Last active
August 31, 2015 18:53
-
-
Save ledell/bd4e227d4e5ff426c41d to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# Update for SuperLearner::CVFolds function that enables stratification by outcome and cluster ID | |
CVFolds2 <- function (N, id, Y, cvControl) { | |
if (!is.null(cvControl$validRows)) { | |
return(cvControl$validRows) | |
} | |
stratifyCV <- cvControl$stratifyCV | |
shuffle <- cvControl$shuffle | |
V <- cvControl$V | |
if (!stratifyCV) { ### Not Stratified | |
if (shuffle) { ## Not Stratified, Shuffled | |
if (is.null(id)) { #Not stratified, Shuffled, Not by ID | |
validRows <- split(sample(1:N), rep(1:V, length = N)) | |
} | |
else { #Not stratified, Shuffled, by ID | |
n.id <- length(unique(id)) | |
id.split <- split(sample(1:n.id), rep(1:V, length = n.id)) | |
validRows <- vector("list", V) | |
for (v in seq(V)) { | |
validRows[[v]] <- which(id %in% unique(id)[id.split[[v]]]) | |
} | |
} | |
} | |
else { ## Not Stratified, Not Shuffled | |
if (is.null(id)) { #Not Stratified, Not Shuffled, Not by ID | |
validRows <- split(1:N, rep(1:V, length = N)) | |
} | |
else { #Not Stratified, Not Shuffled, by ID | |
n.id <- length(unique(id)) | |
id.split <- split(1:n.id, rep(1:V, length = n.id)) | |
validRows <- vector("list", V) | |
for (v in seq(V)) { | |
validRows[[v]] <- which(id %in% unique(id)[id.split[[v]]]) | |
} | |
} | |
} | |
} | |
else { ### Stratified | |
if (length(unique(Y)) != 2) { | |
stop("stratifyCV only implemented for binary Y") | |
} | |
if (sum(Y) < V | sum(!Y) < V) { | |
stop("number of (Y=1) or (Y=0) is less than the number of folds") | |
} | |
if (shuffle) { ## Stratified, Shuffled | |
if (is.null(id)) { #Stratified, Shuffled, not by ID | |
wiY0 <- which(Y == 0) | |
wiY1 <- which(Y == 1) | |
rowsY0 <- split(sample(wiY0), rep(1:V, length = length(wiY0))) | |
rowsY1 <- split(sample(wiY1), rep(1:V, length = length(wiY1))) | |
validRows <- vector("list", length = V) | |
names(validRows) <- paste(seq(V)) | |
for (vv in seq(V)) { | |
validRows[[vv]] <- c(rowsY0[[vv]], rowsY1[[vv]]) | |
} | |
} | |
else { #Stratified, Shuffled, by ID | |
within.split <- suppressWarnings(tapply(1:N, | |
INDEX = Y, FUN = split, 1)) | |
id.Y1 <- unique(id[within.split[[2]]]) | |
id.notY1 <- setdiff(unique(id),id.Y1) | |
n.id.Y1 <- length(id.Y1) | |
n.id.notY1 <- length(id.notY1) | |
id.Y1.split <- split(sample(1:n.id.Y1), rep(1:V, length = n.id.Y1)) | |
id.notY1.split <- split(sample(1:n.id.notY1), rep(1:V, length = n.id.notY1)) | |
validRows <- vector("list", V) | |
for (v in seq(V)) { | |
validRows[[v]] <- c(which(id %in% id.Y1[id.Y1.split[[v]]]), | |
which(id %in% id.notY1[id.notY1.split[[v]]])) | |
} | |
} | |
} | |
else { ## Stratified, Not Shuffled | |
if (is.null(id)) { | |
within.split <- suppressWarnings(tapply(1:N, | |
INDEX = Y, FUN = split, rep(1:V))) | |
validRows <- vector("list", length = V) | |
names(validRows) <- paste(seq(V)) | |
for (vv in seq(V)) { | |
validRows[[vv]] <- c(within.split[[1]][[vv]], | |
within.split[[2]][[vv]]) | |
} | |
} | |
else { #Stratified, Not Shuffled, by ID | |
within.split <- suppressWarnings(tapply(1:N, | |
INDEX = Y, FUN = split, 1)) | |
id.Y1 <- unique(id[within.split[[2]]]) | |
id.notY1 <- setdiff(unique(id),id.Y1) | |
n.id.Y1 <- length(id.Y1) | |
n.id.notY1 <- length(id.notY1) | |
id.Y1.split <- split(1:n.id.Y1, rep(1:V, length = n.id.Y1)) | |
id.notY1.split <- split(1:n.id.notY1, rep(1:V, length = n.id.notY1)) | |
validRows <- vector("list", V) | |
for (v in seq(V)) { | |
validRows[[v]] <- c(which(id %in% id.Y1[id.Y1.split[[v]]]), | |
which(id %in% id.notY1[id.notY1.split[[v]]])) | |
} | |
} | |
} | |
} | |
return(validRows) | |
} |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment