GEIGER: investigating evolutionary radiations

By Luke J. Harmon, Jason T. Weir, Chad D. Brock, Richard E. Glor, Wendell Challenger. Bioinform., 2008

2,366 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Paleontology

View Paper: https://www.semanticscholar.org/paper/8cb9121c58ddaaf1a8a9161d9522c2abad28b9e9

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Citations in the corpus

Thermoregulatory behaviour limits local adaptation of thermal niches and confers sensitivity to climate change (2015, methodology): “Analyses were performed using the ape (Paradis, Claude & Strim- mer 2004), geiger (Harmon et al. 2008) and picante (Kembel et al. 2010) libraries of the R Statistical Package (R Development Core Team 2012).”
A guide to phylogenetic metrics for conservation, community ecology and macroecology (2016, methodology): “We simulated 100 phylogenetic trees with 64 taxa, with a wide distribution of branch lengths (δ statistic) and tree symmetry (IC statistic) using the sim.bdtree function in the R package geiger (Harmon et al., 2008).”
What determines the climatic niche width of species? The role of spatial and temporal climatic variation in three vertebrate clades (2013, methodology): “…analyses were conducted with R software version 2.13.2 (R Development Core Team, 2011) using the following packages: ape version 2.7-3 (Paradis et al., 2004), geiger version 1.3-1 (Harmon et al., 2008), caper version 0.4 (Orme et al., 2011) and CAIC version 1.0 (R version; Purvis & Rambaut, 1995).”
Polyploidy and angiosperm diversification. (2009, methodology): “All calculations were done using GEI- GER 1.0 – 91 ( Harmon et al., 2008 ).”
Flower colour and phylogeny along an altitudinal gradient in the Himalayas of Nepal (2014, methodology): “Pagel’s k was calculated in the R package GEIGER (Harmon et al. 2008).”
Measurement errors should always be incorporated in phylogenetic comparative analysis (2015, methodology): “We evaluated models using the Geiger package (Harmon et al. 2008) because it can readily incorporate predeterminedME or estimate it.”
Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees (2014, background): “99-3 package [50] for the R programming and statistical environment.”
Selectivity in Mammalian Extinction Risk and Threat Types: a New Measure of Phylogenetic Signal Strength in Binary Traits (2010, background): “Cladistic approaches (e.g., tree-length distribution skewness and relative apparent synapomorphy analysis [RASA]) test for clearcut patterns, such as whole clades having the same trait values (Huelsenbeck 1991; Lyons-Weiler et al. 1996).”
SURFACE: detecting convergent evolution from comparative data by fitting Ornstein‐Uhlenbeck models with stepwise Akaike Information Criterion (2013, background): “…2013 British Ecological Society, Methods in Ecology and Evolution, 4, 416–425 models with selective regime shifts, and incorporates functions from the ape (Paradis, Claude & Strimmer 2004), geiger (Harmon et al. 2008), pmc (Boettiger, Coop & Ralph 2012), and igraph (Csardi & Nepusz 2006) packages.”
paleotree: an R package for paleontological and phylogenetic analyses of evolution (2012, background): “This movement has produced a wealth of R libraries dedicated to the analysis of phylogenies and evolutionary patterns (e.g. Paradis, Claude & Strimmer 2004; Harmon et al. 2008; Schliep 2011; Revell 2012).”
Model selection in historical biogeography reveals that founder-event speciation is a crucial process in Island Clades. (2014, methodology): “…extinction rate ( ) for the Psychotria tree are 0.33 and 0 events per million years (estimated with the “birthdeath” function of the R package geiger; Harmon et al. 2008), so, for rough comparability, the base speciation rate was set to base = 0.3 in all simulations, and base was set to 0, 0.1, or…”
Phylogeny, ecology, and the origins of climate-richness relationships (2012, methodology): “Prior to ancestral-state reconstruction, we used the GEIGER package in R (Harmon et al. 2008) to identify the best fitting model of continuous-trait evolution with which to reconstruct ancestral-trait values, based on comparison of AIC values calculated from the likelihood for each model.”