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pavo specifications


Unique identifier OMICS_32093
Name pavo
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, GNU General Public License version 2.0
Computer skills Advanced
Version 2.0.0
Stability Stable
Source code URL
Maintained Yes




No version available



  • person_outline Thomas White

Additional information

Publications for pavo

pavo citations


Daytime eyeshine contributes to pupil camouflage in a cryptobenthic marine fish

Sci Rep
PMCID: 5943592
PMID: 29743512
DOI: 10.1038/s41598-018-25599-y

[…] mpared the achromatic contrasts between the irides and the natural and model pupils with the distribution of the skin patches achromatic contrasts. Visual models were implemented using the R package ‘pavo’ 1.0. […]


Wing scale ultrastructure underlying convergent and divergent iridescent colours in mimetic Heliconius butterflies

PMCID: 5938584
PMID: 29669892
DOI: 10.1098/rsif.2017.0948

[…] Processing and visualization of the reflectance spectra were performed using the R package PAVO v. 1.1 []. The data were smoothed (using the procspec function with fixneg set to zero and span set to 0.3) and then normalized by subtracting the minimum reflectance of a spectrum from all wavel […]


Do the fluorescent red eyes of the marine fish Tripterygion delaisi stand out? In situ and in vivo measurements at two depths

Ecol Evol
PMCID: 5938470
PMID: 29760908
DOI: 10.1002/ece3.4025

[…] tes by adjusting the p‐value for multiple comparisons following Benjamini and Yekutieli (Benjamini & Yekutieli, ) using the “p.adjust” function in R. Visual models were performed using the R package “pavo” (Maia et al., ). […]


Avian learning favors colorful, not bright, signals

PLoS One
PMCID: 5864004
PMID: 29566013
DOI: 10.1371/journal.pone.0194279

[…] frog using an Ocean Optics Jaz A3305 spectrometer (). We measured three different regions on the color band at the top, middle, and bottom of the band. Measurements were averaged and smoothed in the pavo package [] in R [] to create reflectance curves for each signal ().We analyzed spectra using the pavo package [] to examine the chromatic (color, hue) and achromatic (luminance, brightness) contr […]


Carotenoid coloration and health status of urban Eurasian kestrels (Falco tinnunculus)

PLoS One
PMCID: 5805255
PMID: 29420544
DOI: 10.1371/journal.pone.0191956

[…] s due to the glossy surface of the skin. Reflectance of each body patch was measured three times, removing the probe pointer in between measurements. The raw data files were analyzed with the package pavo [].To compare the two different color measurements, color charts and spectral reflectance, we extracted three colorimetric from the reflectance curves within the 400–700 nm spectral range: (a) ca […]


The brown anole dewlap revisited: do predation pressure, sexual selection, and species recognition shape among population signal diversity?

PMCID: 5947042
PMID: 29761044
DOI: 10.7717/peerj.4722
call_split See protocol

[…] a for the seven population sampled by , and for the population from Central Cuba (Santa Clara), due to technical problems with the spectrometer. All analyses of spectral data were run in R using the ‘pavo’ package (). […]


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pavo institution(s)
Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA; CEFE, Univ Montpellier, CNRS, Univ Paul Valery Montpellier 3, EPHE, IRD, Montpellier, France; School of Life and Environmental Sciences, Deakin University, VIC, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia

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