bayes.design: Bayesian design method for sequentially monitoring patients...

Description Usage Arguments Value References Examples

View source: R/sequential_monitor.R

Description

Make animation plots to present sequential monitor stopping rule using Beta-Binomial Bayesian model

Usage

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bayes.design(a,b,r=0, stop.rule="futility", add.size=5, alpha=0.05,
p0 ,delta=0.2,tau1=0.9,tau2=0.9,tau3=0.9,tau4=0.9, time.interval =1)

Arguments

a

the hyperparameter (shape1) of the Beta prior for the experimental drug.

b

the hyperparameter (shape2) of the Beta prior for the experimental drug.

r

the maximum number of patients treated by the experimental drug.

stop.rule

the hyperparameter (shape1) of the Beta prior for the experimental drug.

add.size

a single integer value, random number generator (RNG) state for random number generation.

alpha

the siginificant level to determine the credible interval, set 0.05 by default.

p0

the prespecified reseponse rate.

delta

the minimally acceptable increment of the response rate.

tau1

threshold for stopping rule 1.

tau2

threshold for stopping rule 2.

tau3

threshold for stopping rule 3.

tau4

threshold for stopping rule 4.

time.interval

a positive number to set the time interval of the animation (unit in seconds); default to be 1.

Value

animation plot of determination of stopping boundaries.

References

Yin, G. (2012). Clinical Trial Design: Bayesian and Frequentist Adaptive Methods. New York: Wiley.

Examples

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# Using Multiple Myeloma (MM) data example
MM.r = rep(0,6); MM.mean = 0.1; MM.var = 0.0225
a <- MM.mean^2*(1-MM.mean)/MM.var - MM.mean; b <- MM.mean*(1-MM.mean)^2/MM.var - (1-MM.mean)
bayes.design(a=a,b=b,r=MM.r,stop.rule="futility",p0=0.1)

# Using Acute Promyelocytic Leukaemia (APL) data example
APL.r <- c(0,1,0,0,1,1); APL.mean = 0.3; APL.var = 0.0191
a <- APL.mean^2*(1-APL.mean)/APL.var - APL.mean; b <- APL.mean*(1-APL.mean)^2/APL.var - (1-APL.mean)
bayes.design(a=a,b=b,r=APL.r,stop.rule="efficacy",p0=0.1)

Example output

Loading required package: animation
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Loading required package: nleqslv
$para.a
[1] 0.3

$para.b
[1] 2.7

$`poterior mean`
[1] 0.07500000 0.06000000 0.05000000 0.04285714 0.03750000 0.03333333

[1] "Stop the trial for futility after the inclusion of Inf patients."
sh: 1: convert: Permission denied
I cannot find ImageMagick with convert = 'convert'
[1] FALSE
Warning messages:
1: In min(which(pbeta(p0, a + r, b + n - r) > tau2)) :
  no non-missing arguments to min; returning Inf
2: running command 'convert --version' had status 126 
3: In im.convert(img.files, output = path.expand(movie.name), convert = convert,  :
  Please install ImageMagick first or put its bin path into the system PATH variable
$para.a
[1] 2.998429

$para.b
[1] 6.996335

$`poterior mean`
[1] 0.2727143 0.3333479 0.3076954 0.2857089 0.3333450 0.3750245

[1] "Stop the trial for efficacy after the inclusion of Inf patients."
sh: 1: convert: Permission denied
I cannot find ImageMagick with convert = 'convert'
[1] FALSE
Warning messages:
1: In min(which(pbeta(p0 + delta, a + r, b + n - r, lower.tail = F) >  :
  no non-missing arguments to min; returning Inf
2: running command 'convert --version' had status 126 
3: In im.convert(img.files, output = path.expand(movie.name), convert = convert,  :
  Please install ImageMagick first or put its bin path into the system PATH variable

ph2bye documentation built on May 29, 2017, 9:08 a.m.