.cctm |
Create a 'conditional' ctm model with random effects as offsets |
.check_par |
Helper function to check parameter constarints |
.combine_formulas |
Combine a set of formulas into one (similar to nlme::asOneFormula) |
.constr_adj |
Helper function to adjust the constraints consistently with the parameter restrictions |
.ctm2formula |
Create a dummy fromula from a ctm object |
.gen_param |
Generator for param closure |
.get_cf |
Get the coefficient vector |
.get_par |
Helper function to extract formatted parameters |
.idx |
Get parameter indices of various structures |
.isbars |
Check whether formula contains bars (RE parts) |
.model_name |
Generates proper model name for the tramME model |
.mod_negative |
Helper function to figure out if negative = TRUE in a given model |
.nm2mat |
Add names to the vc matrix |
.nm2vec |
Add names to the vector of theta parameters |
.nobars |
Remove random effects terms from full formulas or calls |
.parallel_default |
Boilerplate parallel-handling function, modified from 'glmmTMB' |
.re_format |
Format random effects |
.re_size |
Calculates the size of the random effect vector implied by the model and the data |
.set_cf |
Set the coefficient vector |
.set_vc |
Set the parameters of the random effect covariance matrix |
.sim_re |
Simulates random effects vector from a tramME object |
.th2vc |
Convert from theta vector to vc matrix |
.tramME2ctm |
Create a corresponding ctm model for a tramME model |
.vc2th |
Convert from vc matrix to theta vector |
AaregME |
Mixed-effects version of 'Aareg' |
anova.tramME |
Comparison of nested tramME models. |
BoxCoxME |
Mixed-effects version of 'BoxCox' |
coef.LmME |
Extract the coefficients of the fixed effects terms of an LmME model. |
coef.SurvregME |
Extract the coefficients of the fixed effects terms of an SurvregME model. |
coef.tramME |
Extract the coefficients of the fixed effects terms. |
coef<-.tramME |
Set coefficients of a tramME model. |
ColrME |
Mixed-effects version of 'Colr' |
confint.LmME |
Confidence intervals for LmME model parameters |
confint.tramME |
Confidence intervals for tramME model parameters |
CoxphME |
Mixed-effects version of 'Coxph' |
duplicate |
Generic for copying objects that are (partly) modified in place |
duplicate.tramME |
Duplicate a tramME object |
duplicate.tramTMB |
Create a duplicate of the tramTMB object |
fe_terms |
Create fixed effects data and initial parameters |
fitmod |
Fit the model. |
fitmod.tramME |
Call the optimizer on a tramME object |
is.pd |
Check positive definiteness |
LehmannME |
Mixed-effects version of 'Lehmann' |
LmME |
ME version of tram::Lm |
logLik.tramME |
Get the log-likelihood of the model |
lpterms |
Generic method for extracting terms of the linear predictor |
lpterms.tramME |
Get inidvidual terms of the linear predictor and their confidence intervals |
model.frame.tramME |
Extract model frame from a tramME model |
model.matrix.tramME |
Model matrix for tramME mdoels |
offset |
Generic method for '"offset"' |
offset.default |
Default method for '"offset"' |
offset.tramME |
Get the offset vector of a tramME object. |
offset<- |
Generic method for '"offset<-"' |
offset<-.tramME |
Set the values of the offsets of a tramME model. |
optim_control |
Set up and control optimization parameters |
optim_tramTMB |
Optimize the tramTMB object |
parboot.tramME |
Do parametric bootsrap using a tarmME model |
plot.trafo.tramME |
Plotting method for 'trafo.tramME' objects |
plot.tramME |
Plotting method for tramME objects |
PolrME |
Mixed-effects version of 'Polr' |
predict.tramME |
Predict method for tramME objects |
print.anova.tramME |
Printing 'anova.tramME' table |
print.simulate.tramME |
Print method for 'simulate.tramME' objects |
print.summary.tramME |
Print method for tramME model summary |
print.tramME |
Print tramME model |
print.VarCorr.tramME |
Print method for the variance-correlation parameters of a tramME object |
ranef |
Extract the conditional modes and conditional variances of random effects |
ranef.LmME |
Extract the conditional modes of random effects of an LmME model |
ranef.tramME |
Extract the conditional modes and conditional variances of random effects |
residuals.LmME |
Residuals of a LmME model |
residuals.tramME |
Residuals of a tramME model |
re_terms |
Create random effects data and initial paramaters |
sigma.LmME |
Extract the SD of the error term of an LmME model. |
simulate.tramME |
Simulate from a tramME model |
summary.tramME |
Summary method for tramME model |
SurvregME |
Mixed-effects version of 'Survreg' |
trafo |
Generic method for extracting baseline transformations |
trafo.tramME |
Get the baseline transformation function and its confidence interval |
tramME_model |
Create an object that defines a tramME_model |
tramTMB |
Create a tramTMB object |
tramTMB_inputs |
Create inputs of the tramTMB model |
VarCorr |
Variances and correlation matrices of random effects |
VarCorr.LmME |
Variances and correlation matrices of random effects of an LmME object |
VarCorr.tramME |
Variances and correlation matrices of random effects |
varcov |
Generic method for 'varcov' |
varcov.LmME |
Extract the variance-covariance matrix of the random effects of an LmME model |
varcov.tramME |
Extract the variance-covariance matrix of the random effects |
varcov<- |
Generic method for '"varcov<-"' |
varcov<-.tramME |
Set the values of the random effects covariance matrices of a tramME model. |
variable.names.tramME |
Return variable names. |
vcov.LmME |
Get the variance-covariance matrix of the parameters of an LmME model |
vcov.tramME |
Calculate the variance-covariance matrix of the parameters |
vcov.tramTMB |
Variance-covariance matrix of the parameters |
weights.tramME |
Get the observation weight vector of a tramME object. |
weights<- |
Generic method for '"weights<-"' |
weights<-.tramME |
Set the values of the observation weights of a tramME model. |