Description Usage Arguments Details Value Author(s) References See Also Examples
Conduct K-adaptive partitioning algorithm for survival data
1 |
formula |
Formula object with a response on the left hand side of the '~' operator, and the covariate terms on the right side. The response has to be a survival object with survival time and censoring status in the Surv function. For more details, see Formula page. |
data |
data frame with variables used in formula. It needs at least three variables including survival time, censoring status, and a covariate. Multivariate covariates can be supported with "+" sign. |
K |
number of subgroups used in the model fitting. The default value is 2:4 which means finding optimal subgroups ranging from 2 to 4. |
type |
Select a type of algorithm in order to find optimal number of subgroups. Two options are provided: |
mindat |
the minimum number of observations at each subgroup. The default value is 5% of observations. |
... |
a list of tuning parameters with the class, "kapsOptions". For more details, see kaps.control. |
This function provides routines to conduct KAPS algorithm which is designed to classify cut-off values by the minimax-based rule.
The function returns an object with class "kaps" with the following slots.
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evaluated function call |
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formula to be used in the model fitting |
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data to be used in the model fitting |
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information about the subgroup classification |
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an index for the optimal subgroup among the candidate K |
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test statistic with the worst pair of subgroups for the split set s |
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the overall test staitstic with K subgroups using the split set s |
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selected pair of subgroups |
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selected covariate in the model fitting |
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selected set of cut-off points |
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minimum number of observations at a subgroup |
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Bonferroni corrected p-value matrix. The first row means overall p-values and the second one denotes p-values of the worst-pair against K. The column in the matrix describes the order of K. |
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adjusted overall test statistic by Bootstrapping |
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adjusted worst-pair test statistic by Bootstrapping |
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candidate K used in the argument |
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list object about the results of each candidate K |
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tuning parameters |
Soo-Heang Eo eo.sooheang@gmail.com
Seung-Mo Hong smhong28@gmail.com
HyungJun Cho hj4cho@korea.ac.kr
S-H Eo, S-M Hong and H Cho (2014). K-adaptive partitioning for survival data, submitted.
show
, plot
, predict
, print
and summary
for the convenient use of kaps()
kaps.control
to control kaps() more detail
count.mindat
to calculate minimum subgroup sample size
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ## Not run:
data(toy)
f <- Surv(time, status) ~ meta
# Fit kaps algorithm without cross-validation.
# It means the step to finding optimal K is not entered.
fit1 <- kaps(f, data = toy, K = 3)
# show the object of kaps (it contains apss S4 class)
fit1
# plot Kaplan-Meire estimates
plot(fit1)
# Fit kaps algorithm for selection optimal number of subgropus.
fit2 <- kaps(f, data = toy, K= 2:4)
fit2
# plot outputs with subgroup selection
require(locfit) # for scatterplot smoothing
plot(fit2)
print(fit2,K=2)
summary(fit2)
summary(fit2,K=2)
# require(party)
# fit4 <- ctree(f, data = toy)
## End(Not run)
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