| Title: | Randomization routines for Clinical Trials |
|---|---|
| Description: | A suite of classes and functions for randomizing patients in clinical trials. |
| Authors: | Vincent Carey <[email protected]> and Robert Gentleman |
| Maintainer: | Robert Gentleman <[email protected]> |
| License: | Artistic 2.0 |
| Version: | 1.51.0 |
| Built: | 2024-07-03 05:47:06 UTC |
| Source: | https://github.com/bioc/randPack |
A class that defines the parameters for a clinical trial.
Objects can be created by calls of the form new("ClinicalExperiment", ...).
name:A string naming the experiment.
factors:A named list, the names are the names of the factors that will be used for randomization. The elements of the list are the names of the factor levels.
treatments:A named integer vector indicating the relative frequency of treatment assignments that are desired. The names are the treatment names.
strataFun:A function that can be applied to instances
of PatientData to obtain the strata that the patient is to
be entered on.
randomization:A list of the randomizers to be used. There is one for each strata.
patientIDs:An instance of the PatientID class
that is used to assign patient IDs to the individuals as they are
randomized into the trial.
signature(object = "ClinicalExperiment"): a print
method.
signature(object = "ClinicalExperiment", value="list"): binds a list of lists of randomizer descriptions to a clinical experiment
instance
Basically the ClinicalExperiment class should contain the static information that describes a clinical trial and in particular how patients will be randomized to treatments in that trial.
There is a name for the trial, then a list of the factors that can be used for randomization. We have yet to decide on how to handle continuous variables (these can be used in some randomization schemes). We also have not yet included strata.
Most of the accessors are simple functions, not methods.
Similar to the classes defined by N. Balasubraminian.
R. Gentleman
treatmentNames, numberOfTreatments,
factorNames
showClass("ClinicalExperiment") data(CT1) CT1@ExperimentshowClass("ClinicalExperiment") data(CT1) CT1@Experiment
container for clinical trial randomization infrastructure and patient data
Objects can be created by calls of the form new("ClinicalTrial", ...).
Experiment:Object of class "ClinicalExperiment".
PatientData:Object of class "environment".
Randomizers:Object of class "list", one
randomizer for each strata.
No methods defined with class "ClinicalTrial" in the signature.
RG and VC
data(CT1) CT1data(CT1) CT1
This function should be used in preference to calls to new to create
instances of the ClinicalTrials class.
createTrial(CExp, seed)createTrial(CExp, seed)
CExp |
An instance of the ClinicalExperiment class. |
seed |
A seed for the random number generator. |
To ensure proper initialization of the different components this
function should be called when creating new instances of the
ClinicalTrial class.
An instance of the ClinicalTrial class.
R. Gentleman
#define the available treatments and their relative allocations trts = c( A = 3L, B = 4L, C = 1L) #describe the permuted block design pbdesc = new("PermutedBlockDesc", treatments = trts, type="PermutedBlock", numBlocks=4L) pIDs = new("PatientID", strata="Test", start=100L, stop=200L) #define the ClinicalExperiment CE1 = new("ClinicalExperiment", name="My first experiment", treatments = trts, factors = list( F1 = c("A", "B", "C"), F2 = c("t1", "t2")), randomization = list(pbdesc), patientIDs = pIDs ) #now create the instance of the trial CT1 = createTrial(CE1, seed=301)#define the available treatments and their relative allocations trts = c( A = 3L, B = 4L, C = 1L) #describe the permuted block design pbdesc = new("PermutedBlockDesc", treatments = trts, type="PermutedBlock", numBlocks=4L) pIDs = new("PatientID", strata="Test", start=100L, stop=200L) #define the ClinicalExperiment CE1 = new("ClinicalExperiment", name="My first experiment", treatments = trts, factors = list( F1 = c("A", "B", "C"), F2 = c("t1", "t2")), randomization = list(pbdesc), patientIDs = pIDs ) #now create the instance of the trial CT1 = createTrial(CE1, seed=301)
demonstration data for use with randPack
data(CT1) data(SampleData) data(alltabs) data(pD1) data(sco)data(CT1) data(SampleData) data(alltabs) data(pD1) data(sco)
The format for CT1 is is:
Formal class 'ClinicalTrial' [package "randPack"] with 3 slots
..@ Experiment :Formal class 'ClinicalExperiment' [package "randPack"] with 6 slots
.. .. ..@ name : chr "My first experiment"
.. .. ..@ factors :List of 2
.. .. .. ..$ F1: chr [1:3] "A" "B" "C"
.. .. .. ..$ F2: chr [1:2] "t1" "t2"
.. .. ..@ treatments : Named int [1:3] 3 4 1
.. .. .. ..- attr(*, "names")= chr [1:3] "A" "B" "C"
.. .. ..@ randomization:List of 2
.. .. .. ..$ Center1:List of 1
.. .. .. .. ..$ :Formal class 'PermutedBlockDesc' [package "randPack"] with 3 slots
.. .. .. .. .. .. ..@ numBlocks : int 4
.. .. .. .. .. .. ..@ treatments: Named int [1:3] 3 4 1
.. .. .. .. .. .. .. ..- attr(*, "names")= chr [1:3] "A" "B" "C"
.. .. .. .. .. .. ..@ type : chr "PermutedBlock"
.. .. .. ..$ Center2:List of 1
.. .. .. .. ..$ :Formal class 'RandomDesc' [package "randPack"] with 3 slots
.. .. .. .. .. .. ..@ numPatients: int 100
.. .. .. .. .. .. ..@ treatments : Named int [1:3] 3 4 1
.. .. .. .. .. .. .. ..- attr(*, "names")= chr [1:3] "A" "B" "C"
.. .. .. .. .. .. ..@ type : chr "Random"
.. .. ..@ strataFun :function (pDesc)
.. .. .. ..- attr(*, "source")= chr "function(pDesc) pDesc@strata"
.. .. ..@ patientIDs :Formal class 'PatientID' [package "randPack"] with 3 slots
.. .. .. .. ..@ strata: chr [1:2] "Center1" "Center2"
.. .. .. .. ..@ start : int [1:2] 1000 2000
.. .. .. .. ..@ stop : int [1:2] 1150 2150
..@ PatientData:<environment: 0x101c86590>
..@ Randomizers:List of 2
.. ..$ Center1:List of 1
.. .. ..$ :Formal class 'PermutedBlock' [package "randPack"] with 3 slots
.. .. .. .. ..@ name : chr "Center1"
.. .. .. .. ..@ treatmentTable: Named int [1:3] 3 4 1
.. .. .. .. .. ..- attr(*, "names")= chr [1:3] "A" "B" "C"
.. .. .. .. ..@ stateVariables:<environment: 0x101c867c0>
.. ..$ Center2:List of 1
.. .. ..$ :Formal class 'Random' [package "randPack"] with 3 slots
.. .. .. .. ..@ name : chr "Center2"
.. .. .. .. ..@ treatmentTable: Named int [1:3] 3 4 1
.. .. .. .. .. ..- attr(*, "names")= chr [1:3] "A" "B" "C"
.. .. .. .. ..@ stateVariables:<environment: 0x101c86a60>
various items used in examples or vignette have been serialized for convenience.
data(CT1) ## maybe str(CT1) ; plot(CT1) ...data(CT1) ## maybe str(CT1) ; plot(CT1) ...
return data frames by strata giving all covariate information along with allocations
getEnrolleeInfo(x)getEnrolleeInfo(x)
x |
An instance of the |
A list of data frames, one per stratum, for all current enrollees.
The first column is named name and gives the patient name, the
last column is named alloc and gives the treatment allocation
for that patient.
RG and VC
data(CT1) getEnrolleeInfo(CT1)data(CT1) getEnrolleeInfo(CT1)
Computes random allocation to treatment of a patient in a trial according to the randomizers etc. defined.
getTreatment(cTrial, pData)getTreatment(cTrial, pData)
cTrial |
An instance of |
pData |
An instance of |
RG and VC
data(pD1) data(CT1) getEnrolleeInfo(CT1) getTreatment(CT1, pD1) getEnrolleeInfo(CT1)data(pD1) data(CT1) getEnrolleeInfo(CT1) getTreatment(CT1, pD1) getEnrolleeInfo(CT1)
This function should be used to create all randomizers. Direct calls to
new should not be used as some coordination etc is needed to
create coherent and complete randomizers.
All of the information about the randomizer should be in the type
argument which must be an instance of the RandomizerDesc class.
makeRandomizer(name, type, seed)makeRandomizer(name, type, seed)
name |
The name of the randomizer. |
type |
An instance of the |
seed |
The initial seed for the randomizer. |
None right now.
An instance of the Randomizer class.
RG and VC
use the Pocock-Simon or Taves algorithm for computing covariate-adaptive 'minimization' allocations for a clinical trial
minimizePocSim(df, features, trtvec, obsdf, trttab, f = function(x, y) sum(abs(x + 1 - y))) minimizeTaves(df, features, trtvec, obsdf, trttab)minimizePocSim(df, features, trtvec, obsdf, trttab, f = function(x, y) sum(abs(x + 1 - y))) minimizeTaves(df, features, trtvec, obsdf, trttab)
df |
a data frame with columns corresponding to covariates rows corresponding to subjects |
features |
character vector of covariates to use |
trtvec |
vector of assignments made so far |
obsdf |
data frame for incoming observation, with values for
all components enumerated in |
trttab |
table of treatment ratios |
f |
score that determines impending allocation |
These functions are generally not called directly. See the vignette; if supplied as the method slot of a MinimizationDesc object the appropriate data are assembled as arguments to these functions.
a treatment code
new("MinimizationDesc", treatments=c(A=1L, B=1L), method=minimizePocSim, type="Minimization", featuresInUse="sex")new("MinimizationDesc", treatments=c(A=1L, B=1L), method=minimizePocSim, type="Minimization", featuresInUse="sex")
A class designed to hold patient data when randomizing participants to a clinical trial.
Objects can be created by calls of the form new("PatientData", ...).
name:That patients name, a length one character
vector.
covariates:A named list, with one element for each variable.
date:An instance of the Date class.
patientID:A length one character vector containing the assigned patient ID.
strata:A length one character vector describing the strata the patient will be randomized to.
No methods defined with class "PatientData" in the signature.
This class is used to hold the internal representation of patient data. We chose to use a named list to hold the covariate information as it might be relatively free form, with different centers (strata) providing different levels of detail. Internal code will need to be careful to handle this properly (and it doesn't currently).
The patientID slot will hold the assigned patient ID, usually this
is provided by the software during randomization, but there are situations
(eg cross-over trials, or trials with specific requirements where this
might be pre-assigned) [current implementation does not handle this case].
RG and VC
showClass("PatientData")showClass("PatientData")
A class to represent ID strings that will be assigned to patients as they are randomized in a clinical trial.
Objects can be created by calls of the form new("PatientID", ...).
strata:A vector of strata identifiers.
start:The starting indices for each strata.
stop:The largest value for each strata.
No methods defined with class "PatientID" in the signature.
Generally patient IDs are assigned at the time a patient is randomized. The scheme used here is very simple, disjoint sets of integers are used for the different strata.
Once all patiend IDs have been allocated further attempts to randomize patients on that strata should fail.
RG and VC
pIDs = new("PatientID", strata = c("Center1", "Center2"), start = c(1000L, 2000L), stop = c(1150L, 2150L) ) validPID(pIDs)pIDs = new("PatientID", strata = c("Center1", "Center2"), start = c(1000L, 2000L), stop = c(1150L, 2150L) ) validPID(pIDs)
These classes form the infrastructure that can be used to create different randomizers for clinical trials or other similar treatment allocation experiments.
Both "Randomizer and "RandomizerDesc" are virtual classes and no objects may be created from them. Their various subclasses, "ForcedAlloc", "Random", "PermutedBlock" and "Urn" can be instantiated.
For "RandomizerDesc":
treatments:A named integer vector. The names correspond to treatment names, the integers are relative allocations.
type:The name of the randomizer, this will be set internally.
For "Randomizer":
name:The name of the randomizer.
treatmentTable:A named integer vector. The names correspond to treatment names and the integer values to relative allocations.
stateVariables:An environment that is used to hold any variables that need to retain state information.
signature(from = "Randomizer", to = "Minimization"): ...
RG and VC
showClass("Randomizer")showClass("Randomizer")
The data were generated using the script in
inst/scripts/makePats.R
and are intended for testing components of the package.
data(SampleData)data(SampleData)
A data frame with 78 observations on the following 7 variables.
nameThe patients name.
sexThe sex of the patient, M or F.
ageThe age of the patient.
dateThe date they were entered into the trial.
strataWhich center they were entered by,
Center1 or Center2.
trtA treatment label, either A or B.
survSurvival time, if treatment is A then
exponential with a mean of 10, for B exponential with mean 12.
Clearly the randomizer will assign the patients to treatments, so the indicator here is irrelevant, but it seemed useful to have some difference in survival, and to keep track of it.
data(SampleData) SampleData[1:10,]data(SampleData) SampleData[1:10,]
The function allows for a relatively simple description of covariates for patients in a clinical trial and then the subsequent simulation of a cohort of the necessary size.
simPats(npat, factList)simPats(npat, factList)
npat |
The number of patients to simulate. |
factList |
A list containing either functions that will be called or named vectors containing relative proportions, for factors. |
A data.frame with npat rows and one column for each variable
given in the factList.
RG and VC
coh1 = list(center=c(C1=.4, C2=.2, C3=.1, C4=.3), sex=c(Male=.5, Female=.5), age = function(x) runif(x, min=50, max=70)) simDat = simPats(100, coh1) simDat[1:5,] table(simDat[,1])coh1 = list(center=c(C1=.4, C2=.2, C3=.1, C4=.3), sex=c(Male=.5, Female=.5), age = function(x) runif(x, min=50, max=70)) simDat = simPats(100, coh1) simDat[1:5,] table(simDat[,1])
These functions should be used to access the information in a
instance of the ClinicalExperiment-class class.
treatmentNames(object) numberOfTreatments(object) treatmentFactors(object) factorNames(object) numberOfFactorLevels(object)treatmentNames(object) numberOfTreatments(object) treatmentFactors(object) factorNames(object) numberOfFactorLevels(object)
object |
An instance of the ClinicalExperiment class. |
These functions provide the names of treatments, the names of factors, and the levels of the factors.
In all cases the information indicated by the name of the function is returned, in an appropriate form.
R. Gentleman
data(CT1) treatmentNames(CT1@Experiment)data(CT1) treatmentNames(CT1@Experiment)