[R] xyplot.zoo trouble with the index when I use microseconds (type POSIXct)

Gabor Grothendieck ggrothend|eck @end|ng |rom gm@||@com
Mon Feb 22 19:32:44 CET 2021


Also, it might be better to simply use seconds as the time. In that
case both plot and xyplot run without error.

 time(DF.w) <- as.POSIXlt(time(DF.w))$sec
 # now run plot or xyplot as before

On Mon, Feb 22, 2021 at 11:56 AM Gabor Grothendieck
<ggrothendieck using gmail.com> wrote:
>
> I assume that this is a lattice problem.  Replacing xyplot with plot
> and using all the same arguments there is no error.
>
>
> On Mon, Feb 22, 2021 at 11:26 AM Laurent Rhelp <LaurentRHelp using free.fr> wrote:
> >
> > Dear R-Help-List,
> >
> >     I have to process time series with a sampling frequency of 1 MHz.
> > I use the POSIXct format for the date-times with microsecond in a zoo
> > object and the xyplot.zoo function to do the graphs.
> > As I show in the below example I had a trouble to plot the labels on the
> > x-axis with an error message. I found a solution but I would like to
> > know if I miss something.
> > The link
> > https://stackoverflow.com/questions/7726034/how-r-formats-posixct-with-fractional-seconds
> >
> > helped me to understand how to print the POSIXct value to see the
> > microseconds thanks to the function myformat.POSIXct:
> >
> > myformat.POSIXct <- function(x, digits=6)
> > {
> >    x2 <- round(unclass(x), digits)
> >    attributes(x2) <- attributes(x)
> >    x <- as.POSIXlt(x2,origin="1970-01-01",tz="GMT")
> >    x$sec <- round(x$sec, digits)
> >    format.POSIXlt(x, paste("%Y-%m-%d %H:%M:%OS",digits,sep=""),tz="GMT")
> >
> > }
> >
> >
> > ## The example giving the error message:
> >
> > library(lattice)
> > library(zoo)
> >
> > ##
> > options(digits = 16) # to see all the digits on the screen
> > options(digits.secs = 6) # to see the microseconds
> > # mock data
> > # a sine with a frequency f0 and two others with a delay
> > Fs <- 1e+6 # sampling frequency 1 MHz
> > Ts <- 1/Fs
> > # frequency of the sinus
> > f0 <- 100000
> > t0 <- 1/f0
> > time <- seq(0, length = 1000, by = Ts)
> > A1 <- 1
> > y1 <- A1 * sin(2*pi*f0*time)
> > y2 <- 2 * A1 * sin(2*pi*f0*(time+0.000002))
> > y3 <- 3 * A1 * sin(2*pi*f0*(time+0.000005))
> > ## creation of a dataframe:
> > ##
> > DF <- data.frame( time = time, y1 = y1, y2 = y2, y3 = y3)
> > # Since I want to allow for the datetime POSIXct format on the x-axis
> > # for the plot I transform my dataframe in a zoo object
> > #
> > # say that my acquisition began at "2021-02-08 09:15:50.000000"
> > #
> > mystart <- as.POSIXct("2021-02-08 09:15:50.000000", format = "%Y-%m-%d
> > %H:%M:%OS",tz="GMT")
> > mystart
> > # To see the correct datetime I use the myformat.POSIXct function
> > myformat.POSIXct(mystart)
> > ##
> > ## using the method seq.POSIXct as following doesn't work:
> > ## mydatetime <- seq( mystart , length = nrow(DF), by = "0.000001 sec")
> > ## head( myformat.POSIXct(mydatetime) )
> > ## if I use the following command it works:
> > mydatetime <- seq( mystart , length = nrow(DF), by = 0.000001)
> > head( myformat.POSIXct(mydatetime) )
> > ## I do the zoo object:
> > DF.z <- zoo(DF[,-1],order.by = mydatetime)
> > ## We don't see the correct value for the index:
> > head(DF.z)
> > # time                    y1 y2                     y3
> > # 2021-02-08 09:15:50.000000 0e+00 0.000000000000000e+00
> > 1.902113032590307e+00  3.673819061467132e-16
> > # 2021-02-08 09:15:50.000000 1e-06 5.877852522924730e-01
> > 1.902113032590307e+00 -1.763355756877419e+00
> > # 2021-02-08 09:15:50.000001 2e-06 9.510565162951535e-01
> > 1.175570504584947e+00 -2.853169548885460e+00
> > # 2021-02-08 09:15:50.000003 3e-06 9.510565162951536e-01
> > 1.133099690464601e-15 -2.853169548885460e+00
> > # 2021-02-08 09:15:50.000004 4e-06 5.877852522924736e-01
> > -1.175570504584946e+00 -1.763355756877420e+00
> > # 2021-02-08 09:15:50.000005 5e-06 5.665498452323003e-16
> > -1.902113032590306e+00 -3.399299071393802e-15
> > # If I use myformat.POSIXct I see that the index is correct in the
> > object DF:
> > head(myformat.POSIXct(index(DF.z)))
> > ## and when I plot I have an error:
> > xyplot(   DF.z
> >            , screens = c(1,1,1)
> >            , type = "l"
> >            , col = c("red","blue","black")
> >
> > )
> >
> > # Error in prettyDate_TMP(x, ...) : range too small for min.n
> >
> > # if I process by hand the plot of the labels on the x-axis it works:
> > #
> > myend <- tail(mydatetime,1)
> >
> > myticks <- seq( mystart , to = myend , length = 5)
> > mylabels <- format(myticks,"%H:%M:%OS")
> >
> > xyplot(      DF.z
> >               , screens = c(1,1,1)
> >               , type = "l"
> >               , col = c("red","blue","black")
> >               , scales = list(
> >                   y= list(relation = "free", abbreviate=TRUE),
> >                   x = list( at = myticks, labels = mylabels
> >                         , rot = 45, cex = 0.5)
> >             )
> > )
> > # The microseconds are well taken into account with the window function
> > # if I want to plot only 100 microseconds but there is of course the same
> > # trouble for the plot
> >
> > myend <- as.POSIXct("2021-02-08 09:15:50.000100", format = "%Y-%m-%d
> > %H:%M:%OS",tz="GMT")
> > myformat.POSIXct(myend)
> >
> > DF.w <- window( DF.z ,start = mystart, end = myend)
> >
> > myticks <- seq( mystart , to = myend , length = 5)
> > mylabels <- format(myticks,"%H:%M:%OS")
> >
> > xyplot(      DF.w
> >               , screens = c(1,1,1)
> >               , type = "l"
> >               , col = c("red","blue","black")
> > )
> >
> > ## Error in prettyDate_TMP(x, ...) : range too small for min.n
> >
> > xyplot(      DF.w
> >               , screens = c(1,1,1)
> >               , type = "l"
> >               , col = c("red","blue","black")
> >               , scales = list(
> >                 y= list(relation = "free", abbreviate=TRUE),
> >                 x = list( at = myticks, labels = mylabels
> >                           , rot = 45, cex = 0.5)
> >               )
> > )
> >
> > May you please tell me if I miss something in the way to use POSIXct
> > with microseconds in a zoo object ?
> >
> > Thank you
> > Laurent
> >
> >
> >
> >
> >
> >
> > --
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> > https://www.avast.com/antivirus
> >
> > ______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
>
>
> --
> Statistics & Software Consulting
> GKX Group, GKX Associates Inc.
> tel: 1-877-GKX-GROUP
> email: ggrothendieck at gmail.com



-- 
Statistics & Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com



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