Description Usage Arguments Value Author(s) Examples

A division of data is specified, for use of linear discriminant analysis, into a training and test set. Feature selection and model fitting is formed, first with I/II as training/test, then with II/I as training/test

1 2 3 |

`x` |
Matrix; rows are features, and columns are observations ('samples') |

`cl` |
Factor that classifies columns into groups that will classify the data for purposes of discriminant calculations |

`traintest` |
Values that specify a division of observations into two groups. In the first pass (fold), one to be training and the other test, with the roles then reversed in a second pass or fold. |

`nfeatures` |
integer: numbers of features for which calculations are required |

`print.acc` |
logical: should accuracies be printed? |

`print.progress` |
logical: should progress by feature number be printed? |

`sub1.2` |
row numbers of features, by order of values of the group
separation measure, for the first subset (I) of the |

`acc1.2` |
accuracies, with I as training set and II as test |

`sub2.1` |
row numbers of features, by order of values of the group
separation measure, for the second subset (II) of the |

`acc2.1` |
accuracies, with II as training set and I as test |

John Maindonald

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mat <- matrix(rnorm(1000), ncol=20)
cl <- factor(rep(1:3, c(7,9,4)))
gp.id <- divideUp(cl, nset=2)
accTrainTest(x=mat, cl=cl, traintest=gp.id,
nfeatures=1:16, print.acc=TRUE, print.progress=TRUE)
## The function is currently defined as
function(x=matrix(rnorm(1000), ncol=20), cl = factor(rep(1:3, c(7,9,4))),
traintest=divideUp(cl, nset=2), nfeatures=NULL, print.acc=FALSE){
traintest <- factor(traintest)
train <- traintest==levels(traintest)[1]
testset <- traintest==levels(traintest)[2]
cl1 <- cl[train]
cl2 <- cl[testset]
ng1 <- length(cl1)
ng2 <- length(cl2)
maxg <- max(c(ng1-length(unique(cl1))-2,
ng2-length(unique(cl2))-2))
if(is.null(nfeatures)){
max.features <- maxg
nfeatures <- 1:max.features
} else
{
if(max(nfeatures)>maxg)nfeatures <- nfeatures[nfeatures<=maxg]
max.features <- max(nfeatures)
}
ord1 <- orderFeatures(x, cl, subset=train)[1:max.features]
ord2 <- orderFeatures(x, cl, subset=testset)[1:max.features]
ord <- unique(c(ord1, ord2))
sub1 <- match(ord1, ord)
sub2 <- match(ord2, ord)
df1 <- data.frame(t(x[ord, train]))
df2 <- data.frame(t(x[ord, testset]))
acc1 <- acc2 <- numeric(max(nfeatures))
for(i in nfeatures){
if(print.progress)cat(paste(i, ":", sep=""))
df1.lda <- lda(df1[, sub1[1:i], drop=FALSE], cl1)
hat2 <- predict(df1.lda, newdata=df2[, sub1[1:i], drop=FALSE])$class
tab <- table(hat2, cl2)
acc1[i] <- sum(tab[row(tab)==col(tab)])/sum(tab)
df2.lda <- lda(df2[, sub2[1:i], drop=FALSE], cl2)
hat1 <- predict(df2.lda, newdata=df1[, sub2[1:i], drop=FALSE])$class
tab <- table(hat1, cl1)
acc2[i] <- sum(tab[row(tab)==col(tab)])/sum(tab)
}
cat("\n")
if(print.acc){
print(round(acc1,2))
print(round(acc2,2))
}
maxacc1 <- max(acc1)
maxacc2 <- max(acc2)
sub1 <- match(maxacc1, acc1)
sub2 <- match(maxacc2, acc2)
nextacc1 <- max(acc1[acc1<1])
nextacc2 <- max(acc1[acc1<2])
lower1 <- maxacc1-sqrt(nextacc1*(1-nextacc1)/ng1)
lower2 <- maxacc2-sqrt(nextacc2*(1-nextacc2)/ng2)
lsub1 <- min((1:ng1)[acc1>lower1])
lsub2 <- min((1:ng2)[acc2>lower2])
lower <- c("Best accuracy, less 1SD ",
paste(paste(round(c(lower1, lower2),2), c(lsub1, lsub2),
sep=" ("), " features) ", sep=""))
best <- c("Best accuracy",
paste(paste(round(c(maxacc1, maxacc2),2), c(sub1, sub2),
sep=" ("), " features)", sep=""))
acc.df <- cbind(lower, best)
dimnames(acc.df) <- list(c("Training/test split",
"I (training) / II (test) ",
"II (training) / I (test) "),c("",""))
print(acc.df, quote=FALSE)
invisible(list(sub1.2=ord1, acc1.2=acc1, sub2.1=ord2, acc2.1=acc2))
}
``` |

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