# Phylogenetic Comparative Methods with Uncertainty Estimates

## 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.