Crm-class: An R6 class encapsulating CRM models This class wraps the...
In precautionary: Safety Diagnostics for Dose-Escalation Trial Designs
Description
Details
Super class
Methods
Note
Examples
Description
An R6 class encapsulating CRM models
This class wraps the functionality of package dfcrm, adding
efficient Rust implementations of some numerical routines.
An R6 class encapsulating CRM models
This class wraps the functionality of package dfcrm, adding
efficient Rust implementations of some numerical routines.
Details
Syntactically, the method chaining supported by R6 classes makes the
invocation of CRM models more transparent. The mutability conferred
by reference semantics enables memoization (caching) of results, which
can speed up DTP calculations significantly.
Presently, this class supports only the 'empiric' (aka 'power') model.
But it is hoped that inheritance will assist in rendering other models
implemented in package dfcrm clearly, with code reuse.
Super class
precautionary::Cpe -> Crm
Methods
Public methods
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Inherited methods
Method new()
Usage
Crm$new(skeleton, scale = sqrt(1.34), target)
Arguments
skeletonCRM skeleton
scaleSigma parameter of prior on beta parameter
targetTarget toxicity rate
Details
Create a new Crm object.
Returns
A Crm object.
Examples
# An example verbatim from dfcrm::crm()
prior <- c(0.05, 0.10, 0.20, 0.35, 0.50, 0.70)
target <- 0.2
level <- c(3, 4, 4, 3, 3, 4, 3, 2, 2, 2)
y <- c(0, 0, 1, 0, 0, 1, 1, 0, 0, 0)
s <- sqrt(1.34)
old <- dfcrm::crm(prior, target, y, level)
new <- Crm$new(skeleton = prior, target = target)$
dontcache()$
observe(level, y)$
est(impl="rusti", abbrev=FALSE)
Method max_dose()
Usage
Crm$max_dose(D)
Arguments
DIncluded to match signature of superclass method.
It is an error to call this method with non-missing D parameter.
Details
Return number of prespecified doses
Returns
Length of CRM skeleton.
Method skeleton()
Usage
Crm$skeleton(skeleton)
Arguments
skeletonA numeric vector to set as the model skeleton.
Details
Set or query CRM skeleton
Returns
Self (invisibly), unless skeleton is missing,
in which case the skeleton, a numeric vector, is returned.
Method dontcache()
Usage
Crm$dontcache()
Details
Set private cache to NULL; useful for performance testing
Returns
Self, invisibly
Method report()
Usage
Crm$report(...)
Arguments
...Optional arguments specifying columns to add to report
Details
Report lifetime duty & performance statistics
Returns
A named vector summarizing lifetime duty and performance
Method stop_func()
Usage
Crm$stop_func(sfunc)
Arguments
sfuncA function taking mtd objects to mtd objects,
attaching suitable stopping information
Details
Set the stopping function
Returns
Self, invisibly
Method no_skip_esc()
Usage
Crm$no_skip_esc(tf)
Arguments
tfAn atomic logical value, TRUE or FALSE
Details
Set the no_skip_esc behavior
Returns
Self, invisibly
Method no_skip_deesc()
Usage
Crm$no_skip_deesc(tf)
Arguments
tfAn atomic logical value, TRUE or FALSE
Details
Set the no_skip_deesc behavior
Returns
Self, invisibly
Method global_coherent_esc()
Usage
Crm$global_coherent_esc(tf)
Arguments
tfAn atomic logical value, TRUE or FALSE
Details
Set the global_coherent_esc behavior
Returns
Self, invisibly
Method conf_level()
Usage
Crm$conf_level(conf)
Arguments
confA numeric confidence less than 1.0
Details
Set the required confidence level for escalation decisions
Returns
Self, invisibly
Method observe()
Usage
Crm$observe(level, tox)
Arguments
levelA patient-wise vector of dose assignments
toxA patient-wise vector of 0/1 toxicity assessments
Details
Set patient-wise toxicity observations
Returns
Self, invisibly
Method tally()
Usage
Crm$tally(x, o)
Arguments
xA dose-wise vector of toxicity counts
oA dose-wise vector of non-toxicity counts
Details
Set dose-wise toxicity observations
Returns
Self, invisibly
Method est()
Usage
Crm$est(impl = "rusti", abbrev = TRUE)
Arguments
implA string choosing the low-level implementation to use.
Possible values include "dfcrm", "rusti" and "ruste".
abbrevLogical; if TRUE (the default), an abbreviated mtd
object is returned to save execution time. If FALSE, a complete object is
returned, suitable for regression testing against package dfcrm.
Details
Estimate the model
Returns
An object of class mtd as per package dfcrm
Method applied()
Usage
Crm$applied(x, o, last_dose = NA, max_dose = NULL)
Arguments
xA dose-wise vector of toxicity counts
oA dose-wise vector of non-toxicity counts
last_doseThe most recently given dose, as required to implement
the global_coherent_esc=TRUE behavior
max_doseUnused; included for compatibility with superclass method
of required impl parameter and optional abbrev flag.
Details
Return dose recommendation for given tox/no-tox tallies.
This function caches results, which greatly saves computation time
in CPE – yielding e.g. a 5x speedup for the VIOLA trial example.
Returns
An object of class mtd as per package dfcrm,
or possibly an abbreviated version of such object as returned by
method Crm$est().
Method clone()
The objects of this class are cloneable with this method.
Usage
Crm$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Note
This specializes the superclass set/get method, consistent
with the non-mutable number of doses of CRM with fixed skeleton.
Examples
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## ------------------------------------------------
## Method `Crm$new`
## ------------------------------------------------
# An example verbatim from dfcrm::crm()
prior <- c(0.05, 0.10, 0.20, 0.35, 0.50, 0.70)
target <- 0.2
level <- c(3, 4, 4, 3, 3, 4, 3, 2, 2, 2)
y <- c(0, 0, 1, 0, 0, 1, 1, 0, 0, 0)
s <- sqrt(1.34)
old <- dfcrm::crm(prior, target, y, level)
new <- Crm$new(skeleton = prior, target = target)$
dontcache()$
observe(level, y)$
est(impl="rusti", abbrev=FALSE)
precautionary documentation built on Aug. 9, 2021, 9:14 a.m.
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Description Details Super class Methods Note Examples
Description
An R6 class encapsulating CRM models
This class wraps the functionality of package dfcrm, adding efficient Rust implementations of some numerical routines.
An R6 class encapsulating CRM models
This class wraps the functionality of package dfcrm, adding efficient Rust implementations of some numerical routines.
Details
Syntactically, the method chaining supported by R6 classes makes the invocation of CRM models more transparent. The mutability conferred by reference semantics enables memoization (caching) of results, which can speed up DTP calculations significantly.
Presently, this class supports only the 'empiric' (aka 'power') model. But it is hoped that inheritance will assist in rendering other models implemented in package dfcrm clearly, with code reuse.
Super class
precautionary::Cpe -> Crm
Methods
Public methods
Inherited methods
Method new()
Usage
Crm$new(skeleton, scale = sqrt(1.34), target)
Arguments
skeletonCRM skeleton
scaleSigma parameter of prior on beta parameter
targetTarget toxicity rate
Details
Create a new Crm object.
Returns
A Crm object.
Examples
# An example verbatim from dfcrm::crm()
prior <- c(0.05, 0.10, 0.20, 0.35, 0.50, 0.70)
target <- 0.2
level <- c(3, 4, 4, 3, 3, 4, 3, 2, 2, 2)
y <- c(0, 0, 1, 0, 0, 1, 1, 0, 0, 0)
s <- sqrt(1.34)
old <- dfcrm::crm(prior, target, y, level)
new <- Crm$new(skeleton = prior, target = target)$
dontcache()$
observe(level, y)$
est(impl="rusti", abbrev=FALSE)
Method max_dose()
Usage
Crm$max_dose(D)
Arguments
DIncluded to match signature of superclass method. It is an error to call this method with non-missing
Dparameter.
Details
Return number of prespecified doses
Returns
Length of CRM skeleton.
Method skeleton()
Usage
Crm$skeleton(skeleton)
Arguments
skeletonA numeric vector to set as the model skeleton.
Details
Set or query CRM skeleton
Returns
Self (invisibly), unless skeleton is missing,
in which case the skeleton, a numeric vector, is returned.
Method dontcache()
Usage
Crm$dontcache()
Details
Set private cache to NULL; useful for performance testing
Returns
Self, invisibly
Method report()
Usage
Crm$report(...)
Arguments
...Optional arguments specifying columns to add to report
Details
Report lifetime duty & performance statistics
Returns
A named vector summarizing lifetime duty and performance
Method stop_func()
Usage
Crm$stop_func(sfunc)
Arguments
sfuncA function taking
mtdobjects tomtdobjects, attaching suitable stopping information
Details
Set the stopping function
Returns
Self, invisibly
Method no_skip_esc()
Usage
Crm$no_skip_esc(tf)
Arguments
tfAn atomic logical value, TRUE or FALSE
Details
Set the no_skip_esc behavior
Returns
Self, invisibly
Method no_skip_deesc()
Usage
Crm$no_skip_deesc(tf)
Arguments
tfAn atomic logical value, TRUE or FALSE
Details
Set the no_skip_deesc behavior
Returns
Self, invisibly
Method global_coherent_esc()
Usage
Crm$global_coherent_esc(tf)
Arguments
tfAn atomic logical value, TRUE or FALSE
Details
Set the global_coherent_esc behavior
Returns
Self, invisibly
Method conf_level()
Usage
Crm$conf_level(conf)
Arguments
confA numeric confidence less than 1.0
Details
Set the required confidence level for escalation decisions
Returns
Self, invisibly
Method observe()
Usage
Crm$observe(level, tox)
Arguments
levelA patient-wise vector of dose assignments
toxA patient-wise vector of 0/1 toxicity assessments
Details
Set patient-wise toxicity observations
Returns
Self, invisibly
Method tally()
Usage
Crm$tally(x, o)
Arguments
xA dose-wise vector of toxicity counts
oA dose-wise vector of non-toxicity counts
Details
Set dose-wise toxicity observations
Returns
Self, invisibly
Method est()
Usage
Crm$est(impl = "rusti", abbrev = TRUE)
Arguments
implA string choosing the low-level implementation to use. Possible values include
"dfcrm","rusti"and"ruste".abbrevLogical; if TRUE (the default), an abbreviated
mtdobject is returned to save execution time. If FALSE, a complete object is returned, suitable for regression testing against package dfcrm.
Details
Estimate the model
Returns
An object of class mtd as per package dfcrm
Method applied()
Usage
Crm$applied(x, o, last_dose = NA, max_dose = NULL)
Arguments
xA dose-wise vector of toxicity counts
oA dose-wise vector of non-toxicity counts
last_doseThe most recently given dose, as required to implement the
global_coherent_esc=TRUEbehaviormax_doseUnused; included for compatibility with superclass method of required
implparameter and optionalabbrevflag.
Details
Return dose recommendation for given tox/no-tox tallies.
This function caches results, which greatly saves computation time in CPE – yielding e.g. a 5x speedup for the VIOLA trial example.
Returns
An object of class mtd as per package dfcrm,
or possibly an abbreviated version of such object as returned by
method Crm$est().
Method clone()
The objects of this class are cloneable with this method.
Usage
Crm$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Note
This specializes the superclass set/get method, consistent with the non-mutable number of doses of CRM with fixed skeleton.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## ------------------------------------------------
## Method `Crm$new`
## ------------------------------------------------
# An example verbatim from dfcrm::crm()
prior <- c(0.05, 0.10, 0.20, 0.35, 0.50, 0.70)
target <- 0.2
level <- c(3, 4, 4, 3, 3, 4, 3, 2, 2, 2)
y <- c(0, 0, 1, 0, 0, 1, 1, 0, 0, 0)
s <- sqrt(1.34)
old <- dfcrm::crm(prior, target, y, level)
new <- Crm$new(skeleton = prior, target = target)$
dontcache()$
observe(level, y)$
est(impl="rusti", abbrev=FALSE)
|
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