“compositions”: A unified R package to analyze compositional data

Boogaart, K. Gerald van den; Tolosana‐Delgado, Raimon

doi:10.1016/j.cageo.2006.11.017

Cited by 460 publications

(239 citation statements)

References 12 publications

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“…Also, estradiol enhances the amplitude of the TCF response in ovariectomized female mice [Jasnow et al, 2006]. TCF and EBC have similarities with respect to the cerebellar regions controlling the behaviors in mice, vermis and interposed nuclei in TCF [Sacchetti et al, 2002], simplex and adjacent HVI lobules and interposed nuclei in EBC [Van Der Giessen et al, 2008], and in addition the two behaviors are cooperatively controlled by amygdala and cerebellum [reviewed in Boele et al, 2010]. However, the modulation by sex hormones may extend to other cerebellar learning behaviors.…”

Section: Discussionmentioning

confidence: 99%

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Sex-Dependent Behavioral Functions of the Purkinje Cell-Specific Gαi/o Binding Protein, Pcp2(L7)

et al. 2012

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We previously reported motor and non-motor enhancements in a mouse mutant with an inactivated Purkinje cell-specific gene, Pcp2(L7), that encodes a GoLoco domain-containing modulator of Gi/o protein-coupled receptors. Effects included elevated learning asymptote with repeated rotarod training, increased acquisition rate in tone-conditioned fear (TCF), and subtle male-specific changes in both acoustic startle habituation and pre-pulse inhibition. We have further analyzed this mutant strain for higher-order behavioral alterations this time with a focus on male-female differences, and here we report a sex-dependent anxiety-like phenotype: male mutants are less anxious, and female mutants more anxious, than same-sex wild-types. Similarly, the fear responses measured during the tone in TCF acquisition are decreased in male mutants and increased in female mutants relative to same-sex wild-types. Overall the dynamics of both acquisition and extinction of TCF is affected in mutants but memory was not affected. Mutants display normal sociability and do not differ from wild-types in the social novelty test; however, compositional analysis supports that both L7 genotype and sex contribute to these behaviors. These results provide direct evidence of higher-order behavioral functions of the cerebellum due to the unambiguous cerebellar specificity of Pcp2(L7) expression, and the lack of any confounding motor defects in the mutant. We attempt to synthesize these new data with what is previously known both about Pcp2(L7) and about the effects of sex and sex hormones on anxiety and fear behaviors: specifically, L7 is a bidirectional and sex-dependent damper that regulates the amplitude and/or rate of sensorimotor responses, potentially acting as a mood stabilizer.

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Section: Discussionmentioning

confidence: 99%

“…Also, if confidence intervals do not span the midline, this indicates a side preference at the significance level of p ≤ 0.05. Analyses and graphical presentation were implemented in R, using the package “compositions” [van den Boogaart and Tolosana-Delgado 2008]. …”

Section: Methodsmentioning

confidence: 99%

Sex-Dependent Behavioral Functions of the Purkinje Cell-Specific Gαi/o Binding Protein, Pcp2(L7)

et al. 2012

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“…Within the R package universe, there are three standalone and well-documented tools for general compositional data analysis: 16 , 17 , and 18 . The function plots an archetypal balance dendrogram.…”

Section: Methodsmentioning

confidence: 99%

Visualizing balances of compositional data: A new alternative to balance dendrograms

Quinn

2018

F1000Res

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Balances have become a cornerstone of compositional data analysis. However, conceptualizing balances is difficult, especially for high-dimensional data. Most often, investigators visualize balances with the balance dendrogram, but this technique is not necessarily intuitive and does not scale well for large data. This manuscript introduces the 'balance' package for the R programming language. This package visualizes balances of compositional data using an alternative to the balance dendrogram. This alternative contains the same information coded by the balance dendrogram, but projects data on a common scale that facilitates direct comparisons and accommodates high-dimensional data. By stripping the branches from the tree, 'balance' can cleanly visualize any subset of balances without disrupting the interpretation of the remaining balances. As an example, this package is applied to a publicly available meta-genomics data set measuring the relative abundance of 500 microbe taxa.

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“…Data preparation, transformations, statistical procedure and plot drawings used the free R software (R Core Team 2008), with the FactoMineR (Lê et al 2008), compositions (Van den Boogaart and Tolosana-Delgado 2008), hotteling (Curran 2013) and ggplot2 packages (Wickham 2009). Mapping used the Quantum GIS free software (QGIS Development Team 2010).…”

Section: Methodsmentioning

confidence: 99%

Impact of nickel mining in New Caledonia assessed by compositional data analysis of lichens

Pasquet¹,

Monier

Monna

et al. 2016

SpringerPlus

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The aim of this study is to explore the use of lichens as biomonitors of the impact of nickel mining and ore treatment on the atmosphere in the New Caledonian archipelago (South Pacific Ocean); both activities emitting also Co, Cr and possibly Fe. Metal contents were analysed in thirty-four epiphytic lichens, collected in the vicinity of the potential sources, and in places free from known historical mining. The highest Ni, Co, and Cr concentrations were, as expected, observed in lichens collected near ore deposits or treatment areas. The elemental composition in the lichens was explored by multivariate analysis, after appropriately transforming the variables (i.e. using compositional data analysis). The sample score of the first principal component (PC1) makes the largest (positive) multiplicative contribution to the log-ratios of metals originating from mining activities (Ni, Cr, Co) divided by Ti. The PC1 scores are used here as a surrogate of pollution levels related to mining and metallurgical activity. They can be viewed as synthetic indicators mapped to provide valuable information for the management and protection of ecosystems or, as a first step, to select locations where air filtration units could be installed, in the future, for air quality monitoring. However, as this approach drastically simplifies the problem, supplying a broadly efficient picture but little detail, recognizing the different sources of contamination may be difficult, more particularly when their chemical differences are subtle. It conveys only relative information: about ratios, not levels, and is therefore recommended as a preliminary step, in combination with close examination of raw concentration levels of lichens. Further validation using conventional air-monitoring by filter units should also prove beneficial.

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“compositions”: A unified R package to analyze compositional data

Cited by 460 publications

References 12 publications

Sex-Dependent Behavioral Functions of the Purkinje Cell-Specific Gαi/o Binding Protein, Pcp2(L7)

Sex-Dependent Behavioral Functions of the Purkinje Cell-Specific Gαi/o Binding Protein, Pcp2(L7)

Visualizing balances of compositional data: A new alternative to balance dendrograms

Impact of nickel mining in New Caledonia assessed by compositional data analysis of lichens

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