sensiPhy v.07.0 (CRAN )

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 influential species 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

• Tree methods: 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.