All functions 


Convert crm_fit object to 

Convert efftox_fit object to 

Convert 

Convert 

Cast 

Cast 

Class used by trialr to fit Wason & Seaman's Augmented Binary method in single arm trials with two postbaseline tumour assessments. 

Class used by trialr to fit Wason & Seaman's Augmented Binary method. 

Calculate the binary probability of success. 

Dose selection function that practices careful escalation. 

Get index of element in vector with value closest to a target 

Calculate codified CRM doses. 

Calculate dosetransition pathways for a CRM study 

Class of model fit by trialr using the CRM dosefinding design. 

Container class for parameters to fit the CRM models in trialr. 

Fit a CRM model to the incrementally observed outcomes on a trial pathway. 

Get the prior beliefs for a CRM trial scenario. 

Process RStan samples from a CRM model. 

Parse a string of dosefinding trial outcomes to binary vector notation. 

Class of dosefinding model fit by trialr using Stan. 

Class to hold the elements of a single dosefinding analysis residing in a pathway of analyses. 

Get the number of efficacy events seen at the doses under investigation. 

EffTox analysis to data.frame 

Plot EffTox utility contours 

Calculate dosetransition pathways for an EffTox study 

Calculate dosetransition pathways for an EffTox study 

Class of model fit by trialr using the EffTox dosefinding design. 

Get the Prob(Tox) for Prob(Eff) and utility pairs 

Get parameters to run the EffTox demo 

Container class for parameters to fit the EffTox model in trialr. 

Parse a string of EffTox outcomes to binary vector notation. 

Fit an EffTox model to the incrementally observed outcomes on a trial pathway. 

Process RStan samples from an EffTox model 

Run EffTox simulations 

Calculate the pindex for EffTox utility contours 

Get dosesuperiority matrix in EffTox 

Get the utility of efficacy & toxicity probability pairs 

Plot densities of EffTox dose utilities 

Get the number of patients treated at the doses under investigation. 

Parse a string of dosefinding trial outcomes. 

Parse a string of phase I/II dosefinding trial outcomes. 

Get data to run the PePS2 trial example 

Process RStan samples from a BEBOP model fit to PePS2 data 

Plot an crm_fit 

Plot an efftox_fit 

Predict probability of success for given tumour size measurements. 

Print augbin_fit object. 

Print crm_fit object. 

Print efftox_fit object. 

Sample data from the Augmented Binary model prior predictive distribution. 

Calculate the probability of success. 

Calculate the probability that the rate of toxicity exceeds some threshold 

Sample pairs of correlated binary events 

Sample LKJ correlation matrices. 

Spread the information in dose_finding_paths object to a wide data.frame format. 

Fit Wason & Seaman's Augmented Binary model for tumour response. 

Simple helper function to demonstrate fitting of an Augmented Binary model. 

Fit a CRM model 

Fit an EffTox model 

Fit the EffTox model presented in Thall et al. (2014) 

Fit the hierarchical response model described by Thall et al. (2003). 

Fit the P2TNE model developed for the PePS2 trial to some outcomes. 

Obtain summary of an crm_fit 

Obtain summary of an efftox_fit 

Get the total weight of patient outcomes at the doses under investigation. 

Get the number of toxicity events seen at the doses under investigation. 

The 'trialr' package. 

Run a simulation study. 

Get the weights of patient outcomes at the doses under investigation. 