Type: Package
Title: Visualize Simon's Two-Stage Design
Version: 0.2.2
Date: 2025-04-27
Description: To visualize the probabilities of early termination, fail and success of Simon's two-stage design. To evaluate and visualize the operating characteristics of Simon's two-stage design.
License: GPL-2
Imports: methods, flextable, ggplot2, officer, geomtextpath, scales
Encoding: UTF-8
Language: en-US
Depends: R (≥ 4.4.0)
Suggests: clinfun, knitr, quarto, rmarkdown
RoxygenNote: 7.3.2
VignetteBuilder: quarto
NeedsCompilation: no
Packaged: 2025-04-28 03:16:36 UTC; tingtingzhan
Author: Tingting Zhan ORCID iD [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Repository: CRAN
Date/Publication: 2025-04-28 03:30:02 UTC

VisualizeSimon2Stage: Visualize Simon's Two-Stage Design

Description

To visualize the probabilities of early termination, fail and success of Simon's two-stage design. To evaluate and visualize the operating characteristics of Simon's two-stage design.

Note

Help files of individual functions are intentionally suppressed in the pdf manual. Users are encouraged to get started with

vignette('intro', package = 'VisualizeSimon2Stage')

Author(s)

Maintainer: Tingting Zhan tingtingzhan@gmail.com (ORCID)

Short Paragraph to Describe a simon_oc Object

Description

To create a short paragraph to describe a simon_oc object.

Usage

Sprintf.simon_oc(model, ...)

Arguments

model

simon_oc object

...

additional parameters, currently not in use

Value

Function Sprintf.simon_oc() returns a character scalar.

Short Paragraph to Describe a ph2simon Object

Description

To create a short paragraph to describe a ph2simon object.

Usage

Sprintf.ph2simon4(model, ...)

Sprintf.ph2simon(model, ...)

Arguments

model

a ph2simon or ph2simon4 object

...

parameters of function ph2simon4(), most importantly type

Value

Function Sprintf.ph2simon() and Sprintf.ph2simon4() return a character scalar.

Convert ph2simon4 to flextable

Description

Convert ph2simon4 to flextable

Usage

## S3 method for class 'simon_pr'
as_flextable(x, ...)

Arguments

x

a ph2simon4

...

additional parameters, currently not in use

Value

Function as_flextable.simon_pr() returns a flextable

Plot Simon's Two-Stage Design

Description

Plot ph2simon object using ggplot2.

Usage

## S3 method for class 'ph2simon'
autoplot(object, ...)

## S3 method for class 'ph2simon4'
autoplot(object, ...)

## S3 method for class 'ph2simon4'
autolayer(
  object,
  r1 = object@r1,
  n1 = object@n1,
  r = object@r,
  n = object@n,
  pu = object@pu,
  pa = object@pa,
  type = object@type,
  ...
)

## S3 method for class 'ph2simon'
autolayer(object, ...)

Arguments

object

a ph2simon or ph2simon4 object

...

parameters of function ph2simon4(), most importantly type

r1, n1, r, n

(optional) integer scalars, see ph2simon4.

pu, pa

double scalars, see function ph2simon

type

see slot ⁠@type⁠ of ph2simon4 object

Value

Function autoplot.ph2simon() returns a ggplot object.

Function autolayer.ph2simon() returns a list of ggproto and labels.

S4 Object ph2simon4

Description

One or more Simon's two-stage designs.

Usage

ph2simon4(object, type = "minimax", ...)

Arguments

object

a ph2simon object

type

character scalar or vector, see Slots

...

additional parameters, currently not in use

Slots

r1,r

non-negative integer scalars or vectors

n1,n

positive integer scalars or vectors

pu,pa

double scalars

alpha,beta

double scalars

nmax

integer

type

character scalars or vectors, type of Simon's two-stage design,

Random Generator based on Simon's Two-Stage Design

Description

Random generator based on Simon's two-stage design.

Usage

r_simon(R, prob, object, ...)

## S3 method for class 'ph2simon'
r_simon(R, prob, object, ...)

## S3 method for class 'ph2simon4'
r_simon(
  R,
  prob,
  object,
  ...,
  r1 = object@r1,
  n1 = object@n1,
  r = object@r,
  n = object@n
)

Arguments

R

positive integer scalar, number of trials R

prob

double scalar, true response rate p

object

a ph2simon or ph2simon4 object

...

parameters of function ph2simon4(), most importantly type

r1, n1, r, n

(optional) integer scalars, see ph2simon4.

Details

Function r_simon() generates R copies of the number of responses y in one Simon's two-stage design. The conclusion of the trials are,

y \leq r_1

indicates early termination

r_1 < y \leq r

indicates failure to reject H_0

y > r

indicates success to reject H_0

Here r is not needed to generate the random number of responses y. Instead, r is needed to determine if the trial is a failure or a success. Therefore, r is not a parameter of function r_simon().

Value

Function r_simon() returns an integer vector of length R, which are the R copies of the number of responses in the Simon's two-stage design.

Show S4 Objects

Description

Show S4 object.

Usage

## S4 method for signature 'simon_oc'
show(object)

## S4 method for signature 'simon_pr'
show(object)

## S4 method for signature 'ph2simon4'
show(object)

Arguments

object

S4 objects, e.g., simon_oc, simon_pr

Value

The show method for S4 objects does not have a returned value.

Operating Characteristics of Simon's Two-Stage Design

Description

Operating characteristics of one Simon's two-stage design.

Usage

simon_oc(prob, R, object, ...)

## S3 method for class 'ph2simon'
simon_oc(prob, R = 10000L, object, ...)

## S3 method for class 'ph2simon4'
simon_oc(
  prob,
  R = 10000L,
  object,
  ...,
  r1 = object@r1,
  n1 = object@n1,
  r = object@r,
  n = object@n
)

Arguments

prob

named double vector, true response rate(s) p of (multiple) drug(s). The names(prob) should be the name(s) of the drug(s).

R

integer scalar, number of simulations. Default 1e4L.

object

ph2simon or ph2simon4 object

...

parameters of function ph2simon4(), most importantly type

r1, n1, r, n

(optional) integer scalars, see ph2simon4.

Value

Function simon_oc() returns simon_oc object.

Slots

maxResp

integer vector of same length as p, the frequencies of each regime having maximum response. The summation of maxResp is the number of simulation copies.

simon_maxResp

integer vector of same length as p, the frequencies of each regime having maximum response and success in Simon's two-stage trial.

Probabilities of one Simon's Two-Stage Design

Description

Probabilities of frail (i.e., early termination) and success (to reject H_0) of one Simon's two-stage design, at given true response rate(s).

Usage

simon_pr(prob, object, ...)

## S3 method for class 'ph2simon'
simon_pr(prob, object, ...)

## S3 method for class 'ph2simon4'
simon_pr(
  prob,
  object,
  r1 = object@r1,
  n1 = object@n1,
  r = object@r,
  n = object@n,
  ...
)

Arguments

prob

double scalar or vector, true response rate(s) p

object

a ph2simon or ph2simon4 object

...

parameters of function ph2simon4(), most importantly type

r1, n1, r, n

(optional) integer scalars, see ph2simon4.

Value

Function simon_pr() returns simon_pr object.

Slots

frail

numeric scalar or vector, probabilities of frail (i.e., early termination) at given true response rate(s) p.

reject

numeric scalar or vector, probabilities of success (to reject H_0) at given true response rate(s) p.

eN

numeric scalar or vector, expected sample size(s) \textrm{E}(n) at given true response rate(s) p.

prob

double scalar or vector, true response rate(s) p

Summarize a Simon's Two-Stage Design

Description

Summarize a Simon's two-stage design

Usage

## S3 method for class 'ph2simon4'
summary(object, ...)

## S3 method for class 'ph2simon'
summary(object, ...)

Arguments

object

a ph2simon or ph2simon4 object

...

parameters of function ph2simon4(), most importantly type

Value

Function summary.ph2simon() returns a list with three (3) elements

'design'

integer matrix

'EN'

double matrix

'p'

double matrix