问题出现的原因是所使用的示例数据集是一个分组数据(groupedData):
library(nlme)
library(bootstrap)
y = Loblolly$height
x = Loblolly
class(x)
[1] "nfnGroupedData" "nfGroupedData" "groupedData" "data.frame"
在bootpred
函数内部,它再次被转换为矩阵。来回转换可能会很混乱,特别是当您需要线性混合模型的因子列时。
您可以编写theta.fit和theta.predict以接受data.frame:
theta.fit = function(df){
nlme(height ~ SSasymp(age, Asym, R0, lrc),
data = df,
fixed = Asym + R0 + lrc ~ 1,
random = Asym ~ 1,
start = c(Asym = 103, R0 = -8.5, lrc = -3.3))
}
theta.predict = function(fit, df){
predict(fit,df)
}
sq.err <- function(y,yhat) { (y-yhat)^2}
现在修改bootpred函数并使用df,我猜你可以再次提供y,或者指定在data.frame中使用的列:
bootpred_df = function (df,y,nboot, theta.fit, theta.predict, err.meas, ...)
{
call <- match.call()
n <- length(y)
saveii <- NULL
fit0 <- theta.fit(df, ...)
yhat0 <- theta.predict(fit0, df)
app.err <- mean(err.meas(y, yhat0))
err1 <- matrix(0, nrow = nboot, ncol = n)
err2 <- rep(0, nboot)
for (b in 1:nboot) {
ii <- sample(1:n, replace = TRUE)
saveii <- cbind(saveii, ii)
fit <- theta.fit(df[ii, ], ...)
yhat1 <- theta.predict(fit, df[ii, ])
yhat2 <- theta.predict(fit, df)
err1[b, ] <- err.meas(y, yhat2)
err2[b] <- mean(err.meas(y[ii], yhat1))
}
optim <- mean(apply(err1, 1, mean,na.rm=TRUE) - err2)
junk <- function(x, i) {
sum(x == i)
}
e0 <- 0
for (i in 1:n) {
o <- apply(saveii, 2, junk, i)
if (sum(o == 0) == 0)
cat("increase nboot for computation of the .632 estimator",
fill = TRUE)
e0 <- e0 + (1/n) * sum(err1[o == 0, i])/sum(o == 0)
}
err.632 <- 0.368 * app.err + 0.632 * e0
return(list(app.err, optim, err.632, call = call))
}
我们现在可以运行它了...但由于这些数据的特性,会出现组(种子)分布不均匀的情况,使得一些变量难以估计...很可能这个问题最好通过改进代码来解决。无论如何,如果你很幸运,它会像下面这样工作:
bootpred_df(Loblolly,Loblolly$height,20,theta.fit,theta.predict,err.meas=sq.err)
[[1]]
[1] 0.4337236
[[2]]
[1] 0.1777644
[[3]]
[1] 0.6532417
$call
bootpred_df(df = Loblolly, y = Loblolly$height, nboot = 20, theta.fit = theta.fit,
theta.predict = theta.predict, err.meas = sq.err)