Phylogenetic Comparative Methods with Uncertainty Estimates

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Documentation for package ‘glinvci’ version 1.2.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

A B C D F G H L M N O P R S V

glinvci-package

glinvci: Confidence intervals and hypothesis testing for GLInv model

-- A --

avail_restrictions

Restrict the parameters space of OU and Brownian motion models.

-- B --

brn	Restrict the parameters space of OU and Brownian motion models.
brn_diagSig	Restrict the parameters space of OU and Brownian motion models.
brn_fixedSig	Restrict the parameters space of OU and Brownian motion models.

-- C --

clone_model	Clone a GLInv model
clone_model.glinv	Clone a GLInv model
clone_model.glinv_gauss	Clone a GLInv model

-- D --

dbrn	Restrict the parameters space of OU and Brownian motion models.
dbrn_diagSig	Restrict the parameters space of OU and Brownian motion models.
dbrn_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_diagH	Restrict the parameters space of OU and Brownian motion models.
dou_diagH_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_diagH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_diagH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
dou_diagH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_diagH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_fixedH	Restrict the parameters space of OU and Brownian motion models.
dou_fixedH_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_fixedH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_fixedH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
dou_fixedH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
dou_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_haltlost	Handling missing data and lost traits in Ornstein-Uhlenbeck processes
dou_logdiagH	Restrict the parameters space of OU and Brownian motion models.
dou_logdiagH_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_logdiagH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_logdiagH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
dou_logdiagH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_logdiagH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_logspdH	Restrict the parameters space of OU and Brownian motion models.
dou_logspdH_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_logspdH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_logspdH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
dou_logspdH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_logspdH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_spdH	Restrict the parameters space of OU and Brownian motion models.
dou_spdH_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_spdH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_spdH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
dou_spdH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_spdH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_symH	Restrict the parameters space of OU and Brownian motion models.
dou_symH_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_symH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_symH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
dou_symH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
dou_symH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
dou_zaplost	Handling missing data and lost traits in Ornstein-Uhlenbeck processes

-- F --

fit.glinv

Fitting a GLInv model via numerical optimisation

-- G --

get_restricted_ou	Convenience function for constructing restricted/reparameterised OU parameterisation function.
glinv	Construct an GLInv model with respect to user-specified parametrisation
glinvci	glinvci: Confidence intervals and hypothesis testing for GLInv model
glinv_gauss	Construct an object representing a GLInv model with respect to the underlying Gaussian process parameters.
grad	Compute the log-likelihood gradients of GLInv models
grad.glinv	Construct an GLInv model with respect to user-specified parametrisation
grad.glinv_gauss	Construct an object representing a GLInv model with respect to the underlying Gaussian process parameters.

-- H --

has_tipvals	Check if a 'glinv_gauss' model contains trait values at their tips.
has_tipvals.glinv	Check if a 'glinv_gauss' model contains trait values at their tips.
has_tipvals.glinv_gauss	Check if a 'glinv_gauss' model contains trait values at their tips.
hbrn	Restrict the parameters space of OU and Brownian motion models.
hbrn_diagSig	Restrict the parameters space of OU and Brownian motion models.
hbrn_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hess	Compute the log-likelihood Hessian of GLInv models
hess.glinv	Construct an GLInv model with respect to user-specified parametrisation
hess.glinv_gauss	Construct an object representing a GLInv model with respect to the underlying Gaussian process parameters.
hou_diagH	Restrict the parameters space of OU and Brownian motion models.
hou_diagH_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_diagH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_diagH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
hou_diagH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_diagH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_fixedH	Restrict the parameters space of OU and Brownian motion models.
hou_fixedH_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_fixedH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_fixedH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
hou_fixedH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
hou_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_haltlost	Handling missing data and lost traits in Ornstein-Uhlenbeck processes
hou_logdiagH	Restrict the parameters space of OU and Brownian motion models.
hou_logdiagH_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_logdiagH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_logdiagH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
hou_logdiagH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_logdiagH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_logspdH	Restrict the parameters space of OU and Brownian motion models.
hou_logspdH_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_logspdH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_logspdH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
hou_logspdH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_logspdH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_spdH	Restrict the parameters space of OU and Brownian motion models.
hou_spdH_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_spdH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_spdH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
hou_spdH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_spdH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_symH	Restrict the parameters space of OU and Brownian motion models.
hou_symH_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_symH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_symH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
hou_symH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
hou_symH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
hou_zaplost	Handling missing data and lost traits in Ornstein-Uhlenbeck processes

-- L --

lik	Compute the likelihood of a GLInv model
lik.glinv	Construct an GLInv model with respect to user-specified parametrisation
lik.glinv_gauss	Construct an object representing a GLInv model with respect to the underlying Gaussian process parameters.

-- M --

marginal_ci

Getting marginal confidence interval for GLInv model

-- N --

nparams_brn	Restrict the parameters space of OU and Brownian motion models.
nparams_brn_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_brn_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou	Get the number of parameters of the unrestricted OU model
nparams_ou_diagH	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_diagH_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_diagH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_diagH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_diagH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_diagH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_fixedH	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_fixedH_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_fixedH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_fixedH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_fixedH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_logdiagH	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_logdiagH_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_logdiagH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_logdiagH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_logdiagH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_logdiagH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_logspdH	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_logspdH_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_logspdH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_logspdH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_logspdH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_logspdH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_spdH	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_spdH_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_spdH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_spdH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_spdH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_spdH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_symH	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_symH_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_symH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_symH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_symH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
nparams_ou_symH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.

-- O --

ouhess	Parameterisation functions of Ornstein-Uhlenbeck model
oujac	Parameterisation functions of Ornstein-Uhlenbeck model
oupar	Parameterisation functions of Ornstein-Uhlenbeck model
ou_diagH	Restrict the parameters space of OU and Brownian motion models.
ou_diagH_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_diagH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_diagH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
ou_diagH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_diagH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_fixedH	Restrict the parameters space of OU and Brownian motion models.
ou_fixedH_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_fixedH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_fixedH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
ou_fixedH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
ou_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_haltlost	Handling missing data and lost traits in Ornstein-Uhlenbeck processes
ou_logdiagH	Restrict the parameters space of OU and Brownian motion models.
ou_logdiagH_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_logdiagH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_logdiagH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
ou_logdiagH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_logdiagH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_logspdH	Restrict the parameters space of OU and Brownian motion models.
ou_logspdH_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_logspdH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_logspdH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
ou_logspdH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_logspdH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_spdH	Restrict the parameters space of OU and Brownian motion models.
ou_spdH_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_spdH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_spdH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
ou_spdH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_spdH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_symH	Restrict the parameters space of OU and Brownian motion models.
ou_symH_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_symH_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_symH_fixedtheta	Restrict the parameters space of OU and Brownian motion models.
ou_symH_fixedtheta_diagSig	Restrict the parameters space of OU and Brownian motion models.
ou_symH_fixedtheta_fixedSig	Restrict the parameters space of OU and Brownian motion models.
ou_zaplost	Handling missing data and lost traits in Ornstein-Uhlenbeck processes

-- P --

parameter_restriction	Restrict the parameters space of OU and Brownian motion models.
plot.glinv	Construct an GLInv model with respect to user-specified parametrisation
print.glinv	Construct an GLInv model with respect to user-specified parametrisation
print.glinv_gauss	Construct an object representing a GLInv model with respect to the underlying Gaussian process parameters.

-- R --

rglinv	Simulate random trait values from models.
rglinv.glinv	Simulate random trait values from models.
rglinv.glinv_gauss	Simulate random trait values from models.

-- S --

set_tips	Set trait values at the tip for a 'glinv_gauss' model.
set_tips.glinv	Set trait values at the tip for a 'glinv_gauss' model.
set_tips.glinv_gauss	Set trait values at the tip for a 'glinv_gauss' model.

-- V --

varest	Estimate the variance-covariance matrix of the maximum likelihood estimator.
varest.glinv	Estimate the variance-covariance matrix of the maximum likelihood estimator.