Package: sensiPhy 0.8.5

Gustavo Paterno

sensiPhy: Sensitivity Analysis for Comparative Methods

An implementation of sensitivity analysis for phylogenetic comparative methods. The package is an umbrella of statistical and graphical methods that estimate and report different types of uncertainty in PCM: (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).

Authors:Gustavo Paterno [cre, aut], Gijsbert Werner [aut], Caterina Penone [aut], Pablo Martinez [ctb]

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sensiPhy.pdf |sensiPhy.html✨
sensiPhy/json (API)
NEWS

# Install 'sensiPhy' in R:
install.packages('sensiPhy', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/paternogbc/sensiphy/issues

Datasets:
  • 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
  • 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

On CRAN:

comparative-methodsecologyevolutionphylogeneticssensitivity-analysis

41 exports 12 stars 2.15 score 65 dependencies 3 mentions 61 scripts 224 downloads

Last updated 4 years agofrom:e20b0003f9. Checks:OK: 3 NOTE: 4. Indexed: no.

TargetResultDate
Doc / VignettesOKAug 28 2024
R-4.5-winNOTEAug 28 2024
R-4.5-linuxNOTEAug 28 2024
R-4.4-winNOTEAug 28 2024
R-4.4-macNOTEAug 28 2024
R-4.3-winOKAug 28 2024
R-4.3-macOKAug 28 2024

Exports:clade_continuousclade_discreteclade_phyglmclade_phylmclade_physiginflu_continuousinflu_discreteinflu_phyglminflu_phylminflu_physigintra_clade_phyglmintra_clade_phylmintra_influ_phyglmintra_influ_phylmintra_phyglmintra_phylmintra_physigintra_samp_phyglmintra_samp_phylmmatch_dataphymiss.phylo.dsamp_continuoussamp_discretesamp_phyglmsamp_phylmsamp_physigsensi_plottree_bdtree_clade_phyglmtree_clade_phylmtree_continuoustree_discretetree_influ_phyglmtree_influ_phylmtree_intra_phyglmtree_intra_phylmtree_phyglmtree_phylmtree_physigtree_samp_phyglmtree_samp_phylm

Dependencies:apecapercliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdeSolvedigestdoParallelexpmfansifarverfastmatchforeachfuturefuture.applygeigergenericsggplot2ggseqlogoglobalsgluegtableigraphisobanditeratorslabelinglatticelifecyclelistenvmagrittrmapsMASSMatrixmgcvmnormtmunsellmvtnormncbitnlmenumDerivoptimParallelparallellyphangornphylolmphytoolspillarpkgconfigquadprogR6RColorBrewerRcpprlangscalesscatterplot3dsubplextibbleutf8vctrsviridisLitewithr

sensiPhy: R-package for sensitivity analysis in phylogenetic comparative methods.

Gustavo Paterno, Caterina Penone, Gijsbert Werner

Rendered fromsensiPhy_vignette.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2019-12-10
Started: 2017-12-08

Readme and manuals

Help Manual

Help pageTopics
Alien Mammals dataset: Example dataset for the package sensiPhyalien
Alien Mammals dataset: Example dataset for the package sensiPhyalien.data
Alien Mammals dataset: Example dataset for the package sensiPhyalien.phy
Influential Clade Detection - Trait Evolution Continuous Charactersclade_continuous
Influential Clade Detection - Trait Evolution Discrete Charactersclade_discrete
Estimate the impact on model estimates of phylogenetic logistic regression after removing clades from the analysis.clade_phyglm
Influential clade detection - Phylogenetic Linear Regressionclade_phylm
Influential clade detection - Phylogenetic signalclade_physig
Influential Species Detection - Trait Evolution Continuous Charactersinflu_continuous
Influential Species Detection - Trait Evolution Discrete Charactersinflu_discrete
Influential species detection - Phylogenetic Logistic Regressioninflu_phyglm
Influential species detection - Phylogenetic Linear Regressioninflu_phylm
Influential species detection - Phylogenetic signalinflu_physig
Interaction between intraspecific variability and influential clade detection - Phylogenetic Logistic Regressionintra_clade_phyglm
Interaction between intraspecific variability and influential clade detection - Phylogenetic Linear Regressionintra_clade_phylm
Interaction between intraspecific variability and influential species - Phylogenetic Logistic Regressionintra_influ_phyglm
Interaction between intraspecific variability and influential species - Phylogenetic Linear Regressionintra_influ_phylm
Intraspecific variability - Phylogenetic Logistic Regressionintra_phyglm
Intraspecific variability - Phylogenetic Linear Regressionintra_phylm
Intraspecific variability - Phylogenetic signalintra_physig
Interaction between intraspecific variability and species sampling - Phylogenetic Logistic Regressionintra_samp_phyglm
Interaction between intraspecific variability and species sampling - Phylogenetic Linear Regressionintra_samp_phylm
Match data and phylogeny based on model formulamatch_dataphy
Phylogenetic signal in missing datamiss.phylo.d
Primates dataset: Example dataset for the package sensiPhyprimates
Primates dataset: Example dataset for the package sensiPhyprimates.data
Primates dataset: Example dataset for the package sensiPhyprimates.phy
Species Sampling uncertainty - Trait Evolution Continuous Characterssamp_continuous
Species Sampling uncertainty - Trait Evolution Discrete Characterssamp_discrete
Sensitivity Analysis Species Sampling - Phylogenetic Logistic Regressionsamp_phyglm
Sensitivity Analysis Species Sampling - Phylogenetic Linear Regressionsamp_phylm
Sensitivity Analysis Species Sampling - Phylogenetic signalsamp_physig
Graphical sensitivity analysis for comparative methodssensi_plot
Graphical diagnostics for class 'clade.physig'sensi_plot.clade.physig
Graphical diagnostics for class 'influ.physig'sensi_plot.influ.physig
Graphical diagnostics for class 'intra.physig'sensi_plot.intra.physig
Graphical diagnostics for class 'samp.physig'sensi_plot.samp.physig
Graphical diagnostics for class 'sensiClade'sensi_plot.sensiClade
Graphical diagnostics for class 'sensiClade.TraitEvol'sensi_plot.sensiClade.TraitEvol
Graphical diagnostics for class 'sensiInflu'sensi_plot.sensiInflu
Graphical diagnostics for class 'sensiInflu.TraitEvol'sensi_plot.sensiInflu.TraitEvol
Graphical diagnostics for class 'sensiIntra'sensi_plot.sensiIntra
Graphical diagnostics for class 'sensiIntra_Clade'sensi_plot.sensiIntra_Clade
Graphical diagnostics for class 'sensiIntra_Influ'sensi_plot.sensiIntra_Influ
Graphical diagnostics for class 'sensiIntra_Samp' and 'sensiTree_samp'sensi_plot.sensiIntra_Samp
Graphical diagnostics for class 'sensiSamp'sensi_plot.sensiSamp
Graphical diagnostics for class 'sensiSamp.TraitEvol'sensi_plot.sensiSamp.TraitEvol
Graphical diagnostics for class 'sensiTree'sensi_plot.sensiTree
Graphical diagnostics for class 'sensiTree_Clade'sensi_plot.sensiTree_Clade
Graphical diagnostics for class 'sensiTree_Influ'sensi_plot.sensiTree_Influ
Graphical diagnostics for class 'sensiIntra_Tree'sensi_plot.sensiTree_Intra
Graphical diagnostics for class 'sensiTree_samp'sensi_plot.sensiTree_Samp
Graphical diagnostics for class 'sensiTree.TraitEvol'sensi_plot.sensiTree.TraitEvol
Graphical diagnostics for class 'tree.physig'sensi_plot.tree.bd
Graphical diagnostics for class 'tree.physig'sensi_plot.tree.physig
Sensitivity Analysis for Comparative MethodssensiPhy
Phylogenetic uncertainty - net diversification ratetree_bd
Interaction between phylogenetic uncertainty and influential clade detection - Phylogenetic Logistic Regressiontree_clade_phyglm
Interaction between phylogenetic uncertainty and influential clade detection - Phylogenetic Linear Regressiontree_clade_phylm
Phylogenetic uncertainty - Trait Evolution Continuous Characterstree_continuous
Phylogenetic uncertainty - Trait Evolution Discrete Characterstree_discrete
Interaction between phylogenetic uncertainty and influential species detection - Phylogenetic Logistic Regressiontree_influ_phyglm
Interaction between phylogenetic uncertainty and influential species detection - Phylogenetic Linear Regressiontree_influ_phylm
Interaction between phylogenetic uncertainty and intraspecific variability - Phylogenetic logistic Regressiontree_intra_phyglm
Interaction between phylogenetic uncertainty and intraspecific variability - Phylogenetic Linear Regressiontree_intra_phylm
Phylogenetic uncertainty - Phylogenetic Logistic Regressiontree_phyglm
Phylogenetic uncertainty - Phylogenetic Linear Regressiontree_phylm
Phylogenetic uncertainty - Phylogenetic signaltree_physig
Interaction between phylogenetic uncertainty and sensitivity to species sampling - Phylogenetic Logistic Regressiontree_samp_phyglm
Interaction between phylogenetic uncertainty and sensitivity to species sampling - Phylogenetic Linear Regressiontree_samp_phylm