Ecologically meaningful transformations for ordination of species data

By Pierre Legendre, E. Gallagher. Oecologia, 2001

3,947 citations recorded by the source corpus.

Subfields: Food Science, Statistics and Probability

View Paper: https://www.semanticscholar.org/paper/48e9e44ca331ca0fc95c70889fa4345c0682b611

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Citations in the corpus

On some properties of the Bray-Curtis dissimilarity and their ecological meaning (2017, background): “This effect may be more substantial for large data matrices in which many species may easily have just a few records leading to sparse matrices predominantly filled up with zeros (Legendre and Gallagher, 2001).”
Contrasting metacommunity structure and beta diversity in an aquatic‐floodplain system (2016, methodology): “Prior to the following analyses, community data were Hellinger transformed as per Legendre and Gallagher (2001) using the decostand function in ‘vegan’ (Oksanen et al. 2013).”
Local and landscape management drive trait‐mediated biodiversity of nine taxa on small grassland fragments (2015, methodology): “Prior to analysis, community data matrices were Hellinger-transformed, weigting rare species lower (Legendre & Gallagher, 2001).”
Hydrological stability drives both local and regional diversity patterns in rock pool metacommunities (2015, methodology): “For this, a response matrix of presence – absence data were Hellinger transformed as recommended by Legendre and Gallagher (2001) because they are more representative for actual distances in a multivariate space.”
Temperature Effects Explain Continental Scale Distribution of Cyanobacterial Toxins (2018, methodology): “The toxin concentration and toxin quota matrices were standardized by Hellinger transformation [80].”
Multiple plant traits shape the genetic basis of herbivore community assembly (2015, methodology): “…willow genotypes, we normalized our community data (siteby-species matrix) using the chord transformation (sum of squared species relative abundances equal to one for each sample; Legendre & Gallagher 2001) and conducted a redundancy analysis (RDA, 1000 permutations; with ‘VEGAN’ package in R).”
Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States (2016, methodology): “For these analyses, the Hellinger transformation (Legendre & Gallagher, 2001) was applied to the OTU count data using vegan’s decostand function prior to PCA on the variance–covariance matrix using vegan’s rda function.”
Pollination services are mediated by bee functional diversity and landscape context (2015, methodology): “This matrix of morphospecies by tree cluster, Y, was subjected to a Hellinger transformation (Legendre & Gallagher 2001) to alleviate the dominant effect of honey bees, which was found to mask variance in non-Apis bees.”
Soil Bacterial and Fungal Response to Wildfires in the Canadian Boreal Forest Across a Burn Severity Gradient (2019, methodology): “We compared community composition across samples using BrayCurtis dissimilarities on Hellinger-transformed relative abundances (Legendre and Gallagher, 2001), which we represented using NMDS ordinations.”
Patterns of pollinator turnover and increasing diversity associated with urban habitats (2017, background): “…matrix (42 sites by bee species) of bee observations to a Hellinger transformation (square root of the relative abundance of each species at each site) to alleviate the masking effect of dominant species (e.g. honey bees) on the covariance structure of the ordination (Legendre and Gallagher 2001).”
Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes (2015, methodology): “The transformed presence/absence data were subsequently analyzed with PCA as recommended by Legendre and Gallagher (2001).”
Total and active microbial communities and phoD as affected by phosphate depletion and pH in soil (2016, methodology): “T-RFs of the archaeal, bacteria and fungal communities were normalized using Hellinger distance (Legendre and Gallagher 2001) and T-RFs were further converted into a binary matrix.”