Sensitivity Analysis for Comparative Methods

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Documentation for package ‘sensiPhy’ version 0.8.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

alien	Alien Mammals dataset: Example dataset for the package sensiPhy
alien.data	Alien Mammals dataset: Example dataset for the package sensiPhy
alien.phy	Alien Mammals dataset: Example dataset for the package sensiPhy
clade_continuous	Influential Clade Detection - Trait Evolution Continuous Characters
clade_discrete	Influential Clade Detection - Trait Evolution Discrete Characters
clade_phyglm	Estimate the impact on model estimates of phylogenetic logistic regression after removing clades from the analysis.
clade_phylm	Influential clade detection - Phylogenetic Linear Regression
clade_physig	Influential clade detection - Phylogenetic signal
influ_continuous	Influential Species Detection - Trait Evolution Continuous Characters
influ_discrete	Influential Species Detection - Trait Evolution Discrete Characters
influ_phyglm	Influential species detection - Phylogenetic Logistic Regression
influ_phylm	Influential species detection - Phylogenetic Linear Regression
influ_physig	Influential species detection - Phylogenetic signal
intra_clade_phyglm	Interaction between intraspecific variability and influential clade detection - Phylogenetic Logistic Regression
intra_clade_phylm	Interaction between intraspecific variability and influential clade detection - Phylogenetic Linear Regression
intra_influ_phyglm	Interaction between intraspecific variability and influential species - Phylogenetic Logistic Regression
intra_influ_phylm	Interaction between intraspecific variability and influential species - Phylogenetic Linear Regression
intra_phyglm	Intraspecific variability - Phylogenetic Logistic Regression
intra_phylm	Intraspecific variability - Phylogenetic Linear Regression
intra_physig	Intraspecific variability - Phylogenetic signal
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
match_dataphy	Match data and phylogeny based on model formula
miss.phylo.d	Phylogenetic signal in missing data
primates	Primates dataset: Example dataset for the package sensiPhy
primates.data	Primates 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
samp_discrete	Species Sampling uncertainty - Trait Evolution Discrete Characters
samp_phyglm	Sensitivity Analysis Species Sampling - Phylogenetic Logistic Regression
samp_phylm	Sensitivity Analysis Species Sampling - Phylogenetic Linear Regression
samp_physig	Sensitivity Analysis Species Sampling - Phylogenetic signal
sensiPhy	Sensitivity Analysis for Comparative Methods
sensi_plot	Graphical sensitivity analysis for comparative methods
sensi_plot.clade.physig	Graphical diagnostics for class 'clade.physig'
sensi_plot.influ.physig	Graphical diagnostics for class 'influ.physig'
sensi_plot.intra.physig	Graphical diagnostics for class 'intra.physig'
sensi_plot.samp.physig	Graphical diagnostics for class 'samp.physig'
sensi_plot.sensiClade	Graphical diagnostics for class 'sensiClade'
sensi_plot.sensiClade.TraitEvol	Graphical diagnostics for class 'sensiClade.TraitEvol'
sensi_plot.sensiInflu	Graphical diagnostics for class 'sensiInflu'
sensi_plot.sensiInflu.TraitEvol	Graphical diagnostics for class 'sensiInflu.TraitEvol'
sensi_plot.sensiIntra	Graphical diagnostics for class 'sensiIntra'
sensi_plot.sensiIntra_Clade	Graphical diagnostics for class 'sensiIntra_Clade'
sensi_plot.sensiIntra_Influ	Graphical diagnostics for class 'sensiIntra_Influ'
sensi_plot.sensiIntra_Samp	Graphical diagnostics for class 'sensiIntra_Samp' and 'sensiTree_samp'
sensi_plot.sensiSamp	Graphical diagnostics for class 'sensiSamp'
sensi_plot.sensiSamp.TraitEvol	Graphical diagnostics for class 'sensiSamp.TraitEvol'
sensi_plot.sensiTree	Graphical diagnostics for class 'sensiTree'
sensi_plot.sensiTree.TraitEvol	Graphical diagnostics for class 'sensiTree.TraitEvol'
sensi_plot.sensiTree_Clade	Graphical diagnostics for class 'sensiTree_Clade'
sensi_plot.sensiTree_Influ	Graphical diagnostics for class 'sensiTree_Influ'
sensi_plot.sensiTree_Intra	Graphical diagnostics for class 'sensiIntra_Tree'
sensi_plot.sensiTree_Samp	Graphical diagnostics for class 'sensiTree_samp'
sensi_plot.tree.bd	Graphical diagnostics for class 'tree.physig'
sensi_plot.tree.physig	Graphical diagnostics for class 'tree.physig'
tree_bd	Phylogenetic uncertainty - net diversification rate
tree_clade_phyglm	Interaction between phylogenetic uncertainty and influential clade detection - Phylogenetic Logistic Regression
tree_clade_phylm	Interaction between phylogenetic uncertainty and influential clade detection - Phylogenetic Linear Regression
tree_continuous	Phylogenetic uncertainty - Trait Evolution Continuous Characters
tree_discrete	Phylogenetic uncertainty - Trait Evolution Discrete Characters
tree_influ_phyglm	Interaction between phylogenetic uncertainty and influential species detection - Phylogenetic Logistic Regression
tree_influ_phylm	Interaction between phylogenetic uncertainty and influential species detection - Phylogenetic Linear Regression
tree_intra_phyglm	Interaction between phylogenetic uncertainty and intraspecific variability - Phylogenetic logistic Regression
tree_intra_phylm	Interaction between phylogenetic uncertainty and intraspecific variability - Phylogenetic Linear Regression
tree_phyglm	Phylogenetic uncertainty - Phylogenetic Logistic Regression
tree_phylm	Phylogenetic uncertainty - Phylogenetic Linear Regression
tree_physig	Phylogenetic uncertainty - Phylogenetic signal
tree_samp_phyglm	Interaction between phylogenetic uncertainty and sensitivity to species sampling - Phylogenetic Logistic Regression
tree_samp_phylm	Interaction between phylogenetic uncertainty and sensitivity to species sampling - Phylogenetic Linear Regression