将事件开始和结束转换为 R 中的状态向量

Question

我希望将事件开始和结束日期列表转换为状态向量，其中开始和结束之间的任何一天都是 1，外面是 0（例如 2,4 -> c( 0,1,1,1,0,0))

每个主题（由 id 键入）可能有多个开始和结束日期，在不同的行中，需要合并。

我有一个非常依赖 lapply 的解决方案（如果需要我可以访问超级计算机，所以可以将它们切换到 mclapply），但更希望将事情矢量化为尽可能多，因为输入数据可能很大 (~250MB)。

任何人都可以在这里找到减少任何步骤的途径吗？

require(data.table)

#The days that will be assessed for state
period = as.integer(1:8)
#Indices for days (they are not necessarily sequential)
dayInds = as.integer(1:length(period))

#Events for same ID will never overlap
dt = data.table(id = c("a","a","b","c","d","d","e"),
                start = c(1,6,3,3,3,5,5),
                end =   c(4,7,6,7,4,6,5))

# setkeyv(dt,colnames(dt))
setkeyv(dt,c("start","end"))

#Setup output table
stateData = data.table(id = dt$id)
#Remove "-" from days before index, they could get confusing, and initialise
#columns with zero
dayStrings = paste("d",gsub("-", "m", period),sep="")
stateData[,(dayStrings) := 0L]

#Find whether there is an overlap between a specified day in period and a
#subject's events
getStateOnDay = function(dayInd) {
  #Get day
  day = period[dayInd]
  #Create a table with the same number of rows as input dt, with a one day long
  #event on the input day
  overlapDays = unlist(foverlaps(data.table(start = day,end = day),
                                 dt,
                                 which=TRUE,
                                 nomatch = 0L)$yid)
  #Set those days to 1 in the state table
  set(stateData,overlapDays,dayInd+1L,1L)

}

#Get states for each row
lapply(dayInds,getStateOnDay)


#Create table for data with one row for each unique ID
reducedStateData = data.table(id = unique(stateData$id))
reducedStateData[,(dayStrings) := 0L]

#Sum a vector of logicals using OR
orSum = function(inputVec) {
  return(Reduce("|", c(inputVec)))
}

#Function for finding for each ID if they were in the state on a given day
reduceStatesByID = function(dayInd) {
  set(reducedStateData,
      NULL,
      dayInd+1L,
      stateData[,c(1,dayInd+1),with=FALSE][,as.integer(lapply(.SD, orSum)), by=id][,V1])
  return(NA)
}

#Apply reduction and sort
lapply(dayInds,reduceStatesByID)
setkey(reducedStateData,id)

Answer 1

这是使用 Map 和序列的尝试，然后 dcast-ed 为宽格式：

dcast(
  dt[, .(d=unlist(Map(seq, start, end)), val=1), by=id],
  id ~ d, value.var="val", fun.aggregate=sum, na.rm=TRUE
)

#   id 1 2 3 4 5 6 7
#1:  a 1 1 1 1 0 1 1
#2:  b 0 0 1 1 1 1 0
#3:  c 0 0 1 1 1 1 1
#4:  d 0 0 1 1 1 1 0
#5:  e 0 0 0 0 1 0 0

@Frank 在评论中的建议似乎更快，可能主要是因为避免了 by=:

dt[
    , .(t = unlist(L <- Map(seq, start, end)), id = rep(id, lengths(L)))
  ][, dcast(.SD, id ~ t, fun.agg = length)]

Answer 2

这是一种使用 data.table 极其高效的 set 函数的方法，它是在构造一个具有正确维度 (res) 的空 data.table 以及从原始矩阵和新矩阵中的行 (resRows)。

# construct empty data.table (ids and appropriate number of variables with 0s)
res <- data.table(id=unique(dt$id), matrix(0L, dt[, uniqueN(id)], max(dt$end)))

# get values for rows from id variable for placement into final data.table
resRows <- dt[, cumsum(rowid(id) == 1L)]

# fill in appropriate elements in data.table with 1s using set
for(i in seq_along(resRows)) set(res, resRows[i], dt[i, seq(start, end)] + 1L, 1L)

这个returns

res
   id V1 V2 V3 V4 V5 V6 V7
1:  a  1  1  1  1  0  1  1
2:  b  0  0  1  1  1  1  0
3:  c  0  0  1  1  1  1  1
4:  d  0  0  1  1  1  1  0
5:  e  0  0  0  0  1  0  0

将事件开始和结束转换为 R 中的状态向量

Transforming event start and ends to state vectors in R

reduce

r

time-series

data.table