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sensiPhy v0.8.0 (ON CRAN)
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@paternogbc paternogbc released this 19 Dec 05:26
· 47 commits to master since this release
v0.8.0
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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
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