and non‐Gaussian data: a practical guide for biologists (2010, methodology): “Second, randomization procedures can be used to test the null-hypothesis RM = 0 against the alternative hypothesis RM > 0 (Manly, 2006).”