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).


News

sensiPhy 0.8.1

Additions:

The vigentee now include two new sections:

  1. Using sensiPhy to analyse results from other packages
  2. How long does it take?

Also available at the online tutorial: https://github.com/paternogbc/sensiPhy/wiki

Bug fix

  • Corrected issue #182: intra_physig problem with se argument.

sensiPhy 0.8.0

Major additions

sensiPhy now performs sensitivity analysis for a new class of methods which allows users to perform sensitivity analyses of both continuous and discrete (binary) macro-evolutionary models of trait evolution (e.g. Mkn models for binary traits, OU, BM, lambda etc. for continuous traits).

sensiPhy nor performs sensitivity analysis of phylogenetic uncertainty for simple metrics of diversification and speciation rates (Magallon and Sanderson (2000) method) or speciation rate using bd.km (Kendall-Moran method)

New functions (trait evolution)

Influential species:
  • influ_continuous(): Performs sensitivity analysis of influential species for models of trait evolution (continuous characters)

  • influ_discrete(): Performs sensitivity analysis of influential species for models of trait evolution (binary discrete characters)

Influential clades:
  • clade_continuous(): Performs sensitivity analysis of influential clades for models of trait evolution (continuous characters)

  • clade_discrete(): Performs sensitivity analysis of influential clades for for models of trait evolution (binary discrete characters)

Sampling size
  • samp_continuous(): Performs sensitivity analysis of species sampling for models of trait evolution (continuous characters)

  • samp_discrete(): Performs sensitivity analysis of species sampling for models of trait evolution (binary discrete characters)

Phylogenetic uncertainty
  • tree_continuous(): Performs sensitivity analysis of phylogenetic uncertainty for models of trait evolution (continuous characters)

  • tree_discrete(): Performs sensitivity analysis of phylogenetic uncertainty for models of trait evolution (binary discrete characters)

New functions (diversification rates)

Phylogenetic uncertainty
  • tree_bd(): Performs estimates of diversification rate evaluating uncertainty in trees topology.

New functions (Diagnostic plots and stats)

  • summary() and sensi_plot methods were implemented (for all new functions) to provide a quick and intuitive overview of results from sensitivite analysis.

Bug fix

  • Corrected progressbar bug when track=FALSE in physig functions

sensiPhy 0.7.0

Core changes

sensiPhy now imports the package phytools

Major additions

  • sensiPhy now performs sensitivity analysis by interacting two types of uncertainty at the same time (tree and intra against influ, clade and samp methods)
  • sensiPhy now performs sensitivity analysis for phylogenetic signal

New functions

Phylogenetic signal
  • influ_physig(): Performs sensitivity analysis of influential species for phylogenetic signal estimate (k or lambda)
  • clade_physig(): Performs sensitivity analysis of influential clades for phylogenetic signal estimate (k or lambda)
  • samp_physig(): Performs sensitivity analysis of species sampling for phylogenetic signal estimate (k or lambda)
  • tree_physig(): Performs sensitivity analysis of phylogenetic signal estimate (k or lambda) accounting for phylogenetic uncertainty
  • intra_physig(): Performs sensitivity analysis of phylogenetic signal estimate (k or lambda) accounting for intra-specific variation and measurement errors
Interactions for phylolm models
  • tree_intra_phylm(): Performs sensitivity analysis of interaction between phylogenetic uncertainty and intraspecific variability for phylolm models (linear regression)
  • tree_intra_phyglm(): Performs sensitivity analysis of interaction between phylogenetic uncertainty and intraspecific variability for phylolm models (logistic regression)
  • tree_clade_phylm(): Performs sensitivity analysis of interaction between phylogenetic uncertainty and sensitivity to species sampling for phylolm models (linear regression)
  • tree_clade_phyglm(): Performs sensitivity analysis of interaction between phylogenetic uncertainty and sensitivity to species sampling for phylolm models (logistic regression)
  • tree_influ_phylm(): Performs sensitivity analysis of interaction between phylogenetic uncertainty and influential species detection for phylolm models (linear regression)
  • tree_influ_phyglm(): Performs sensitivity analysis of interaction between phylogenetic uncertainty and influential species detection for phylolm models (logistic regression)
  • tree_samp_phylm(): Performs sensitivity analysis of interaction between phylogenetic uncertainty and sensitivity to species sampling for phylolm models (linear regression)
  • tree_samp_phyglm(): Performs sensitivity analysis of interaction between phylogenetic uncertainty and sensitivity to species sampling for phylolm models (logistic regression)
  • intra_clade_phylm(): Performs sensitivity analysis of interaction between intraspecific variability and influential clades for phylolm models (linear regression)
  • intra_clade_phyglm(): Performs sensitivity analysis of interaction between intraspecific variability and influential clades for phylolm models (logistic regression)
  • intra_influ_phylm(): Performs sensitivity analysis of interaction between intraspecific variability and influential species detection for phylolm models (linear regression)
  • intra_influ_phyglm(): Performs sensitivity analysis of interaction between intraspecific variability and influential species detection for phylolm models (logistic regression)
  • intra_samp_phylm(): Performs sensitivity analysis of interaction between intraspecific variability and species sampling for phylolm models (linear regression)
  • intra_samp_phyglm(): Performs sensitivity analysis of interaction between intraspecific variability and species sampling for phylolm models (logistic regression)

Improvements

  • match_data_phy() now accepts datasets with no information on species names as row names. If the number of species corresponds to the number of tips a warning informs the user that the function assumes that the dataset and the phylogeny are in the same order.

Naming standardization between functions:

  • For all sensiPhy function the following changes were made:
  1. slope -> estimate
  2. DF -> DIF
  3. model estimates -> sensi.estimates

Bug fix

  • Treemethods: Data order was matching order of the first tree of the multiphylo file only. This bug is now fixed. Data and order matching is now done at each iteration.

sensiPhy 0.6.0

New Functions

  • miss.phylo.d() - Calculates phylogenetic signal for missing data (D statistic; Fritz & Purvis 2010). Missingness is recoded into a binary variable.

Improvements:

  • The package now includes a Vignette with a quick introduction to all sensiPhy functions.

  • clade_phylm() and clade_phyglm() now account for clade sample size bias. This is done by estimating a null distribution of intercepts and slopes considering only the number of species in the clade.

  • summary() methods for clade_phylm() & clade_phyglm() now includes a randomization test to account for the number of species in clades (tests if change in model parameters (without the focal clade) is within the null distribution - one-tailed test).

  • sensi_plot() for clade analysis now include a histogram with the simulated DFslopes (null distribution).

  • sensi_plot() for influential species analysis (influ_phylm / influ_phyglm) now prints the names of the most influential species on the regression plot.

  • sensi_plot() now uses font size = 12 for better visualization.

  • Packages datasets ("primates", "alien") now loads data and phylogeny in independent objects to faciliate usage in examples.

sensiPhy 0.5.0

First submission to CRAN.

Reference manual

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install.packages("sensiPhy")

0.8.2 by Gustavo Paterno, a month ago


https://github.com/paternogbc/sensiPhy


Report a bug at https://github.com/paternogbc/sensiPhy/issues


Browse source code at https://github.com/cran/sensiPhy


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


Documentation:   PDF Manual  


GPL-2 license


Imports caper, phytools, geiger

Depends on ape, phylolm, ggplot2

Suggests knitr, rmarkdown


See at CRAN