Package: glinvci 1.2.4
Woodrow Kiang
glinvci: Phylogenetic Comparative Methods with Uncertainty Estimates
A framework for analytically computing the asymptotic confidence intervals and maximum-likelihood estimates of a class of continuous-time Gaussian branching processes defined by Mitov V, Bartoszek K, Asimomitis G, Stadler T (2019) <doi:10.1016/j.tpb.2019.11.005>. The class of model includes the widely used Ornstein-Uhlenbeck and Brownian motion branching processes. The framework is designed to be flexible enough so that the users can easily specify their own sub-models, or re-parameterizations, and obtain the maximum-likelihood estimates and confidence intervals of their own custom models.
Authors:
glinvci_1.2.4.tar.gz
glinvci_1.2.4.tar.gz(r-4.5-noble)glinvci_1.2.4.tar.gz(r-4.4-noble)
glinvci.pdf |glinvci.html✨
glinvci/json (API)
| # Install 'glinvci' in R: |
| install.packages('glinvci', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hckiang/glinvci/issues
Last updated 6 months agofrom:4c896146c1. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 16 2024 |
| R-4.5-linux-x86_64 | OK | Oct 16 2024 |
Exports:avail_restrictionsbrnbrn_diagSigbrn_fixedSigclone_modeldbrndbrn_diagSigdbrn_fixedSigdou_diagHdou_diagH_diagSigdou_diagH_fixedSigdou_diagH_fixedthetadou_diagH_fixedtheta_diagSigdou_diagH_fixedtheta_fixedSigdou_diagSigdou_fixedHdou_fixedH_diagSigdou_fixedH_fixedSigdou_fixedH_fixedthetadou_fixedH_fixedtheta_diagSigdou_fixedSigdou_fixedthetadou_fixedtheta_diagSigdou_fixedtheta_fixedSigdou_haltlostdou_logdiagHdou_logdiagH_diagSigdou_logdiagH_fixedSigdou_logdiagH_fixedthetadou_logdiagH_fixedtheta_diagSigdou_logdiagH_fixedtheta_fixedSigdou_logspdHdou_logspdH_diagSigdou_logspdH_fixedSigdou_logspdH_fixedthetadou_logspdH_fixedtheta_diagSigdou_logspdH_fixedtheta_fixedSigdou_spdHdou_spdH_diagSigdou_spdH_fixedSigdou_spdH_fixedthetadou_spdH_fixedtheta_diagSigdou_spdH_fixedtheta_fixedSigdou_symHdou_symH_diagSigdou_symH_fixedSigdou_symH_fixedthetadou_symH_fixedtheta_diagSigdou_symH_fixedtheta_fixedSigdou_zaplostfitget_restricted_ouglinvglinv_gaussgradhas_tipvalshbrnhbrn_diagSighbrn_fixedSighesshou_diagHhou_diagH_diagSighou_diagH_fixedSighou_diagH_fixedthetahou_diagH_fixedtheta_diagSighou_diagH_fixedtheta_fixedSighou_diagSighou_fixedHhou_fixedH_diagSighou_fixedH_fixedSighou_fixedH_fixedthetahou_fixedH_fixedtheta_diagSighou_fixedSighou_fixedthetahou_fixedtheta_diagSighou_fixedtheta_fixedSighou_haltlosthou_logdiagHhou_logdiagH_diagSighou_logdiagH_fixedSighou_logdiagH_fixedthetahou_logdiagH_fixedtheta_diagSighou_logdiagH_fixedtheta_fixedSighou_logspdHhou_logspdH_diagSighou_logspdH_fixedSighou_logspdH_fixedthetahou_logspdH_fixedtheta_diagSighou_logspdH_fixedtheta_fixedSighou_spdHhou_spdH_diagSighou_spdH_fixedSighou_spdH_fixedthetahou_spdH_fixedtheta_diagSighou_spdH_fixedtheta_fixedSighou_symHhou_symH_diagSighou_symH_fixedSighou_symH_fixedthetahou_symH_fixedtheta_diagSighou_symH_fixedtheta_fixedSighou_zaplostlikmarginal_cinparams_brnnparams_brn_diagSignparams_brn_fixedSignparams_ounparams_ou_diagHnparams_ou_diagH_diagSignparams_ou_diagH_fixedSignparams_ou_diagH_fixedthetanparams_ou_diagH_fixedtheta_diagSignparams_ou_diagH_fixedtheta_fixedSignparams_ou_diagSignparams_ou_fixedHnparams_ou_fixedH_diagSignparams_ou_fixedH_fixedSignparams_ou_fixedH_fixedthetanparams_ou_fixedH_fixedtheta_diagSignparams_ou_fixedSignparams_ou_fixedthetanparams_ou_fixedtheta_diagSignparams_ou_fixedtheta_fixedSignparams_ou_logdiagHnparams_ou_logdiagH_diagSignparams_ou_logdiagH_fixedSignparams_ou_logdiagH_fixedthetanparams_ou_logdiagH_fixedtheta_diagSignparams_ou_logdiagH_fixedtheta_fixedSignparams_ou_logspdHnparams_ou_logspdH_diagSignparams_ou_logspdH_fixedSignparams_ou_logspdH_fixedthetanparams_ou_logspdH_fixedtheta_diagSignparams_ou_logspdH_fixedtheta_fixedSignparams_ou_spdHnparams_ou_spdH_diagSignparams_ou_spdH_fixedSignparams_ou_spdH_fixedthetanparams_ou_spdH_fixedtheta_diagSignparams_ou_spdH_fixedtheta_fixedSignparams_ou_symHnparams_ou_symH_diagSignparams_ou_symH_fixedSignparams_ou_symH_fixedthetanparams_ou_symH_fixedtheta_diagSignparams_ou_symH_fixedtheta_fixedSigou_diagHou_diagH_diagSigou_diagH_fixedSigou_diagH_fixedthetaou_diagH_fixedtheta_diagSigou_diagH_fixedtheta_fixedSigou_diagSigou_fixedHou_fixedH_diagSigou_fixedH_fixedSigou_fixedH_fixedthetaou_fixedH_fixedtheta_diagSigou_fixedSigou_fixedthetaou_fixedtheta_diagSigou_fixedtheta_fixedSigou_haltlostou_logdiagHou_logdiagH_diagSigou_logdiagH_fixedSigou_logdiagH_fixedthetaou_logdiagH_fixedtheta_diagSigou_logdiagH_fixedtheta_fixedSigou_logspdHou_logspdH_diagSigou_logspdH_fixedSigou_logspdH_fixedthetaou_logspdH_fixedtheta_diagSigou_logspdH_fixedtheta_fixedSigou_spdHou_spdH_diagSigou_spdH_fixedSigou_spdH_fixedthetaou_spdH_fixedtheta_diagSigou_spdH_fixedtheta_fixedSigou_symHou_symH_diagSigou_symH_fixedSigou_symH_fixedthetaou_symH_fixedtheta_diagSigou_symH_fixedtheta_fixedSigou_zaplostouhessoujacouparrglinvset_tipsvarest
Dependencies:apeBBdigestgenericslatticelbfgsb3cnlmenloptrnumDerivoptimxplyrpracmaquadprogRcppRcppArmadillorlang
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clone a GLInv model | clone_model clone_model.glinv clone_model.glinv_gauss |
| Fitting a GLInv model via numerical optimisation | fit.glinv |
| Convenience function for constructing restricted/reparameterised OU parameterisation function. | get_restricted_ou |
| Construct an GLInv model with respect to user-specified parametrisation | glinv grad.glinv hess.glinv lik.glinv plot.glinv print.glinv |
| Construct an object representing a GLInv model with respect to the underlying Gaussian process parameters. | glinv_gauss grad.glinv_gauss hess.glinv_gauss lik.glinv_gauss print.glinv_gauss |
| glinvci: Confidence intervals and hypothesis testing for GLInv model | glinvci-package glinvci |
| Compute the log-likelihood gradients of GLInv models | grad |
| Check if a 'glinv_gauss' model contains trait values at their tips. | has_tipvals has_tipvals.glinv has_tipvals.glinv_gauss |
| Compute the log-likelihood Hessian of GLInv models | hess |
| Compute the likelihood of a GLInv model | lik |
| Getting marginal confidence interval for GLInv model | marginal_ci |
| Get the number of parameters of the unrestricted OU model | nparams_ou |
| Handling missing data and lost traits in Ornstein-Uhlenbeck processes | dou_haltlost dou_zaplost hou_haltlost hou_zaplost ou_haltlost ou_zaplost |
| Parameterisation functions of Ornstein-Uhlenbeck model | ouhess oujac oupar |
| Restrict the parameters space of OU and Brownian motion models. | avail_restrictions brn brn_diagSig brn_fixedSig dbrn dbrn_diagSig dbrn_fixedSig dou_diagH dou_diagH_diagSig dou_diagH_fixedSig dou_diagH_fixedtheta dou_diagH_fixedtheta_diagSig dou_diagH_fixedtheta_fixedSig dou_diagSig dou_fixedH dou_fixedH_diagSig dou_fixedH_fixedSig dou_fixedH_fixedtheta dou_fixedH_fixedtheta_diagSig dou_fixedSig dou_fixedtheta dou_fixedtheta_diagSig dou_fixedtheta_fixedSig dou_logdiagH dou_logdiagH_diagSig dou_logdiagH_fixedSig dou_logdiagH_fixedtheta dou_logdiagH_fixedtheta_diagSig dou_logdiagH_fixedtheta_fixedSig dou_logspdH dou_logspdH_diagSig dou_logspdH_fixedSig dou_logspdH_fixedtheta dou_logspdH_fixedtheta_diagSig dou_logspdH_fixedtheta_fixedSig dou_spdH dou_spdH_diagSig dou_spdH_fixedSig dou_spdH_fixedtheta dou_spdH_fixedtheta_diagSig dou_spdH_fixedtheta_fixedSig dou_symH dou_symH_diagSig dou_symH_fixedSig dou_symH_fixedtheta dou_symH_fixedtheta_diagSig dou_symH_fixedtheta_fixedSig hbrn hbrn_diagSig hbrn_fixedSig hou_diagH hou_diagH_diagSig hou_diagH_fixedSig hou_diagH_fixedtheta hou_diagH_fixedtheta_diagSig hou_diagH_fixedtheta_fixedSig hou_diagSig hou_fixedH hou_fixedH_diagSig hou_fixedH_fixedSig hou_fixedH_fixedtheta hou_fixedH_fixedtheta_diagSig hou_fixedSig hou_fixedtheta hou_fixedtheta_diagSig hou_fixedtheta_fixedSig hou_logdiagH hou_logdiagH_diagSig hou_logdiagH_fixedSig hou_logdiagH_fixedtheta hou_logdiagH_fixedtheta_diagSig hou_logdiagH_fixedtheta_fixedSig hou_logspdH hou_logspdH_diagSig hou_logspdH_fixedSig hou_logspdH_fixedtheta hou_logspdH_fixedtheta_diagSig hou_logspdH_fixedtheta_fixedSig hou_spdH hou_spdH_diagSig hou_spdH_fixedSig hou_spdH_fixedtheta hou_spdH_fixedtheta_diagSig hou_spdH_fixedtheta_fixedSig hou_symH hou_symH_diagSig hou_symH_fixedSig hou_symH_fixedtheta hou_symH_fixedtheta_diagSig hou_symH_fixedtheta_fixedSig nparams_brn nparams_brn_diagSig nparams_brn_fixedSig nparams_ou_diagH nparams_ou_diagH_diagSig nparams_ou_diagH_fixedSig nparams_ou_diagH_fixedtheta nparams_ou_diagH_fixedtheta_diagSig nparams_ou_diagH_fixedtheta_fixedSig nparams_ou_diagSig nparams_ou_fixedH nparams_ou_fixedH_diagSig nparams_ou_fixedH_fixedSig nparams_ou_fixedH_fixedtheta nparams_ou_fixedH_fixedtheta_diagSig nparams_ou_fixedSig nparams_ou_fixedtheta nparams_ou_fixedtheta_diagSig nparams_ou_fixedtheta_fixedSig nparams_ou_logdiagH nparams_ou_logdiagH_diagSig nparams_ou_logdiagH_fixedSig nparams_ou_logdiagH_fixedtheta nparams_ou_logdiagH_fixedtheta_diagSig nparams_ou_logdiagH_fixedtheta_fixedSig nparams_ou_logspdH nparams_ou_logspdH_diagSig nparams_ou_logspdH_fixedSig nparams_ou_logspdH_fixedtheta nparams_ou_logspdH_fixedtheta_diagSig nparams_ou_logspdH_fixedtheta_fixedSig nparams_ou_spdH nparams_ou_spdH_diagSig nparams_ou_spdH_fixedSig nparams_ou_spdH_fixedtheta nparams_ou_spdH_fixedtheta_diagSig nparams_ou_spdH_fixedtheta_fixedSig nparams_ou_symH nparams_ou_symH_diagSig nparams_ou_symH_fixedSig nparams_ou_symH_fixedtheta nparams_ou_symH_fixedtheta_diagSig nparams_ou_symH_fixedtheta_fixedSig ou_diagH ou_diagH_diagSig ou_diagH_fixedSig ou_diagH_fixedtheta ou_diagH_fixedtheta_diagSig ou_diagH_fixedtheta_fixedSig ou_diagSig ou_fixedH ou_fixedH_diagSig ou_fixedH_fixedSig ou_fixedH_fixedtheta ou_fixedH_fixedtheta_diagSig ou_fixedSig ou_fixedtheta ou_fixedtheta_diagSig ou_fixedtheta_fixedSig ou_logdiagH ou_logdiagH_diagSig ou_logdiagH_fixedSig ou_logdiagH_fixedtheta ou_logdiagH_fixedtheta_diagSig ou_logdiagH_fixedtheta_fixedSig ou_logspdH ou_logspdH_diagSig ou_logspdH_fixedSig ou_logspdH_fixedtheta ou_logspdH_fixedtheta_diagSig ou_logspdH_fixedtheta_fixedSig ou_spdH ou_spdH_diagSig ou_spdH_fixedSig ou_spdH_fixedtheta ou_spdH_fixedtheta_diagSig ou_spdH_fixedtheta_fixedSig ou_symH ou_symH_diagSig ou_symH_fixedSig ou_symH_fixedtheta ou_symH_fixedtheta_diagSig ou_symH_fixedtheta_fixedSig parameter_restriction |
| Simulate random trait values from models. | rglinv rglinv.glinv rglinv.glinv_gauss |
| Set trait values at the tip for a 'glinv_gauss' model. | set_tips set_tips.glinv set_tips.glinv_gauss |
| Estimate the variance-covariance matrix of the maximum likelihood estimator. | varest varest.glinv |
