[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 17:56:29 CET 2021


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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