Compositional Data Analysis in Practice

Greenacre, Michael

doi:10.1201/9780429455537

Cited by 153 publications

(168 citation statements)

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“…The objective is to define a set of FA ratios that adequately describe the FA compositional data set, which are acceptable from both a biological and a statistical point of view. The statistical methodology has been described and justified in detail in an archeometric application by Greenacre (, ). Here we give a summary of the main features of this new analytical approach and the steps involved in the selection of the FA ratios.…”

Section: Methodsmentioning

confidence: 99%

“…Logratios make sense for multivariate analysis as well, as demonstrated by various publications promoting logratio analysis (LRA) as the appropriate way to ordinate compositional data (Aitchison , ; Aitchison and Greenacre ; Greenacre and Lewi ; Pawlowsky‐Glahn and Buccianti ; Greenacre , ). LRA involves analyzing all the pairwise logratios in a global analysis, including optional weights for the FAs that are by default proportional to their mean percentage.…”

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confidence: 99%

“…PCA, on the other hand, suffers severely from a lack of subcompositional coherence (Greenacre ). For example, a covariance or correlation between FAs changes in the presence (or absence) of other FAs, after renormalization of the percentages—for example, see Greenacre (). Since PCA, for example, is an analysis of the covariance or correlation matrix, this rules out PCA as a suitable multivariate method to analyze FA data.…”

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confidence: 99%

“…A strategy is thus necessary to replace zeros in a data set with appropriate positive values, for example, half the corresponding detection limit, or another fraction of it (see, e.g., Palarea‐Albaladejo et al and references therein). Greenacre () shows how a sensitivity analysis can be performed on a data set which is subjected to varying small values used to replace the zeros. Alternatively, the CA approach can be used (Greenacre , ), adopted by Stewart (), because CA has no problems with analyzing data zeros—in fact, it is the ability of CA to handle large sparse data matrices (i.e., data with a very high percentage of zero values) that makes it a method of choice in ecological data analysis as well as in archeology and linguistics.…”

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confidence: 99%

“…Few authors have used the logratio approach in FA analysis, although it is extensively used in the geochemical literature (e.g., see the journal Mathematical Geosciences , formerly Mathematical Geology , for many publications). In the FA literature Neubauer and Jensen () consider how to select FAs that discriminate between predator diets in a controlled experiment, using centered logratios, that is, the logarithms of each FA divided by the geometric mean of all the FAs, computed for each individual (for an introduction to logratio transformations and analysis from a practitioner's viewpoint, see Greenacre ). Werker and Hall () measure a subset of 10 FAs in an experiment and display logratios of nine of them relative to the most frequent one, 16:0, which are called additive logratios (Aitchison ).…”

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confidence: 99%

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The selection and analysis of fatty acid ratios: A new approach for the univariate and multivariate analysis of fatty acid trophic markers in marine pelagic organisms

Graeve

Greenacre

2020

Limnology & Ocean Methods

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Fatty acid (FA) compositions provide insights about storage and feeding modes of marine organisms, characterizing trophic relationships in the marine food web. Such compositional data, which are normalized to sum to 1, have values-and thus derived statistics as well-that depend on the particular mix of components that constitute the composition. In FA studies, if the set of FAs under investigation is different in two separate studies, all the summary statistics and relationships between the FAs that are common to the two studies are artificially changed due to the normalization, and thus incomparable. Ratios of FAs, however, are invariant to the particular choice of FAs under consideration-they are said to be subcompositionally coherent. Here, we document the collaboration between a biochemist (M.G.) and a statistician (M.J.G.) to determine a suitable small set of FA ratios that effectively replaces the original data set for the purposes of univariate and multivariate analysis. This strategy is applied to two FA data sets, on copepods and amphipods, respectively, and is widely applicable in other contexts. The selection of ratios is performed in such a way as to satisfy substantive requirements in the context of the respective data set, namely to explain phenomena of interest relevant to the particular species, as well as the statistical requirement to explain as much variance in the FA data set as possible. Benefits of this new approach are (1) univariate statistics that can be validly compared between different studies, and (2) a simplified multivariate analysis of the reduced set of ratios, giving practically the same results as the analysis of the full FA data set.

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Section: Methodsmentioning

confidence: 99%

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The selection and analysis of fatty acid ratios: A new approach for the univariate and multivariate analysis of fatty acid trophic markers in marine pelagic organisms

Graeve

Greenacre

2020

Limnology & Ocean Methods

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Correlated evolution of dispersal traits and habitat preference in the melicgrasses

Brightly,

Bedoya,

Carlson

et al. 2024

American J of Botany

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PremiseSeed dispersal is a critical process impacting individual plants and their communities. Plants have evolved numerous strategies and structures to disperse their seeds, but the evolutionary drivers of this diversity remain poorly understood in most lineages. We tested the hypothesis that the evolution of wind dispersal traits within the melicgrasses (Poaceae: Meliceae Link ex Endl.) was correlated with occupation of open and disturbed habitats.MethodsTo evaluate wind dispersal potential, we collected seed dispersal structures (diaspores) from 24 melicgrass species and measured falling velocity and estimated dispersal distances. Species’ affinity for open and disturbed habitats were recorded using georeferenced occurrence records and land cover maps. To test whether habitat preference and dispersal traits were correlated, we used phylogenetically informed multilevel models.ResultsMelicgrasses display several distinct morphologies associated with wind dispersal, suggesting likely convergence. Open habitat taxa had slower‐falling diaspores, consistent with increased wind dispersal potential. However, their shorter stature meant that dispersal distances, at a given wind speed, were not higher than those of their forest‐occupying relatives. Species with affinities for disturbed sites had slower‐falling diaspores and greater wind dispersal distances, largely explained by lighter diaspores.ConclusionsOur results are consistent with the hypothesized evolutionary relationship between habitat preference and dispersal strategy. However, phylogenetic inertia and other plant functions (e.g., water conservation) likely shaped dispersal trait evolution in melicgrasses. It remains unclear if dispersal trait changes were precipitated by or predated changing habitat preferences. Nevertheless, our study provides promising results and a framework for disentangling dispersal strategy evolution.

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Geospatial model of composition of water service lines in Flint,Michigan: Validation using excavation data and a new compositional geostatistical approach

Goovaerts¹

2023

AWWA Water Science

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Following the Flint drinking water crisis, a service line (SL) replacement program was implemented to replace lead SLs and galvanized SLs connecting residences to Flint's water system, leading to the excavation and inspection over a 5‐year period (2016–2020) of a total of 26,750 lines, representing close to 50% of all tax parcels in the City of Flint. These recent data were used to validate an earlier geospatial model created by residual indicator kriging (IK) to predict the probability that a home has a lead, galvanized, or copper private‐side SL based on neighboring house inspections (i.e., 3254 homes visited in 2017) and secondary information (i.e., built year and city records on SL composition). Receiver operating characteristic curves indicated an average frequency of detection (i.e., area under the curve [AUC]) of 0.9 for copper and galvanized material and 0.6 for lead service lines. Predicting the composition of SL at unmonitored residences by IK, however, can result in negative probabilities of occurrence and probabilities that do not sum to 1. These limitations were overcome by adopting simplicial IK, whereby data undergo a logratio transform before the geospatial analysis. This first application of a compositional approach to SL data improved the detection of lead SLs (AUC = 0.8 vs. 0.6) while providing coherent predictions. Incorporating secondary information, in particular using standardized cokriging and a new rescaled cross‐semivariogram estimator introduced to correct for geographical clustering of house inspections, increased the accuracy of the prediction.

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Compositional Data Analysis in Practice

Cited by 153 publications

References 0 publications

The selection and analysis of fatty acid ratios: A new approach for the univariate and multivariate analysis of fatty acid trophic markers in marine pelagic organisms

The selection and analysis of fatty acid ratios: A new approach for the univariate and multivariate analysis of fatty acid trophic markers in marine pelagic organisms

Correlated evolution of dispersal traits and habitat preference in the melicgrasses

Geospatial model of composition of water service lines in Flint,Michigan: Validation using excavation data and a new compositional geostatistical approach

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