[R] Error in as.xts
Rui Barradas
ruipbarradas at sapo.pt
Mon Jul 16 20:32:17 CEST 2012
Hello,
I couldn't reproduce your error, with the csv file, your code run at the
first try. Here is exactly what I've done
dat <- read.csv("diveData_2008.csv", header=TRUE, stringsAsFactors=FALSE)
# This 'DateTime' will be used again later.
DateTime <- with(dat, paste(date, time))
DateTime <- as.POSIXct(DateTime, format="%m/%d/%Y %H:%M")
# Create the xts object, slightly different, [ not as.xts() ]
diveData_2008 <- xts(dat ,order.by=DateTime)
# Your code
diveCond <- data.frame(matrix(0, nrow=61, ncol=17))
names(diveCond) <- c("dive_id", "timestamp", "visability", "r_wvht",
"r_dpd", "r_apt", "r_mwd", "r_wtmp", "l_salinity", "l_o2",
"l_hs", "l_tp", "l_wdir", "l_along", "l_cross", "l_mab",
"l_depth")
dive_id <- 0
for(i in unique(as.character(index(diveData_2008)))){
dive_id <- dive_id+1
diveCond$dive_id[dive_id] <- dive_id
diveCond$timestamp[dive_id] <- as.character(i)
diveCond$visability[dive_id] <- as.numeric(diveData_2008[i][1,11])
}
# See ?aggregate and note that the function is
# is FUN = `[`with further args 1 (the dots '...')
# to extract the first row in each sub-df
aggr <- aggregate(TRANSECT ~ index(diveData_2008), data = diveData_2008,
`[`, 1)
names(aggr)[1] <- "timestamp"
merge(data.frame(timestamp=unique(DateTime)), aggr, all.x=TRUE)
The output of this merge() is similar to your diveCond, but with much
less columns, it only has the columns with values different from zero.
The aggregate alone wouldn't include the <NA> value, only the ones with
an actual timestamp.
Anyway, there was no error in the creation of diveCond. This leads me to
the final note. If something is going wrong break the instructions nto
smaller simpler ones. See, for instance, how I've broken the DateTime
variable, without putting everything in the as.POSIXct, just the end
value after paste. Though the possible error wasn't there, it's allways
better to debug simpler code, EVEN if at the cost of making longer, with
more lines.
Hope this helps,
Rui Barradas
Em 16-07-2012 15:27, Yolande Tra escreveu:
> Hello,
> Can I ask you another question? Attached is the file created from
> as.xts. After submitting the following code, I got an error. Please
> help. Thanks.
>
> diveCond <- data.frame(matrix(0, nrow=61, ncol=17))
>
> names(diveCond) <- c("dive_id", "timestamp", "visability", "r_wvht",
> "r_dpd", "r_apt", "r_mwd", "r_wtmp", "l_salinity", "l_o2", "l_hs",
> "l_tp", "l_wdir", "l_along", "l_cross", "l_mab", "l_depth")
>
> dive_id <- 0
>
> for(i in unique(as.character(index(diveData_2008)))){
>
> dive_id <- dive_id+1
>
> diveCond$dive_id[dive_id] <- dive_id
>
> diveCond$timestamp[dive_id] <- as.character(i)
>
> diveCond$visability[dive_id] <- as.numeric(diveData_2008[i][1,11])
>
> }
>
> Error in if (length(c(year, month, day, hour, min, sec)) == 6 && c(year,:
>
> missing value where TRUE/FALSE needed
>
> In addition: Warning messages:
>
> 1: In as_numeric(YYYY) : NAs introduced by coercion
>
> 2: In as_numeric(YYYY) : NAs introduced by coercion
>
> Thanks,
>
> Yolande
>
>
>
> On Mon, Jul 16, 2012 at 2:51 AM, Rui Barradas <ruipbarradas at sapo.pt
> <mailto:ruipbarradas at sapo.pt>> wrote:
>
> Hello,
>
> I can see several things that are not right or may go wrong.
> (Without an actual dataset, this is just a series of hints.)
>
> 1. The read.csv statement. Like read.table, it creates a data.frame,
> which defaults to reading strings as factors, coded internally as
> integers. Sometimes there are problems, when using them and you are
> converting the dates/times to POSIXct. You can try to use read.csv
> option
>
> stringsAsFactors = FALSE
>
> and then do the conversions. These conversions would include
> converting 'species' and 'site' to factor, if you want them as factors.
>
> 2. Are there typos in your posted code example?
> 2.a) You read into data.frame 'd1' but then use d$date and d$TIME.
> 2.b) In 'd1' the column is named 'time', not 'TIME'.
>
> 3. Try to create the date/time and assign it to a variable, for
> instance,
>
> dtvar <- as.POSIXct(...etc...)
>
> Now you can check length(dtvar) and NROW(d1) to see if they are
> equal. You can also see if the conversion was allright. This is a
> general rule: if there's an error in a complicated instruction,
> break it into smaller ones.
>
> Hope this helps,
>
> Rui Barradas
>
> Em 16-07-2012 03:10, Yolande Tra escreveu:
>
> Hi
> I got the following error using as.xts
> Error in xts(x, order.by <http://order.by/> = order.by
> <http://order.by/>, frequency = frequency, ...) :
> NROW(x) must match length(order.by <http://order.by/>)
> Here is how the data looks like
>
> d1 <-
> read.csv(file.path(dataDir,"__AppendixA-FishCountsTable-__2009.csv"),
>
> as.is <http://as.is/>=T)
>
> d1[1:3,]
>
> dive_id date time species count size site
> depth level
> TRANSECT VIS_M
> 1 62 10/12/2009 12:44 E. lateralis 2 15 Hopkins 15
> B
> 1 4
> 2 62 10/12/2009 12:44 E. lateralis 1 22 Hopkins 15
> B
> 1 4
> 3 62 10/12/2009 12:44 E. lateralis 1 25 Hopkins 15
> B
> 1 4
>
> diveData_2009 <- as.xts( d1,order.by
> <http://order.by/>=as.POSIXct(__strptime(paste(d$date,
>
> d$TIME ), "%d/%m/%Y %H:%M") ))
> Error in xts(x, order.by <http://order.by/> = order.by
> <http://order.by/>, frequency = frequency, ...) :
> NROW(x) must match length(order.by <http://order.by/>)
>
> I could not figure out how to correct it
> Thank you for your help
> Yolande
>
> [[alternative HTML version deleted]]
>
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