Rphylopars features


Estimation of phylogenetic and phenotypic covariance parameters

Function: function(trait_data,tree,model="BM",pheno_error,phylo_correlated=TRUE,pheno_correlated=TRUE,REML=TRUE,full_alpha=TRUE,phylocov_start,phenocov_start,model_par_start,phylocov_fixed,phenocov_fixed,model_par_fixed,skip_optim=FALSE,skip_EM=FALSE,EM_Fels_limit=1e3,repeat_optim_limit=1,EM_missing_limit=50,repeat_optim_tol = 1e-2,model_par_evals=10,max_delta=1e4,EM_verbose=FALSE,optim_verbose=FALSE,npd=FALSE,nested_optim=FALSE,usezscores=TRUE)

Description: This function estimates parameters for the phylogenetic and phenotypic variance-covariance matrices for datasets with missing observations, multiple within-species observations, and a variety of evolution models ("BM", "star", "lambda", "kappa", "delta", "OU", "mvOU"). This function also automatically performs ancestral state reconstruction and missing data imputation.

Simulate traits for phylopars estimation

Function: function(ntaxa=15,ntraits=4,nreps=1,nmissing=0,tree,v,anc,intraspecific,model="BM",parameters,nsim=1,return.type="data.frame")

Description: This function simulates data for use with the PhyloPars R package.

Write data and tree files for PhyloPars web compatability

Function: write.phylopars(trait_data, tree, data_file, tree_file, species_identifier = "species")

Description: This function creates a tab-separated data file and a Newick-formatted tree file for use with the online PhyloPars implementation.