posterior_linpred.blrmfit: Posterior of linear predictor

In OncoBayes2: Bayesian Logistic Regression for Oncology Dose-Escalation Trials

Posterior of linear predictor

Description

Calculates the posterior of the linear predictor.

Usage

## S3 method for class 'blrmfit'
posterior_linpred(object, transform = FALSE, newdata, draws, ...)

Arguments

object	fitted model object
transform	logical (defaults to FALSE) indicating if the linear predictor on the logit link scale is transformed with inv_logit to the 0-1 response scale.
newdata	optional data frame specifying for what to predict; if missing, then the data of the input model object is used
draws	number of returned posterior draws; by default the entire posterior is returned
...	not used in this function

Details

Simulates the posterior of the linear predictor of the model object for the specified data set.

Value

Matrix of dimensions draws by nrow(newdata) where row correspond to a draw of the posterior and each column corresponds to a row in newdata. The columns are labelled with the row.names of newdata.

Group and strata definitions

The groups and strata as defined when running the blrm_exnex analysis cannot be changed at a later stage. As a result no evaluations can be performed for groups which have not been present in the data set used for running the analysis. However, it is admissible to code the group (and/or stratum) column as a factor which contains empty levels. These groups are thus not contained in the fitting data set and they are assigned by default to the first stratum. In addition priors must be setup for these groups (and/or strata). These empty group (and/or strata) levels are then allowed in subsequent evaluations. This enables the evaluation of the hierarchical model in terms of representing a prior for future groups.

Examples

## Setting up dummy sampling for fast execution of example
## Please use 4 chains and 100x more warmup & iter in practice
.user_mc_options <- options(OncoBayes2.MC.warmup=10, OncoBayes2.MC.iter=20, OncoBayes2.MC.chains=1,
                            OncoBayes2.MC.save_warmup=FALSE)


## run single-agent analysis which defines blrmfit model object
example_model("single_agent", silent=TRUE)

## obtain posterior of linear prediction on 0-1 scale
post_prob_dlt <- posterior_linpred(blrmfit, TRUE, newdata=hist_SA)
## name columns to obtain nice bayesplot labels
colnames(post_prob_dlt) <- hist_SA$drug_A

library(bayesplot)
library(ggplot2)
mcmc_intervals(post_prob_dlt, prob=0.5, prob_outer=0.95) +
    coord_flip() +
    vline_at(c(0.16, 0.33), linetype=2) +
    ylab("Dose [mg]") +
    ggtitle("Posterior Probability of a DLT") +
    scale_x_continuous(breaks=c(0.1,0.16,0.33, 0.5, 0.75))

## Recover user set sampling defaults
options(.user_mc_options)

OncoBayes2 documentation built on July 26, 2023, 5:30 p.m.