# Sensitivity Analysis for Comparative Methods

## Documentation for package ‘sensiPhy’ version 0.8.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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