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sensiPhy (version 0.8.4)

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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Install

install.packages('sensiPhy')

Monthly Downloads

219

Version

0.8.4

License

GPL-2

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Repository

https://github.com/paternogbc/sensiPhy

Maintainer

Gustavo Paterno

Last Published

December 10th, 2019

Functions in sensiPhy (0.8.4)

Influential Species Detection - Trait Evolution Discrete Characters

Intraspecific variability - Phylogenetic signal

Intraspecific variability - Phylogenetic Linear Regression

intra_clade_phyglm

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

Influential species detection - Phylogenetic signal

Intraspecific variability - Phylogenetic Logistic Regression

intra_influ_phylm

Interaction between intraspecific variability and influential species - Phylogenetic Linear Regression

intra_samp_phyglm

Interaction between intraspecific variability and species sampling - Phylogenetic Logistic Regression

intra_samp_phylm

Interaction between intraspecific variability and species sampling - Phylogenetic Linear Regression

Influential species detection - Phylogenetic Logistic Regression

Match data and phylogeny based on model formula

Influential species detection - Phylogenetic Linear Regression

Primates dataset: Example dataset for the package sensiPhy

Sensitivity Analysis for Comparative Methods

intra_clade_phylm

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

Graphical sensitivity analysis for comparative methods

Phylogenetic signal in missing data

sensi_plot.sensiSamp

Graphical diagnostics for class 'sensiSamp'

sensi_plot.sensiClade.TraitEvol

Graphical diagnostics for class 'sensiClade.TraitEvol'

sensi_plot.sensiClade

Graphical diagnostics for class 'sensiClade'

samp_continuous

Species Sampling uncertainty - Trait Evolution Continuous Characters

sensi_plot.intra.physig

Graphical diagnostics for class 'intra.physig'

Primates dataset: Example dataset for the package sensiPhy

sensi_plot.sensiTree

Graphical diagnostics for class 'sensiTree'

tree_clade_phylm

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

sensi_plot.sensiTree.TraitEvol

Graphical diagnostics for class 'sensiTree.TraitEvol'

tree_continuous

Phylogenetic uncertainty - Trait Evolution Continuous Characters

sensi_plot.samp.physig

Graphical diagnostics for class 'samp.physig'

Primates dataset: Example dataset for the package sensiPhy

intra_influ_phyglm

Interaction between intraspecific variability and influential species - Phylogenetic Logistic Regression

Sensitivity Analysis Species Sampling - Phylogenetic Logistic Regression

Species Sampling uncertainty - Trait Evolution Discrete Characters

sensi_plot.influ.physig

Graphical diagnostics for class 'influ.physig'

sensi_plot.sensiIntra

Graphical diagnostics for class 'sensiIntra'

sensi_plot.clade.physig

Graphical diagnostics for class 'clade.physig'

sensi_plot.sensiIntra_Clade

Graphical diagnostics for class 'sensiIntra_Clade'

sensi_plot.sensiSamp.TraitEvol

Graphical diagnostics for class 'sensiSamp.TraitEvol'

sensi_plot.sensiTree_Clade

Graphical diagnostics for class 'sensiTree_Clade'

Sensitivity Analysis Species Sampling - Phylogenetic signal

sensi_plot.sensiInflu.TraitEvol

Graphical diagnostics for class 'sensiInflu.TraitEvol'

Sensitivity Analysis Species Sampling - Phylogenetic Linear Regression

sensi_plot.sensiInflu

Graphical diagnostics for class 'sensiInflu'

sensi_plot.sensiTree_Intra

Graphical diagnostics for class 'sensiIntra_Tree'

sensi_plot.sensiTree_Influ

Graphical diagnostics for class 'sensiTree_Influ'

sensi_plot.tree.bd

Graphical diagnostics for class 'tree.physig'

sensi_plot.tree.physig

Graphical diagnostics for class 'tree.physig'

sensi_plot.sensiTree_Samp

Graphical diagnostics for class 'sensiTree_samp'

sensi_plot.sensiIntra_Influ

Graphical diagnostics for class 'sensiIntra_Influ'

tree_influ_phylm

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

Phylogenetic uncertainty - Trait Evolution Discrete Characters

Phylogenetic uncertainty - net diversification rate

tree_clade_phyglm

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

sensi_plot.sensiIntra_Samp

Graphical diagnostics for class 'sensiIntra_Samp' and 'sensiTree_samp'

tree_influ_phyglm

Interaction between phylogenetic uncertainty and influential species detection - Phylogenetic Logistic Regression

tree_intra_phyglm

Interaction between phylogenetic uncertainty and intraspecific variability - Phylogenetic logistic Regression

tree_samp_phyglm

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

Phylogenetic uncertainty - Phylogenetic Linear Regression

Phylogenetic uncertainty - Phylogenetic signal

tree_samp_phylm

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

tree_intra_phylm

Interaction between phylogenetic uncertainty and intraspecific variability - Phylogenetic Linear Regression

Phylogenetic uncertainty - Phylogenetic Logistic Regression

Alien Mammals dataset: Example dataset for the package sensiPhy

influ_continuous

Influential Species Detection - Trait Evolution Continuous Characters

Influential clade detection - Phylogenetic signal

Influential clade detection - Phylogenetic Linear Regression

Alien Mammals dataset: Example dataset for the package sensiPhy

clade_continuous

Influential Clade Detection - Trait Evolution Continuous Characters

Influential Clade Detection - Trait Evolution Discrete Characters

Alien Mammals dataset: Example dataset for the package sensiPhy

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