The ecodist Package for Dissimilarity-based Analysis of Ecological Data

By Sarah C. Goslee, Dean L. Urban. 2007

2,515 citations recorded by the source corpus.

Ecologists are concerned with the relationships between species composition and environmental framework incorporating space explicitly is an extremely flexible tool for answering these questions. The R package ecodist brings together methods for working with dissimilarities, including some not available in other R packages. We present some of the features of ecodist, particularly simple and partial Mantel tests, and make recommendations for their effective use. Although the partial Mantel test is often used to account for the effects of space, the assumption of linearity greatly reduces its effectiveness for complex spatial patterns. We introduce a modification of the Mantel correlogram designed to overcome this restriction and allow consideration of complex nonlinear structures. This extension of the method allows the use of partial multivariate correlograms and tests of relationship between variables at different spatial scales. Some of the possibilities are demonstrated using both artificial data and data from an ongoing study of plant community composition in grazinglands of the northeastern United States.

Subfields: Ecological Modeling, Nature and Landscape Conservation

View Paper: https://www.semanticscholar.org/paper/d74d61a3b9543569505c889feda3e8286ceceece

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In Ecological Modeling

In Nature and Landscape Conservation

Citations in the corpus

Addressing the removal of rare species in multivariate bioassessments: The impact of methodological choices (2012, methodology): “7.0 using statistics libraries simba (Jurasinski, 2007), vegan (Oksanen et al., 2008), ecodist (Goslee and Urban, 2007), MASS (Venables and Ripley, 2011) and labdsv (Roberts, 2010).”
Re-Evaluating Causal Modeling with Mantel Tests in Landscape Genetics (2013, methodology): “Following Cushman et al. [6] and to assess the relationship between genetic and landscape distance matrices, we used Mantel tests [41] as implemented in the “Ecodist” package [42] in R [43].”
The distance decay of similarity in communities of ectomycorrhizal fungi in different ecosystems and scales (2013, methodology): “The Mantel and Moran’s I tests were performed in Ecodist (Goslee & Urban 2007) and Ape (Paradis, Claude & Strimmer 2004) packages of R, respectively.”
Drivers of bacterial β-diversity depend on spatial scale (2011, methodology): “To investigate the relationship between bacterial community similarity and plant community similarity, geographic distance, and environmental distance across all spatial scales, we first applied a ranked partial mantel test (which assume a monotonic, but not linear, relationship) in the ecodist R pa”
Impacts of agricultural intensification on bird communities: New insights from a multi-level and multi-facet approach of biodiversity (2016, methodology): “To analyse the relationships between beta diversity components and environmental gradients (Tuomisto and Ruokolainen, 2006), Multiple Regressions were performed on distance Matrices (MRM; Legendre et al.,1994) (package {ecodist}; Goslee and Urban, 2007).”
Warming leads to higher species turnover in a coastal ecosystem (2010, methodology): “The partial Mantel test was run using package ecodist in R (Goslee & Urban, 2007).”
Aggregation on the edge: effects of hypoxia avoidance on the spatial distribution of brown shrimp and demersal fishes in the Northern Gulf of Mexico (2012, methodology): “Regressions were conducted with the ‘ecodist’ package in S-Plus version 7.0 (Goslee & Urban 2007).”
Functional homogenization exceeds taxonomic homogenization among European fish assemblages (2014, methodology): “Statistical analyses were carried out using R (R Core Team, 2013), including the libraries betapart for computing dissimilarity indices (Baselga & Orme, 2012; Baselga et al., 2013) and ecodist for MRM analyses (Goslee & Urban, 2007).”
Nitrogen deposition and precipitation induced phylogenetic clustering of arbuscular mycorrhizal fungal communities (2017, methodology): “The relationships between AMF communities and soil/plant variables and plant communities were assessed using Mantel test with the “ecodist” and “vegan” packages (Goslee and Urban, 2007).”
Spatial scaling and multi-model inference in landscape genetics: Martes americana in northern Idaho (2010, background): “1.3 (Goslee and Urban 2007) in R with 10,000 permutations (R Development Core Team 2007).”
Partial Distance Correlation with Methods for Dissimilarities (2013, positive): “This method (permutation of raw data) for the partial Mantel test is implemented in the ecodist package [6] and also the vegan package [20] for R.”
Soil pH mediates the balance between stochastic and deterministic assembly of bacteria (2018, methodology): “These analyses were performed using the “mantel” function of “ecodist” R package [49].”
Effects of sample size, number of markers, and allelic richness on the detection of spatial genetic pattern (2012, methodology): “For each scenario, we performed a partial Mantel test to correlate genetic distance to IBR distance accounting for IBD distance using the library ‘ecodist’ version 1.1.3 (Goslee & Urban 2007) in the statistical software package R (R Development Core Team 2009).”
Multidimensional Scaling Using Majorization: SMACOF in R (2008, methodology): “For the latter variant there are also some functionalities in vegan (Oksanen, Kindt, Legendre, O’Hara, Henry, and Stevens 2009), labdsv (Roberts 2006), ecodist (Goslee and Urban 2007), and xgobi (Maechler 2005).”
Plant diversity represents the prevalent determinant of soil fungal community structure across temperate grasslands in northern China (2017, methodology): “The relationships between fungal community and plant community, geographic distance and abiotic variables were assessed using Mantel test with the “ecodist” and “vegan” packages in R (Goslee and Urban, 2007; R Development Core Team., 2013).”
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle (2019, methodology): “…and S6A were computed on pairwise genetic distances between core gene alignments produced by Roary using the nmds function in the ecodist R package (Goslee and Urban, 2007) The phylogenetic trees in Figures 1A, 3C and S3A were generated using GraPhlAn (version 1.1.3, (Asnicar et al., 2015)) and…”
Evaluating nesting microhabitat for ground-nesting bees using emergence traps (2014, methodology): “…of nest location or was orrelated to the distribution of nesting resources within he site, using multiple regression on Bray–Curtis distance atrices (Lichstein, 2006; Mandelik, Winfree, Neeson, & remen, 2012), which is an extension of the Mantel test in he R package ecodist (Goslee & Urban, 2007).”