Picante: R tools for integrating phylogenies and ecology

By Steven W. Kembel, Peter D. Cowan, Matthew R. Helmus, William K. Cornwell, Hélène Morlon, David D. Ackerly, Simon P. Blomberg, Campbell O. Webb. Bioinform., 2010

6,166 citations recorded by the source corpus.

Subfields: Global and Planetary Change, Nature and Landscape Conservation, Paleontology

View Paper: https://www.semanticscholar.org/paper/2e096517da04193fc894caa3331d69c4e0bcd513

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Citations in the corpus

Deciphering the associations between soil microbial diversity and ecosystem multifunctionality driven by long‐term fertilization management (2018, methodology): “The degree of the non- random phylogenetic structure of each community in the soil was evaluated by calculating the nearest relative index (NRI) using the “ses.mpd” function (NRI is equivalent to −1 times the output of “ses.mdp”; Kembel et al., 2010).”
Two new graphical methods for mapping trait evolution on phylogenies (2013, methodology): “Phylogenetic comparative biology in R has exploded in recent years, with many new packages and functions (e.g. Harmon et al. 2008; Kembel et al. 2010; Boettiger, Coop & Ralph 2012; Fitzjohn 2012).”
Emerging patterns in the comparative analysis of phylogenetic community structure (2009, methodology): “…2007; (3) Webb, Ackerly & Kembel 2008; (4) Webb et al. (2008); (5) PST only; (6) Contact Hardy; (7) Steers 2001; Cavender-Bares et al. 2004; (8) Kembel et al. 2008; (9) Helmus et al. 2007a, b; (10) Proches et al. 2006; (11) depending on measure of co-occurrence used; (12) Cavender-Bares &…”
Microbial colonization of microplastics in the Caribbean Sea (2020, methodology): “All statistical analyses and graphs were completed in RStudio (version 1.2.1335) using the “vegan” (Oksanen et al. 2018) and “picante” (Kembel et al. 2010) packages, except the analyses of the relative abundances of the diatoms identified using SEM, which were visualized using a heatmap made in…”
Global diversity and distribution of arbuscular mycorrhizal fungi (2011, positive): “All analyses were preformed in Picante v. 0.7-2 (Kembel et al., 2010).”
Inferring community assembly mechanisms from functional diversity patterns: the importance of multiple assembly processes (2012, methodology): “create null communities, and the picante package (Kembel et al. 2010)”
Specialized metabolic functions of keystone taxa sustain soil microbiome stability (2021, methodology): “using the picante R package [65] and implemented a previously developed null modeling approach to calculate the β-nearest taxon index (βNTI) to infer the community assembly processes [5].”
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data (2011, background): “Contact: artemis@sanger.ac.uk; tjc@sanger.ac.uk Received on September 6, 2011; revised on November 10, 2011; accepted on December 17, 2011”
Protein Complexes in Bacteria (2015, methodology): “) retaining the same species order but with a randomized distribution of conservation fractions were prepared using the R function randomizeMatrix (in the picante package [27]) and the ‘richness’ null model to respect overall conservation levels.”
Nitrogen deposition and precipitation induced phylogenetic clustering of arbuscular mycorrhizal fungal communities (2017, methodology): “To characterize the phylogenetic structure of AMF communities within each sample, we calculated the mean nearest taxon distance (MNTD) and the mean pairwise phylogenetic distance (MPD) (Webb et al., 2002) using the ‘picante’ package (Kembel et al., 2010).”
Genome-wide identification of novel small RNAs in Pseudomonas aeruginosa (2013, methodology): “Read alignments onto the reference genome were visualized using Tablet 1.11.08.10 (Milne et al., 2010).”
Community‐level plant palatability increases with elevation as insect herbivore abundance declines (2017, methodology): “We tested the significance of this test by comparing the observed K value to a null distribution generated by comparing 999 randomizations of trait values across the tips of the phylogenetic tree (Kembel et al. 2010).”
Dispersal traits drive the phylogenetic distance decay of similarity in Neotropical stream metacommunities (2015, methodology): “All analyses were run in R using the packages picante (Kembel et al., 2010) and vegan (Oksanen et al., 2013).”