Issues with Indexing and Merging XTS Objects in R - r

Question

Apologies in advance if this is answered elsewhere. I have searched for roughly 24 hrs and have come up empty at every turn.
This is the data set I am working with
Sys.setenv(TZ='GMT')
dat = read.csv("SPY_MINUTE_TRADE.csv", header = TRUE) #QuantQuote sample minute data
dat[,2] <- sprintf('%04d', dat[,2]) #add a zero to front of time IE 400 becomes 0400 aka 4AM
#Create a zoo object ordered by day and time from the dat dataframe
datzoo <- read.zoo(file=dat, sep=",", header=TRUE,
index.column=1:2, format="%Y%m%d %H%M", tz="",
colClasses = rep(c("character", "numeric"), c(2, 8)))
Spy <- as.xts(datzoo)
# Create regular series from 00:00 to 23:59 of 1 minute prints
y <- xts(seq(from = 1, to = 60*24, by = 1), as.POSIXlt((0),
origin="2013-03-30 00:00", tz='GMT')+seq(from = 0, to = 60*60*24-1, by = 60))
colnames(y) <- "TempIndex"
#Merge the regular ts (y) with Spy and remove the original Spy column
SpyReg <- merge(y,Spy, join='left')
SpyReg$TempIndex <- NULL
#Capture the index of Spy
ISpy <- index(Spy)
I have a few questions about the above code...
1) SpyReg["2012-03-30 04:00:00 GMT"] returns
OPEN HIGH LOW CLOSE VOLUME SPLITS EARNINGS DIVIDENDS
Spy["2012-03-30 04:00:00 GMT"] returns the correct values of Spy for the given index
OPEN HIGH LOW CLOSE VOLUME SPLITS EARNINGS DIVIDENDS
2012-03-30 04:00:00 140.66 140.66 140.66 140.66 2160 1 0 0
However,
SpyReg["T04:00:00/T04:01:00"]
OPEN HIGH LOW CLOSE VOLUME SPLITS EARNINGS DIVIDENDS
2013-03-30 04:00:00 NA NA NA NA NA NA NA NA
2013-03-30 04:01:00 NA NA NA NA NA NA NA NA
why is this, when both are xts objects of the same index type, month, and time? Shouldn't SpyReg[""2012-03-30 04:00:00 GMT"] return:
OPEN HIGH LOW CLOSE VOLUME SPLITS EARNINGS DIVIDENDS
2013-03-30 04:00:00 NA NA NA NA NA NA NA NA
2) Why did the merge not give SpyReg the Spy value for the same index (such as the 4AM print?) I tried all 4 "join" options, but none worked...
3) I assume there is a MUCH more elegant way to solve this problem than what I am trying to do. After creating Spy, it was not regular, minute by minute. I wanted to create a regular xts object that had no gaps and flowed continuously minute by minute from midnight to 23:59, add the entries from Spy into it, then do a na.locf to replace the rest of the NAs with the original data.

Answer 1

Setting the index of an xts object to POSIXlt can cause some strange behaviors. I'd simply recommend you use POSIXct instead.
URL <- "http://quantquote.com/sample/SPY_MINUTE_TRADE.csv"
Spy <- read.zoo(URL, sep=",", header=TRUE, index.column=1:2, FUN=function(x)
as.POSIXct(sprintf("%8d %04d",x[,1],x[,2]), format="%Y%m%d %H%M", tz=""))
Spy <- as.xts(Spy)
Now you can merge Spy with an 'empty' xts object that has the regular index values you want.
SpyReg <- merge(Spy, xts(, seq(start(Spy),end(Spy),by="1 min")), fill=na.locf)