plot.kb: Plot Objects Generated by the Keyboard Design Package

In hongyingsun1101/KEYBOARDR: Bayesian Designs for Early Phase Clinical Trials

Description

This function plots the objects returned by the other functions in the Keyboard package.

Usage

## S3 method for class 'kb'
plot(x, ..., name = deparse(substitute(x)))

Arguments

x	The object (returned by another function) to be plotted.
...	Ignored arguments.
name	The name of the object to be plotted. (Users should not input this parameter).

Details

(1) For get.oc.kb() and get.oc.comb.kb(), the operating characteristics of the Keyboard design, which include:
(i) the overall dose selection percentage of the simulations generated,
(ii) the number of patients treated at each dose, and
(iii) the toxicities presented at each dose.

(2) For get.oc.obd.kb() and get.oc.obd2.kb(), the operating characteristics of the Keyboard design for phase I/II, which includes:
(i) the overall dose selection percentage of the simulations generated,
(ii) the number of patients treated at each dose,
(iii) the toxicities presented at each dose, and
(iv) the efficacies presented at each dose.

(3) For select.mtd.kb() and select.mtd.comb.kb(): an infographic showing the estimates of the toxicity probability for each dose, with corresponding 95% credible intervals.

Value

This function returns a figure.

Author(s)

Hongying Sun, Li Tang, and Haitao Pan

See Also

summary.kb

Examples

### Single-agent trial ###

## Get the operating characteristics for a Keyboard single-agent trial
oc <- get.oc.kb(target=0.3, p.true=c(0.05, 0.15, 0.3, 0.45, 0.6),
                ncohort=10, cohortsize=3, ntrial=1000)
summary.kb(oc)

plot.kb(oc)
plot.kb(oc$selpercent)
plot.kb(oc$npatients)
plot.kb(oc$ntox)

## Select the MTD based on a trial's data
n <- c(3, 3, 15, 9, 0)
y <- c(0, 0, 4, 4, 0)
selmtd <- select.mtd.kb(target=0.3, npts=n, ntox=y)
summary.kb(selmtd)

plot.kb(selmtd)


### Drug-combination trial ###

## Get the operating characteristics for a Keyboard drug-combination trial
p.true <- matrix(c(0.01, 0.03, 0.10, 0.20, 0.30,
                   0.03, 0.05, 0.15, 0.30, 0.60,
                   0.08, 0.10, 0.30, 0.60, 0.75), byrow=TRUE, ncol=5)
oc.comb <- get.oc.comb.kb(target=0.3, p.true=p.true, ncohort=20, 
 cohortsize=3, n.earlystop=12, startdose=c(1, 1), ntrial=100)
summary.kb(oc.comb)

plot.kb(oc.comb)
plot.kb(oc.comb$selpercent)
plot.kb(oc.comb$nptsdose)
plot.kb(oc.comb$ntoxdose)

## Select the MTD based on a trial's data
n <- matrix(c(3, 5, 0, 0, 0,
              7, 6, 15, 0, 0,
              0, 0, 4, 0, 0), ncol=5, byrow=TRUE)
y <- matrix(c(0, 1, 0, 0, 0,
              1, 1, 4, 0, 0,
              0, 0, 2, 0, 0), ncol=5, byrow=TRUE)
sel.comb <- select.mtd.comb.kb(target=0.3, npts=n, ntox=y)
summary.kb(sel.comb)

plot.kb(sel.comb)

### oc.obd.kb
toxicity.low <- 0.15
toxicity.moderate <- 0.33
toxicity.high <- 0.40
efficacy.low <- 0.20
efficacy.moderate <- 0.40
efficacy.high <- 0.60
target.toxicity <- 0.30
target.efficacy <- 0.40
p.true <-c(0.08,0.30,0.60,0.80)
q.true <- c(0.25,0.40,0.25,0.50)
oc.obd.kb <- get.oc.obd.kb(toxicity.low = toxicity.low,
             toxicity.moderate= toxicity.moderate,
             toxicity.high = toxicity.high,
             efficacy.low = efficacy.low,
             efficacy.moderate = efficacy.moderate,
             efficacy.high = efficacy.high,
             target.toxicity=target.toxicity,
             target.efficacy= target.efficacy,
             p.true= p.true, q.true= q.true)
summary.kb(oc.obd.kb)
plot.kb(oc.obd.kb)
plot.kb(oc.obd.kb$selpercent1)
plot.kb(oc.obd.kb$selpercent2)
plot.kb(oc.obd.kb$selpercent3)
plot.kb(oc.obd.kb$npatients)
plot.kb(oc.obd.kb$ntox)
plot.kb(oc.obd.kb$neff)

hongyingsun1101/KEYBOARDR documentation built on July 14, 2020, 10:41 a.m.