/
weartimefuncts.R
225 lines (193 loc) · 6.04 KB
/
weartimefuncts.R
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nthOccurance <-
function(dataVct, value, nth = NA, reverse = FALSE)
{
loc = c()
if(reverse){
dataVct = rev(dataVct)
}
if(is.na(value)){
value = "NA"
dataVct[is.na(dataVct)] = "NA"
}
temp = 1:length(dataVct)
if(length(nth)==1){
if( is.na(nth)){
loc = temp[match(dataVct, value, nomatch = 0)==1]
}else{
loc = temp[match(dataVct, value, nomatch = 0)==1][nth]
}
}else{
loc = temp[match(dataVct, value, nomatch = 0)==1][nth]
}
if(reverse){
loc = length(dataVct) - loc +1
}
if(sum(is.na(loc)) == length(loc)){
loc = 0
}
return(loc)
}
marking <-
function(dataset,
frame,
cts = "counts",
streamFrame = NULL,
allowanceFrame= 2,
newcolname = "wearing")
{
cat("frame is ", frame, "\n")
cat("streamFrame is ", streamFrame, "\n")
cat("allowanceFrame is ", allowanceFrame, "\n")
ct = as.vector(dataset[,names(dataset) == cts])
if(is.null(streamFrame)){
streamFrame = round(0.5*frame)
}
#all the NA's in the original counts data will be treated as 0 counts
ct1 = ct
ct[is.na(ct)] = 0
size = dim(dataset)[1]
wearing = rep("nw", size)
ct_bool = ct > 0
rowPos = nthOccurance (dataVct = ct_bool, value= TRUE)
#getting section start and end positions
startpos = rowPos[1]
endpos = c()
prev = TRUE
for(q in 2: (length(rowPos)))
{
if(prev)
{
if( rowPos[q] - rowPos[q-1]>1 )
{
endpos = c(endpos, rowPos[q-1])
startpos = c(startpos, rowPos[q])
}
}
else
{
startpos = c(startpos, rowPos[q])
prev = TRUE
}
if(q == length(rowPos))
{endpos = c(endpos, rowPos[q])}
}#end of q
#ele3 should be handled here on startpos/endpos level
allowancewin = endpos-startpos
for(r in 1:length(allowancewin))
{
if(allowancewin[r] < allowanceFrame)
{
#upstream
usStart = startpos[r] - streamFrame
usEnd = startpos[r] - 1
if(usStart <=0)
{usStart = 1}
if(usEnd <= 0)
{usStart = 1}
if(usEnd-usStart == 0){
usSignal = "nowearing"
}else {
if(sum(ct_bool[usStart:usEnd]) >0){
usSignal = "wearing"
}else {
usSignal = "nowearing"
}
}
#downstream
dsEnd = endpos[r] + streamFrame
dsStart = endpos[r] + 1
if(dsEnd >size)
{dsEnd = size}
if(dsStart > size)
{dsStart = size}
if(dsEnd-dsStart == 0){
dsSignal = "nowearing"
}else {
if(sum(ct_bool[dsStart:dsEnd]) >0){
dsSignal = "wearing"
}else {
dsSignal = "nowearing"
}
}
if(usSignal == "nowearing" & dsSignal == "nowearing")
{
startpos[r] = -1
endpos[r] = -1
}
}#end of if/allowancewin
}#end of for/r
startpos = startpos[startpos != -1]
endpos = endpos[endpos!=-1]
#end of ele3
#now get the non-wearing gap
#frame is the gap allowed between time section. ie if 90 minutes allowed
#between two wearing sections, them frame = 90
gap = startpos[-1] - endpos[1:length(endpos)-1]
endgap = endpos[1:length(gap)]
startgap = startpos[-1]
endgap[gap<= frame] = NA
startgap [gap <= frame] = NA
startgap = c(startpos[1], startgap)
endgap = c(endgap, endpos[length(gap)+1])
newstartpos = startgap[!is.na(startgap)]
newendpos = endgap[!is.na(endgap)]
for(w in 1: length(newendpos)){
wearing[newstartpos[w]:newendpos[w]] = "w"
}
tlen= length(wearing)
wearing[tlen] = wearing[tlen-1]
wearing[is.na(ct1)] = NA
oldnames = names(dataset)
rst = cbind(dataset, wearing = wearing)
names(rst) = c(oldnames, newcolname)
return(rst)
}
dataCollapser <-
function (dataset, TS, by, col, func = sum, ...)
{
ts = as.vector(dataset[, TS])
ct = as.numeric(dataset[, col])
timeRange = range(as.vector(ts))
epoch = as.numeric(as.POSIXlt(ts[2]) - as.POSIXlt(ts[1]))
ratio = by/epoch
newrange = c(0:(ceiling(length(ts)/ratio) - 1)) * by
step1 = rep(as.POSIXlt(timeRange[1], tz = "GMT"), length(newrange))
newts = gsub(" GMT", "", step1 + newrange)
newct = rep(NA, length(newrange))
i = 1
prevts = while (i <= length(newts)) {
start = (i - 1) * ratio + 1
end = i * ratio
if (end > length(ct)) {
end = length(ct)
}
newct[i] = func(ct[start:end], ...)
i = i + 1
}
tf = data.frame(timestamp = newts, counts = newct)
names(tf) = c(TS, col)
return(tf)
}
est.on.off <- function(data, frame, allowanceFrame)
{
# data has 2 columns and is 1 sec epoch data with times as character, for example:
# time counts
# 2010-04-09 08:45:00 32
# 2010-04-09 08:45:01 28
# 2010-04-09 08:45:02 44
# collapse to 1 min epoch data
data <- dataCollapser(data, TS = "time", by = 60, col = "counts")
data <- marking(data,frame,cts = "counts",streamFrame = NULL,allowanceFrame,newcolname = "wearing")
n <- dim(data)[1]
inds.off <- (2:(n))[(data$wearing[-n]=="w")&(data$wearing[-1]=="nw")]
inds.on <- (2:(n))[(data$wearing[-n]=="nw")&(data$wearing[-1]=="w")]
if (data$wearing[1]=="w")
on.start.times <- as.character(data$time[c(1,inds.on)])
if (data$wearing[1]!="w")
on.start.times <- as.character(data$time[c(inds.on)])
if (data$wearing[n]!="nw")
off.start.times <- as.character(data$time[c(inds.off,n)])
if (data$wearing[n]=="nw")
off.start.times <- as.character(data$time[c(inds.off)])
return(list(on.start.times=on.start.times,off.start.times=off.start.times))
}