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sensiPhy (version 0.8.5)

Sensitivity Analysis for Comparative Methods

Description

An implementation of sensitivity analysis for phylogenetic comparative methods. The package is an umbrella of statistical and graphical methods that estimate and report different types of uncertainty in PCM: (i) Species Sampling uncertainty (sample size; influential species and clades). (ii) Phylogenetic uncertainty (different topologies and/or branch lengths). (iii) Data uncertainty (intraspecific variation and measurement error).

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Version

Install

install.packages('sensiPhy')

Monthly Downloads

219

Version

0.8.5

License

GPL-2

Issues

5

Pull Requests

0

Stars

12

Forks

4

Maintainer

Gustavo Paterno

Last Published

April 2nd, 2020

Functions in sensiPhy (0.8.5)

clade_phylm

Influential clade detection - Phylogenetic Linear Regression
alien.data

Alien Mammals dataset: Example dataset for the package sensiPhy
influ_discrete

Influential Species Detection - Trait Evolution Discrete Characters
influ_continuous

Influential Species Detection - Trait Evolution Continuous Characters
clade_physig

Influential clade detection - Phylogenetic signal
clade_continuous

Influential Clade Detection - Trait Evolution Continuous Characters
clade_phyglm

Estimate the impact on model estimates of phylogenetic logistic regression after removing clades from the analysis.
clade_discrete

Influential Clade Detection - Trait Evolution Discrete Characters
intra_phylm

Intraspecific variability - Phylogenetic Linear Regression
alien

Alien Mammals dataset: Example dataset for the package sensiPhy
intra_physig

Intraspecific variability - Phylogenetic signal
alien.phy

Alien Mammals dataset: Example dataset for the package sensiPhy
primates.phy

Primates dataset: Example dataset for the package sensiPhy
samp_continuous

Species Sampling uncertainty - Trait Evolution Continuous Characters
intra_influ_phylm

Interaction between intraspecific variability and influential species - Phylogenetic Linear Regression
samp_phyglm

Sensitivity Analysis Species Sampling - Phylogenetic Logistic Regression
samp_discrete

Species Sampling uncertainty - Trait Evolution Discrete Characters
intra_phyglm

Intraspecific variability - Phylogenetic Logistic Regression
sensi_plot.influ.physig

Graphical diagnostics for class 'influ.physig'
sensi_plot.clade.physig

Graphical diagnostics for class 'clade.physig'
influ_physig

Influential species detection - Phylogenetic signal
intra_samp_phyglm

Interaction between intraspecific variability and species sampling - Phylogenetic Logistic Regression
sensi_plot.sensiInflu

Graphical diagnostics for class 'sensiInflu'
sensi_plot.sensiInflu.TraitEvol

Graphical diagnostics for class 'sensiInflu.TraitEvol'
tree_bd

Phylogenetic uncertainty - net diversification rate
sensi_plot

Graphical sensitivity analysis for comparative methods
sensi_plot.sensiTree.TraitEvol

Graphical diagnostics for class 'sensiTree.TraitEvol'
sensi_plot.tree.physig

Graphical diagnostics for class 'tree.physig'
sensi_plot.sensiTree

Graphical diagnostics for class 'sensiTree'
sensiPhy

Sensitivity Analysis for Comparative Methods
sensi_plot.tree.bd

Graphical diagnostics for class 'tree.physig'
intra_clade_phyglm

Interaction between intraspecific variability and influential clade detection - Phylogenetic Logistic Regression
influ_phylm

Influential species detection - Phylogenetic Linear Regression
influ_phyglm

Influential species detection - Phylogenetic Logistic Regression
tree_intra_phylm

Interaction between phylogenetic uncertainty and intraspecific variability - Phylogenetic Linear Regression
tree_phyglm

Phylogenetic uncertainty - Phylogenetic Logistic Regression
tree_samp_phyglm

Interaction between phylogenetic uncertainty and sensitivity to species sampling - Phylogenetic Logistic Regression
tree_clade_phyglm

Interaction between phylogenetic uncertainty and influential clade detection - Phylogenetic Logistic Regression
tree_samp_phylm

Interaction between phylogenetic uncertainty and sensitivity to species sampling - Phylogenetic Linear Regression
match_dataphy

Match data and phylogeny based on model formula
samp_phylm

Sensitivity Analysis Species Sampling - Phylogenetic Linear Regression
intra_influ_phyglm

Interaction between intraspecific variability and influential species - Phylogenetic Logistic Regression
intra_clade_phylm

Interaction between intraspecific variability and influential clade detection - Phylogenetic Linear Regression
primates

Primates dataset: Example dataset for the package sensiPhy
miss.phylo.d

Phylogenetic signal in missing data
tree_continuous

Phylogenetic uncertainty - Trait Evolution Continuous Characters
primates.data

Primates dataset: Example dataset for the package sensiPhy
tree_influ_phylm

Interaction between phylogenetic uncertainty and influential species detection - Phylogenetic Linear Regression
sensi_plot.sensiTree_Intra

Graphical diagnostics for class 'sensiIntra_Tree'
sensi_plot.sensiClade

Graphical diagnostics for class 'sensiClade'
tree_intra_phyglm

Interaction between phylogenetic uncertainty and intraspecific variability - Phylogenetic logistic Regression
sensi_plot.sensiIntra

Graphical diagnostics for class 'sensiIntra'
sensi_plot.sensiIntra_Clade

Graphical diagnostics for class 'sensiIntra_Clade'
samp_physig

Sensitivity Analysis Species Sampling - Phylogenetic signal
tree_clade_phylm

Interaction between phylogenetic uncertainty and influential clade detection - Phylogenetic Linear Regression
intra_samp_phylm

Interaction between intraspecific variability and species sampling - Phylogenetic Linear Regression
sensi_plot.sensiClade.TraitEvol

Graphical diagnostics for class 'sensiClade.TraitEvol'
sensi_plot.sensiTree_Samp

Graphical diagnostics for class 'sensiTree_samp'
sensi_plot.sensiSamp

Graphical diagnostics for class 'sensiSamp'
sensi_plot.sensiSamp.TraitEvol

Graphical diagnostics for class 'sensiSamp.TraitEvol'
tree_phylm

Phylogenetic uncertainty - Phylogenetic Linear Regression
sensi_plot.sensiTree_Clade

Graphical diagnostics for class 'sensiTree_Clade'
tree_influ_phyglm

Interaction between phylogenetic uncertainty and influential species detection - Phylogenetic Logistic Regression
sensi_plot.samp.physig

Graphical diagnostics for class 'samp.physig'
sensi_plot.sensiIntra_Influ

Graphical diagnostics for class 'sensiIntra_Influ'
sensi_plot.intra.physig

Graphical diagnostics for class 'intra.physig'
sensi_plot.sensiIntra_Samp

Graphical diagnostics for class 'sensiIntra_Samp' and 'sensiTree_samp'
tree_discrete

Phylogenetic uncertainty - Trait Evolution Discrete Characters
sensi_plot.sensiTree_Influ

Graphical diagnostics for class 'sensiTree_Influ'
tree_physig

Phylogenetic uncertainty - Phylogenetic signal