spacodiR specifications

Information


Unique identifier OMICS_08681
Name spacodiR
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 2.0
Computer skills Advanced
Version 0.13.0115
Stability Stable
Requirements
Rcpp, colorspace, picante
Maintained Yes

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Publication for spacodiR

spacodiR in publications

 (3)
PMCID: 5743486
PMID: 29299283
DOI: 10.1002/ece3.3564

[…] the respective age threshold. all calculations of phylogenetic community structure were carried out on phylogenetic, cophenetic distance matrices, using the packages “vegan” (oksanen et al., ) and “spacodir” (eastman, paine, & hardy, ) in the r statistical package (r development core team, ) and spacodi 0.10 (hardy, ). to identify clades that significantly contributed to phylogenetic […]

PMCID: 4482738
PMID: 26115369
DOI: 10.1371/journal.pone.0130151

[…] tests were implemented in the vegan package in r., both phylogenetic community structure analyses and trait dispersion analyses were implemented in r v3.0.1 [] using picante, ape, geiger, ade4, spacodir, fd and cluster packages. to investigate variation in community structure with spatial scale, we repeated all analyses at the plot (0.25 ha) and subplot (0.01 ha) scales., mean phylogenetic […]

PMCID: 4061019
PMID: 24936786
DOI: 10.1371/journal.pone.0098920

[…] magnoliales clades. for each clade the coefficients described above were calculated under the 1s model (999 randomization of tree tips). this was done by using the spacodi.per.nodes function in the spacodir ., for 17 families, phylogenetic studies allowed the resolution of most relationships between genera (). a total of 23 calibration points () were used to generate the dated phylogenetic tree […]


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spacodiR institution(s)
Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow; Institut für Evolutionsbiologie und Umweltwissenschaften, Universität Zürich, Zürich, Switzerland; Evolutionary Biology and Ecology Unit, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium

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