RSF_eval: Function to calculate error rate using the Random Survival...

In HCsnip: Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree

Description

This function constructs survival forest using training sample's follow-up as response and cluster labels as covariate. Constructed forest is used to calculate cumulative hazard function (CHF) for each new sample based its cluster label. CHFs are compared with new samples' actual survival time to calculate the error rate. Error rate ranges from 0 to 1, with 0 representing perfect.

Usage

RSF_eval(partition, surv.time, status, te.partition, te.surv.time, te.status, ...)

Arguments

partition	Partition (clustering) corresponds to the training set samples. Cluster labels in the partition will be used as covariate to construct SF.
surv.time	A numeric vector contains the follow-up information of patients in partition , will be used as response to construct SF.
status	A binary vector contains survival status of patients in the partition, normally 0=alive, 1=dead, will be used as response to construct SF.
te.partition	Partition to be evaluated
te.surv.time	A numeric vector contains the follow-up information of patient's in te.partition
te.status	A binary vector contains survival status of patients in te.partition, normally 0=alive, 1=dead.
...	Arguments for rfsrc from the randomForestSRC package

Value

A vector of error rates. Length is equal the number of trees constructed. Default is 1000.

Author(s)

Askar Obulkasim

References

Ishwaran,H. et al., (2008). "Random survival forest", Ann. App. Statist., 2, 841-860.

Obulkasim,A. et al., (2013). "Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree", submitted.

See Also

rfsrc

Examples

data(BullingerLeukemia)
attach(BullingerLeukemia)
cl <- HCsnipper(em[, 1:30], min = 5)
cl <- cl$partitions[cl$id, ]
pred <- cluster_pred(em[, 1:100], cl[1, ], surv.time[1:30],
                     status[1:30], 31:100)
Err <- RSF_eval(cl[1, ], surv.time[1:30], status[1:30], pred, 
               surv.time[31:100], status[31:100])

HCsnip documentation built on Nov. 17, 2017, 11:17 a.m.