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Protocols

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

Versioning


No version available

Documentation


Maintainer


Publication for spacodiR

spacodiR citations

 (5)
call_split

Phylogenetic turnover during subtropical forest succession across environmental and phylogenetic scales

2017
Ecol Evol
PMCID: 5743486
PMID: 29299283
DOI: 10.1002/ece3.3564
call_split See protocol

[…] n 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 turnover be […]

library_books

Stochastic assembly in a subtropical forest chronosequence: evidence from contrasting changes of species, phylogenetic and functional dissimilarity over succession

2016
Sci Rep
PMCID: 5013490
PMID: 27599883
DOI: 10.1038/srep32596

[…] r in the process of succession.Chao-Jaccard’s dissimilarity index was calculated using the R package ‘vegan’. The Bst and τst values and null models of Bst and τst was calculated using the R package ‘spacodiR’. Linear mixed models were fitted using the R package ‘lme4’. The significance of fixed effect variables were computed using ‘lmerTest’ package, and multiple comparisons were conducted using […]

call_split

Using Plant Functional Traits and Phylogenies to Understand Patterns of Plant Community Assembly in a Seasonal Tropical Forest in Lao PDR

2015
PLoS One
PMCID: 4482738
PMID: 26115369
DOI: 10.1371/journal.pone.0130151
call_split See protocol

[…] 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 Dis […]

call_split

Characterizing the Phylogenetic Tree Community Structure of a Protected Tropical Rain Forest Area in Cameroon

2014
PLoS One
PMCID: 4061019
PMID: 24936786
DOI: 10.1371/journal.pone.0098920
call_split See protocol

[…] d 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 . […]

library_books

Cryptic Diversity in Indo Australian Rainbowfishes Revealed by DNA Barcoding: Implications for Conservation in a Biodiversity Hotspot Candidate

2012
PLoS One
PMCID: 3400673
PMID: 22829879
DOI: 10.1371/journal.pone.0040627

[…] rtitioning approach of Hardy and Senterre . The index of phylogenetic community structure, denoted as ∏ST, was computed and its significance was tested through 10,000 permutations using the R package SpacodiR . This index provides a standardized estimate of phylogenetic community structure: ∏ST <0 in case of phylogenetic dispersion across communities (i.e., species present in the same locality ten […]


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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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