Keyboard (version 0.1.3)

plot_kb: Plot Objects Generated by the Keyboard Design Package

Description

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

Usage

plot_kb(x, ..., name = deparse(substitute(x)))

Value

This function returns a figure.

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).

Author

Xiaomeng Yuan, Chen Li, Hongying Sun, Li Tang and Haitao Pan

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.

See Also

summary_kb

Examples

# \donttest{
### 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) # use previous plot or next plot button to switch plots
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)
# }