sensiPhy: Sensitivity Analysis for Comparative Methods

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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) Sampling uncertainty (sample size; influential species and clades). (ii) Phylogenetic uncertainty. (iii) Data uncertainty (intraspecific variation and measurement error).

Author
Gustavo Paterno [cre, aut], Gijsbert Werner [aut], Caterina Penone [aut]
Date of publication
2016-07-18 20:37:24
Maintainer
Gustavo Paterno <paternogbc@gmail.com>
License
GPL-2
Version
0.5.0
URLs

View on CRAN

Man pages

alien
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
primates
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

Files in this package

sensiPhy
sensiPhy/NAMESPACE
sensiPhy/NEWS.md
sensiPhy/data
sensiPhy/data/primates.rda
sensiPhy/data/alien.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/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/MD5
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/sensi_plot.sensiTree.Rd
sensiPhy/man/influ_phyglm.Rd
sensiPhy/man/sensiPhy.Rd
sensiPhy/man/sensi_plot.sensiInflu.Rd
sensiPhy/man/sensi_plot.sensiIntra.Rd
sensiPhy/man/tree_phyglm.Rd
sensiPhy/man/alien.Rd
sensiPhy/man/primates.Rd
sensiPhy/man/sensi_plot.Rd
sensiPhy/man/samp_phyglm.Rd
sensiPhy/man/clade_phylm.Rd
sensiPhy/man/clade_phyglm.Rd
sensiPhy/man/tree_phylm.Rd
sensiPhy/man/match_dataphy.Rd
sensiPhy/man/samp_phylm.Rd