PRIM.real.data.min {rfcdmin} | R Documentation |
The HIV-protein stimulated st.1829 FCS R-object and the unstimulated unst.1829 FCS R-object from the VRCmin data were used to exemplify the PRIM algorithm on a real dataset. The three steps for the finding of a single rule were saved as output. The out.peel is the 'PRIM.step' class object of the Peeling step. The out.expand is the 'PRIM.step' class object of the Expansion Step. The out.cv is the 'PRIM.crossval.step' class object of the cross-validation step. From these output objects we obtain the necessary indices and vectors for making plots that are exemplified in PRIM.pdf.
data(PRIM.real.data.min)
The class information, extraction, plotting, implementation tools for the 'PRIM.step' and the 'PRIM.crossval.step' class objects are detailed in the rfcprim package.
See VRCmin
See VRCmin and rfcprim.
data(PRIM.real.data) ## the following code was used to generate the output if (FALSE){ data(VRCmin) ## the HIV-protein stimulation status Y <- c(rep(1, dim.FCS(st.1829)[1]), rep(0, dim.FCS(unst.1829)[1])) ## the dataset X <- rbind(as(st.1829, "matrix"), as(unst.1829, "matrix")) if (require(rfcprim)){ out.peel <- peel.step(X, Y, min.box.size = 500, alpha=0.10, verbose=TRUE) out.expand <- expand.step(X, Y, out.peel@best.box.idx, beta=0.01, verbose=TRUE) out.cv <- crossval.step(X, Y, num.testdata=2, prob.testdata=c(0.50, 0.50), alpha=0.10, target.mu.Y=1, min.box.size=500, choose.best.box.decision=c("max.mean.box", "final.box"), beta=0.01, verbose=TRUE) box.idx.list <- list(out.peel@best.box.idx, out.expand@best.box.idx) box.support.PS <- out.peel@box.support.vec means.PS <- out.peel@means.vec type.PS <- out.peel@type.vec box.support.ES <- out.expand@box.support.vec means.ES <- out.expand@means.vec type.ES <- out.expand@type.vec best.box.X.ranges <- out.expand@best.box.X.ranges Rule1.idx <- out.expand@best.box.idx TD1 <- out.cv[1, "testdata.idx.list"] TD2 <- out.cv[2, "testdata.idx.list"] box.idx.listTD1 <- list(out.cv[1,"step.set.list"]@peel.step@best.box.idx, out.cv[1, "step.set.list"]@expand.step@best.box.idx) box.idx.listTD2 <- list(out.cv[2,"step.set.list"]@peel.step@best.box.idx, out.cv[2, "step.set.list"]@expand.step@best.box.idx) } }