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Overcoming the Spurious Groups Problem in Between-Group PCA

Jean Thioulouse 1 Sabrina Renaud 2 Anne-Béatrice Dufour 1 Stéphane Dray 1 
1 Ecologie quantitative et évolutive des communautés
Département écologie évolutive [LBBE]
2 Ecologie et évolution des populations
Département écologie évolutive [LBBE]
Abstract : Several papers have recently raised the occurrence of some problems with between-group Principal Component Analysis (bgPCA). This method inflates the differences between the groups, and can even display completely artificial differences when none exist, for example when applied to random numbers tables with many variables (columns) and few individuals (rows). Lately, cross-validation has been proposed as a way to circumvent this problem. Here we present some tools and several functions of the ade4 package for the R statistical software to compute a bgPCA, test the presence of statistically significant groups, perform a cross-validation of this analysis and compute associated statistics. We also describe how to use these functions to avoid running into the spurious groups problem. Several examples, including a real data set and random numbers tables, are used to validate this approach in var
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Submitted on : Friday, September 17, 2021 - 6:39:56 PM
Last modification on : Monday, June 27, 2022 - 3:56:07 PM
Long-term archiving on: : Saturday, December 18, 2021 - 7:13:17 PM


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Jean Thioulouse, Sabrina Renaud, Anne-Béatrice Dufour, Stéphane Dray. Overcoming the Spurious Groups Problem in Between-Group PCA. Evolutionary Biology, Springer, 2021, ⟨10.1007/s11692-021-09550-0⟩. ⟨hal-03348141⟩



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