sensiPhy: Sensitivity Analysis for Comparative Methods

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).

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
https://github.com/paternogbc/sensiPhy

View on CRAN

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
clade_phylm Man page
influ_phyglm Man page
influ_phylm Man page
intra_phyglm Man page
intra_phylm Man page
match_dataphy Man page
miss.phylo.d Man page
primates Man page
primates.data Man page
primates.phy Man page
samp_phyglm Man page
samp_phylm Man page
sensiPhy Man page
sensiPhy-package Man page
sensi_plot Man page
sensi_plot.sensiClade Man page
sensi_plot.sensiInflu Man page
sensi_plot.sensiIntra Man page
sensi_plot.sensiSamp Man page
sensi_plot.sensiTree Man page
tree_phyglm Man page
tree_phylm Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.