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GEIGER specifications


Unique identifier OMICS_15703
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0.6
Stability Stable
methods, MASS, mvtnorm, digest, coda, colorspace, R(≥2.15.0), deSolve(≥1.7), subplex, ape(≥3.0-6), Rcpp(≥ 0.9.0), ncbit
Maintained Yes


No version available



  • person_outline Matt Pennell

Publication for GEIGER

GEIGER citations


Multiple origins of green blood in New Guinea lizards

Sci Adv
PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] single-parameter model that assumed forward and reverse transition rates were equal (ER). To determine the model fit, we examined the AIC for each model using the fitDiscrete command from the package geiger v2.0.6 (). Because the three models gave comparable support (table S4), we applied a fourth mixed model for which we integrated stochastic character maps across all three transition models. For […]


Low acclimation capacity of narrow‐ranging thermal specialists exposes susceptibility to global climate change

Ecol Evol
PMCID: 5938462
PMID: 29760904
DOI: 10.1002/ece3.4006
call_split See protocol

[…] to test for the phylogenetic influence of measured traits (e.g., acclimation ability, CTMax, thermal range, latitudinal extent). Lambda tests were employed using “Fit Continuous” model tests in the “geiger” package of R (v.3.0.2, R Development Core Team, ). In all cases, lambda was chosen as the best model with lambda scores for traits between 0.00 and 0.086. These low lambda values indicate that […]


Trophic specialization drives morphological evolution in sea snakes

R Soc Open Sci
PMCID: 5882731
PMID: 29657807
DOI: 10.1098/rsos.172141
call_split See protocol

[…] that among the estimated ancestors. Statistical significance of C1 was evaluated using phylogenetic simulation: the variables were simulated along the phylogeny using BM, using ‘sim.char’ function in geiger v. 2.0.6 [], and the observed test measure C1 was compared to a distribution of 1000 simulated values using the maximum clade credibility tree. These tests were implemented using convevol v. 1. […]


Verrucomicrobia are prevalent in north temperate freshwater lakes and display class level preferences between lake habitats

PLoS One
PMCID: 5874073
PMID: 29590198
DOI: 10.1371/journal.pone.0195112
call_split See protocol

[…] t were significantly more abundant in spring from both comparisons was then selected as those which had a preference for spring. Significance of DESeq results was determined by calculating Pagel’s λ (geiger package []). DESeq results were visualized alongside the Verrucomicrobia tree using Interactive Tree of Life [] and tree bootstrap values were calculated using the phangorn package []. […]


Environmental determinism, and not interspecific competition, drives morphological variability in Australasian warblers (Acanthizidae)

Ecol Evol
PMCID: 5916309
PMID: 29721264
DOI: 10.1002/ece3.3925
call_split See protocol

[…] s, (2) regions, and (3) adaptive peaks estimated by SURFACE, for each of the 100 trees sampled from the posterior distribution, using phytools (Revell, ). Models were implemented using the R packages geiger (Harmon, Weir, Brock, Glor, & Challenger, ) and OUwie (Beaulieu & O'Meara, ) and compared by means of the sample size‐corrected Akaike's Information Criterion (AICc). […]


Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

Genome Biol Evol
PMCID: 5888179
PMID: 29635329
DOI: 10.1093/gbe/evy063

[…] ize and intron content (group I and group II introns) were separately mapped onto the ML tree. The following R packages were used: contMap function of phytools () for genome size analysis and ape (), geiger (), and phytools () for intron content. Visualization was done using TreeGradients () or phytools. […]


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GEIGER funding source(s)
This work was supported by the University of British Columbia Biodiversity Research Centre and an NSF IGERT Fellowship (NSF BCS- 0549425).

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