| getDataset {rpact} | R Documentation |
Creates a dataset object and returns it.
getDataset(..., floatingPointNumbersEnabled = FALSE)
getDataSet(..., floatingPointNumbersEnabled = FALSE)
... |
A |
floatingPointNumbersEnabled |
If |
The different dataset types DatasetMeans, of DatasetRates, or
DatasetSurvival can be created as follows:
An element of DatasetMeans for one sample is created by
getDataset(sampleSizes =, means =, stDevs =) where
sampleSizes, means, stDevs are vectors with stage-wise sample sizes,
means and standard deviations of length given by the number of available stages.
An element of DatasetMeans for two samples is created by
getDataset(sampleSizes1 =, sampleSizes2 =, means1 =, means2 =,
stDevs1 =, stDevs2 =) where
sampleSizes1, sampleSizes2, means1, means2,
stDevs1, stDevs2 are vectors with
stage-wise sample sizes, means and standard deviations for the two treatment groups
of length given by the number of available stages.
An element of DatasetRates for one sample is created by
getDataset(sampleSizes =, events =) where sampleSizes, events are vectors
with stage-wise sample sizes and events of length given by the number of available stages.
An element of DatasetRates for two samples is created by
getDataset(sampleSizes1 =, sampleSizes2 =, events1 =, events2 =) where
sampleSizes1, sampleSizes2, events1, events2
are vectors with stage-wise sample sizes
and events for the two treatment groups of length given by the number of available stages.
An element of DatasetSurvival is created by
getDataset(events =, logRanks =, allocationRatios =) where
events, logRanks, and allocation ratios are the stage-wise events,
(one-sided) logrank statistics, and allocation ratios.
An element of DatasetMeans, DatasetRates, and DatasetSurvival
for more than one comparison is created by adding subsequent digits to the variable names.
The system can analyze these data in a multi-arm many-to-one comparison setting where the
group with the highest index represents the control group.
Prefix overall[Capital case of first letter of variable name]... for the variable
names enables entering the overall (cumulative) results and calculates stage-wise statistics.
Since rpact version 3.2, the prefix cumulative[Capital case of first letter of variable name]... or
cum[Capital case of first letter of variable name]... can alternatively be used for this.
n can be used in place of samplesizes.
Note that in survival design usually the overall (cumulative) events and logrank test statistics are provided
in the output, so
getDataset(cumulativeEvents=, cumulativeLogRanks =, cumulativeAllocationRatios =)
is the usual command for entering survival data. Note also that for cumulativeLogranks also the
z scores from a Cox regression can be used.
For multi-arm designs, the index refers to the considered comparison. For example,
getDataset(events1=c(13, 33), logRanks1 = c(1.23, 1.55), events2 = c(16, NA), logRanks2 = c(1.55, NA))
refers to the case where one active arm (1) is considered at both stages whereas active arm 2
was dropped at interim. Number of events and logrank statistics are entered for the corresponding
comparison to control (see Examples).
For enrichment designs, the comparison of two samples is provided for an unstratified
(sub-population wise) or stratified data input.
For non-stratified (sub-population wise) data input the data sets are defined for the sub-populations
S1, S2, ..., F, where F refers to the full populations. Use of getDataset(S1 = , S2, ..., F = )
defines the data set to be used in getAnalysisResults() (see examples)
For stratified data input the data sets are defined for the strata S1, S12, S2, ..., R, where R
refers to the remainder of the strata such that the union of all sets is the full population.
Use of getDataset(S1 = , S12 = , S2, ..., R = ) defines the data set to be used in
getAnalysisResults() (see examples)
For survival data, for enrichment designs the log-rank statistics can only be entered as stratified
log-rank statistics in order to provide strong control of Type I error rate. For stratified data input,
the variables to be specified in getDataset() are cumEvents, cumExpectedEvents,
cumVarianceEvents, and cumAllocationRatios or overallEvents, overallExpectedEvents,
overallVarianceEvents, and overallAllocationRatios. From this, (stratified) log-rank tests and
and the independent increments are calculated.
Returns a Dataset object.
The following generics (R generic functions) are available for this result object:
names() to obtain the field names,
print() to print the object,
summary() to display a summary of the object,
plot() to plot the object,
as.data.frame() to coerce the object to a data.frame,
as.matrix() to coerce the object to a matrix.
## Not run:
# Create a Dataset of Means (one group):
datasetOfMeans <- getDataset(
n = c(22, 11, 22, 11),
means = c(1, 1.1, 1, 1),
stDevs = c(1, 2, 2, 1.3)
)
datasetOfMeans
datasetOfMeans$show(showType = 2)
datasetOfMeans2 <- getDataset(
cumulativeSampleSizes = c(22, 33, 55, 66),
cumulativeMeans = c(1.000, 1.033, 1.020, 1.017),
cumulativeStDevs = c(1.00, 1.38, 1.64, 1.58)
)
datasetOfMeans2
datasetOfMeans2$show(showType = 2)
as.data.frame(datasetOfMeans2)
# Create a Dataset of Means (two groups):
datasetOfMeans3 <- getDataset(
n1 = c(22, 11, 22, 11),
n2 = c(22, 13, 22, 13),
means1 = c(1, 1.1, 1, 1),
means2 = c(1.4, 1.5, 3, 2.5),
stDevs1 = c(1, 2, 2, 1.3),
stDevs2 = c(1, 2, 2, 1.3)
)
datasetOfMeans3
datasetOfMeans4 <- getDataset(
cumulativeSampleSizes1 = c(22, 33, 55, 66),
cumulativeSampleSizes2 = c(22, 35, 57, 70),
cumulativeMeans1 = c(1, 1.033, 1.020, 1.017),
cumulativeMeans2 = c(1.4, 1.437, 2.040, 2.126),
cumulativeStDevs1 = c(1, 1.38, 1.64, 1.58),
cumulativeStDevs2 = c(1, 1.43, 1.82, 1.74)
)
datasetOfMeans4
df <- data.frame(
stages = 1:4,
n1 = c(22, 11, 22, 11),
n2 = c(22, 13, 22, 13),
means1 = c(1, 1.1, 1, 1),
means2 = c(1.4, 1.5, 3, 2.5),
stDevs1 = c(1, 2, 2, 1.3),
stDevs2 = c(1, 2, 2, 1.3)
)
datasetOfMeans5 <- getDataset(df)
datasetOfMeans5
# Create a Dataset of Means (three groups) where the comparison of
# treatment arm 1 to control is dropped at the second interim stage:
datasetOfMeans6 <- getDataset(
cumN1 = c(22, 33, NA),
cumN2 = c(20, 34, 56),
cumN3 = c(22, 31, 52),
cumMeans1 = c(1.64, 1.54, NA),
cumMeans2 = c(1.7, 1.5, 1.77),
cumMeans3 = c(2.5, 2.06, 2.99),
cumStDevs1 = c(1.5, 1.9, NA),
cumStDevs2 = c(1.3, 1.3, 1.1),
cumStDevs3 = c(1, 1.3, 1.8))
datasetOfMeans6
# Create a Dataset of Rates (one group):
datasetOfRates <- getDataset(
n = c(8, 10, 9, 11),
events = c(4, 5, 5, 6)
)
datasetOfRates
# Create a Dataset of Rates (two groups):
datasetOfRates2 <- getDataset(
n2 = c(8, 10, 9, 11),
n1 = c(11, 13, 12, 13),
events2 = c(3, 5, 5, 6),
events1 = c(10, 10, 12, 12)
)
datasetOfRates2
# Create a Dataset of Rates (three groups) where the comparison of
# treatment arm 2 to control is dropped at the first interim stage:
datasetOfRates3 <- getDataset(
cumN1 = c(22, 33, 44),
cumN2 = c(20, NA, NA),
cumN3 = c(20, 34, 44),
cumEvents1 = c(11, 14, 22),
cumEvents2 = c(17, NA, NA),
cumEvents3 = c(17, 19, 33))
datasetOfRates3
# Create a Survival Dataset
datasetSurvival <- getDataset(
cumEvents = c(8, 15, 19, 31),
cumAllocationRatios = c(1, 1, 1, 2),
cumLogRanks = c(1.52, 1.98, 1.99, 2.11)
)
datasetSurvival
# Create a Survival Dataset with four comparisons where treatment
# arm 2 was dropped at the first interim stage, and treatment arm 4
# at the second.
datasetSurvival2 <- getDataset(
cumEvents1 = c(18, 45, 56),
cumEvents2 = c(22, NA, NA),
cumEvents3 = c(12, 41, 56),
cumEvents4 = c(27, 56, NA),
cumLogRanks1 = c(1.52, 1.98, 1.99),
cumLogRanks2 = c(3.43, NA, NA),
cumLogRanks3 = c(1.45, 1.67, 1.87),
cumLogRanks4 = c(1.12, 1.33, NA)
)
datasetSurvival2
# Enrichment: Stratified and unstratified data input
# The following data are from one study. Only the first
# (stratified) data input enables a stratified analysis.
# Stratified data input
S1 <- getDataset(
sampleSize1 = c(18, 17),
sampleSize2 = c(12, 33),
mean1 = c(125.6, 111.1),
mean2 = c(107.7, 77.7),
stDev1 = c(120.1, 145.6),
stDev2 = c(128.5, 133.3))
S2 <- getDataset(
sampleSize1 = c(11, NA),
sampleSize2 = c(14, NA),
mean1 = c(100.1, NA),
mean2 = c( 68.3, NA),
stDev1 = c(116.8, NA),
stDev2 = c(124.0, NA))
S12 <- getDataset(
sampleSize1 = c(21, 17),
sampleSize2 = c(21, 12),
mean1 = c(135.9, 117.7),
mean2 = c(84.9, 107.7),
stDev1 = c(185.0, 92.3),
stDev2 = c(139.5, 107.7))
R <- getDataset(
sampleSize1 = c(19, NA),
sampleSize2 = c(33, NA),
mean1 = c(142.4, NA),
mean2 = c(77.1, NA),
stDev1 = c(120.6, NA),
stDev2 = c(163.5, NA))
dataEnrichment <- getDataset(S1 = S1, S2 = S2, S12 = S12, R = R)
dataEnrichment
# Unstratified data input
S1N <- getDataset(
sampleSize1 = c(39, 34),
sampleSize2 = c(33, 45),
stDev1 = c(156.503, 120.084),
stDev2 = c(134.025, 126.502),
mean1 = c(131.146, 114.4),
mean2 = c(93.191, 85.7))
S2N <- getDataset(
sampleSize1 = c(32, NA),
sampleSize2 = c(35, NA),
stDev1 = c(163.645, NA),
stDev2 = c(131.888, NA),
mean1 = c(123.594, NA),
mean2 = c(78.26, NA))
F <- getDataset(
sampleSize1 = c(69, NA),
sampleSize2 = c(80, NA),
stDev1 = c(165.468, NA),
stDev2 = c(143.979, NA),
mean1 = c(129.296, NA),
mean2 = c(82.187, NA))
dataEnrichmentN <- getDataset(S1 = S1N, S2 = S2N, F = F)
dataEnrichmentN
## End(Not run)