Hey Guys, maybe we could just include our changes in here and later we organize everything on the NEWS.md file. ;)
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:
slope -> estimate
DF -> DIF
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.
Hey Guys, maybe we could just include our changes in here and later we organize everything on the NEWS.md file. ;)
Core changes
sensiPhy
now imports the packagephytools
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 signalNew 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 uncertaintyintra_physig()
: Performs sensitivity analysis of phylogenetic signal estimate (k or lambda) accounting for intra-specific variation and measurement errorsInteractions 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:
sensiPhy
function the following changes were made: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.