sensiPhy: Sensitivity Analysis for Comparative Methods
Version 0.6.0

An implementation of sensitivity analysis in phylogenetic regression models, for both linear and logistic phylogenetic regressions. The package is an umbrella of statistical and graphical methods that estimate and report different types of uncertainty in PGLS models: (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).

Browse man pages Browse package API and functions Browse package files

AuthorGustavo Paterno [cre, aut], Gijsbert Werner [aut], Caterina Penone [aut]
Date of publication2017-01-14 00:59:22
MaintainerGustavo Paterno <paternogbc@gmail.com>
LicenseGPL-2
Version0.6.0
URL https://github.com/paternogbc/sensiPhy
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("sensiPhy")

Man pages

alien: Alien Mammals dataset: Example dataset for the package...
alien.data: Alien Mammals dataset: Example dataset for the package...
alien.phy: Alien Mammals dataset: Example dataset for the package...
clade_phyglm: Influential clade detection - Phylogenetic Logistic...
clade_phylm: Influential clade detection - Phylogenetic Linear Regression
influ_phyglm: Influential species detection - Phylogenetic Logistic...
influ_phylm: Influential species detection - Phylogenetic Linear...
intra_phyglm: Intraspecific variability - Phylogenetic Logistic Regression
intra_phylm: Intraspecific variability - 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_phyglm: Sensitivity Analysis Species Sampling - Phylogenetic Logistic...
samp_phylm: Sensitivity Analysis Species Sampling - Phylogenetic Linear...
sensiPhy: Sensitivity Analysis for Comparative Methods
sensi_plot: Graphical sensitivity analysis for comparative methods
sensi_plot.sensiClade: Graphical diagnostics for class 'sensiClade'
sensi_plot.sensiInflu: Graphical diagnostics for class 'sensiInflu'
sensi_plot.sensiIntra: Graphical diagnostics for class 'sensiIntra'
sensi_plot.sensiSamp: Graphical diagnostics for class 'sensiSamp'
sensi_plot.sensiTree: Graphical diagnostics for class 'sensiTree'
tree_phyglm: Phylogenetic uncertainty - Phylogenetic Logistic Regression
tree_phylm: Phylogenetic uncertainty - Phylogenetic Linear Regression

Functions

alien Man page
alien.data Man page
alien.phy Man page
clade_phyglm Man page Source code
clade_phylm Man page Source code
influ_phyglm Man page Source code
influ_phylm Man page Source code
intra_phyglm Man page Source code
intra_phylm Man page Source code
match_dataphy Man page Source code
miss.phylo.d Man page Source code
multiplot Source code
primates Man page
primates.data Man page
primates.phy Man page
print.data.phy Source code
print.sensiClade Source code
print.sensiInflu Source code
print.sensiIntra Source code
print.sensiSamp Source code
print.sensiTree Source code
samp_phyglm Man page Source code
samp_phylm Man page Source code
sensiPhy Man page
sensiPhy-package Man page
sensi_plot Man page Source code
sensi_plot.sensiClade Man page Source code
sensi_plot.sensiInflu Man page Source code
sensi_plot.sensiIntra Man page Source code
sensi_plot.sensiSamp Man page Source code
sensi_plot.sensiTree Man page Source code
summary.sensiClade Source code
summary.sensiInflu Source code
summary.sensiIntra Source code
summary.sensiSamp Source code
summary.sensiTree Source code
tree_phyglm Man page Source code
tree_phylm Man page Source code
which_plot Source code

Files

inst
inst/doc
inst/doc/Introduction_to_sensiPhy.R
inst/doc/Introduction_to_sensiPhy.html
inst/doc/Introduction_to_sensiPhy.Rmd
NAMESPACE
NEWS.md
data
data/primates.rda
data/alien.phy.rda
data/alien.data.rda
data/primates.phy.rda
data/alien.rda
data/primates.data.rda
R
R/samp_phyglm.R
R/sensiPhy.R
R/samp_phylm.R
R/influ_phyglm.R
R/match_dataphy.R
R/intra_phyglm.R
R/document-data.R
R/miss.phylo.d.R
R/intra_phylm.R
R/influ_phylm.R
R/tree_phyglm.R
R/sensi_plot.sensiSamp.R
R/clade_phyglm.R
R/sensi_plot.sensiIntra.sensiTree.R
R/print_methods.R
R/sensi_plot.R
R/clade_phylm.R
R/sensi_plot.sensiClade.R
R/utils_plot.R
R/sensi_plot.sensiInflu.R
R/summary_methods.R
R/tree_phylm.R
vignettes
vignettes/Introduction_to_sensiPhy.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/sensi_plot.sensiSamp.Rd
man/influ_phylm.Rd
man/sensi_plot.sensiClade.Rd
man/intra_phylm.Rd
man/intra_phyglm.Rd
man/miss.phylo.d.Rd
man/sensi_plot.sensiTree.Rd
man/influ_phyglm.Rd
man/sensiPhy.Rd
man/alien.phy.Rd
man/sensi_plot.sensiInflu.Rd
man/sensi_plot.sensiIntra.Rd
man/primates.phy.Rd
man/tree_phyglm.Rd
man/alien.Rd
man/primates.Rd
man/sensi_plot.Rd
man/alien.data.Rd
man/samp_phyglm.Rd
man/clade_phylm.Rd
man/clade_phyglm.Rd
man/tree_phylm.Rd
man/primates.data.Rd
man/match_dataphy.Rd
man/samp_phylm.Rd
sensiPhy documentation built on May 19, 2017, 11:42 a.m.