Multiple Comparisons Using R


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Plot of adjusted p-values vs.

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Multiple Comparisons Using R

The dashed line represents a one-to-one line. Note that Holm and Hochberg have the same values as Hommel, and so are hidden by Hommel. Non-commercial reproduction of this content, with attribution, is permitted. For-profit reproduction without permission is prohibited. If you use the code or information in this site in a published work, please cite it as a source. Also, if you are an instructor and use this book in your course, please let me know. My contact information is on the About the Author page. This site uses advertising from Media. Multiple Comparisons in Parametric Models General linear models Extensions to general parametric models The multcomp package.

An R Companion for the Handbook of Biological Statistics

Applications Multiple comparisons with a control All pairwise comparisons Dose response analyses Variable selection in regression models Simultaneous confidence bands Multiple comparisons under heteroscedasticity Multiple comparisons in logistic regression models Multiple comparisons in survival models Multiple comparisons in mixed-effects models. Further Topics Resampling-based multiple comparison procedures Group sequential and adaptive designs Combining multiple comparisons with modeling.

He is also an adjunct professor at the Hannover Medical School in Germany. The book is primarily targeted at practitioners who will find the illustrative examples utilizing real data helpful.

Multiple Comparisons

Methodologically interested readers are provided with interesting concepts and a good survey on multiple comparisons literature in the bibliography. Nice stand-out features of the book are its clarity and conciseness, its coverage of group sequential and adaptive designs, and the nice illustration through actual problems using R software and the CRAN library of R routines for multiple testing. Chernick, Technometrics , August An excellent first chapter gently explains to the reader why multiple comparison techniques are required.

Successive chapters delve into more and more sophisticated scenarios for multiple comparisons. The benefits of applying multiple testing in the context of ordinary linear models are in my opinion not often stressed in undergraduate statistics courses. It was refreshing to see an entire chapter devoted to this idea. The over references make this an excellent entry point into the literature … Do consider it [the book] if you are a user of R, who is also a researcher or teacher of linear modelling, and needs to apply multiple comparisons in their work.

Your work will be the better for it. I found the book to be a rare gem; it is very seldom indeed that a reviewer has difficulty finding things to criticize. The book is concise, but covers all the common topics and a little more. It is simply written, yet manages to explain the key concepts remarkably well. In recent decades, alternative management techniques integrating conservation concerns into industrial forestry have become increasingly widespread.

In order to compare the effects of various management methods on forest site and biodiversity, a systematic forestry experiment was conducted in a managed, mature oak—hornbeam forest.

Multiple Comparisons Using R - MultXpert

The present work introduces the 2-year responses of environmental variables and understory vegetation to different silvicultural treatments. These belong either to clear-cutting clear-cutting, retention tree group , to shelterwood preparation cutting , or to continuous cover forestry systems gap-cutting. The experiment follows a complete block design with four replicates. Light availability was significantly higher in all the treatments than in the uncut control, with highest values in the clear-cuts. Soil moisture was highest in the gap-cuts and clear-cuts, while in the retention tree group, it did not differ from the control.

Species richness, cover, and height of the understory considerably differed from the control in the clear-cuts and gap-cuts, while in the retention tree group, only species richness was higher. The establishment of ruderal, non-forest species altered the species composition in the clear-cuts. Based on these short-term responses, we conclude that as a result of the extreme environmental changes, clear-cutting in oak—hornbeam forests changes the understory vegetation considerably.


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Retention tree groups can maintain legacies of the understory composition for some years. Despite the experienced high vegetation cover, gap-cutting preserves the forest characteristics of the understory better than clear-cutting. These results confirm that in oak—hornbeam forests, continuous cover forestry may be more sustainable from conservational aspect than clear-cutting system. To assess the overall significance of 'plant species' we compared the explanatory power of models including and excluding the fixed effect i.

Post-hoc Tukey tests were used to evaluate differences between plant species in ease of cracking and attractiveness to ants using the glht function in the R package 'multcomp' [22]. Non-foraging tool use in European Honey-buzzards: Examples of tool-use behaviors by birds outside foraging contexts are scarce and limited to a handful of species. We report a field experiment aimed to test whether an observed suite of odd behaviors by European Honey-buzzards Pernis apivorus represents use of green twigs cut from trees and woody shrubs as a tool to attract ants for anting.

Specifically, we tested whether buzzards are selective in their choice of twigs, under the assumption that birds would prefer easy-to-collect twigs from plants that effectively attract ants. Experimental results lend support to our hypothesis that European Honey-buzzards cut green twigs of Montpellier maple trees Acer monspessulanum and, to a lesser extent, of Pyrenean oaks Quercus pyrenaica for their immediate use as ant attractors.


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Fresh twigs of both tree species attracted large numbers of ants, suggesting that their preferential use in the reported behavior of Honey-buzzards is not a random selection of the available plant material. Maple twigs, however, were the easiest to break and oak twigs the hardest compared to other plants in the community.


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  5. This suggests that the relative ease of cracking of maple twigs may account for the preference Honey-buzzards have for this plant species as compared with Pyrenean oak, whose twigs demand considerable more effort from the birds to break. Our results lend support to the inclusion of the reported behavioral sequence by this raptor species as a potential example of tool use in birds outside the usual foraging context.

    Aerobiological behavior of Paleolithic decorated caves: The preservation of decorated caves is a great challenge that has been reinforced by the microbial crisis occurring at emblematic sites such as the Lascaux and Altamira caves. To date, little is known about the microbial behavior of caves. Past studies concentrated on caves with microbial disorders and were generally carried out in a time frame that was too short to gain an adequate picture of healthy microbial behaviors, the sine qua non of detecting potential imbalance.

    Multiple Comparisons in R

    The aim of this study was to determine whether models of aerobiological behavior could be identified in several decorated caves. We monitored aerial rates of fungi and bacteria in five decorated caves of the Gard department France for periods of 2 years or more. A model behavior was identified in each cave.

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