[R] xyplot.zoo trouble with the index when I use microseconds (type POSIXct)
Laurent Rhelp
L@urentRHe|p @end|ng |rom |ree@|r
Mon Feb 22 18:33:22 CET 2021
Le 22/02/2021 à 18:01, Deepayan Sarkar a écrit :
> On Mon, Feb 22, 2021 at 9:56 PM 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
> At least the immediate problem is that
>
> lattice:::prettyDate_TMP(range(mydatetime))
> # Error in lattice:::prettyDate_TMP(range(mydatetime)) :
> # range too small for min.n
>
> grDevices:::prettyDate(range(mydatetime))
> # [1] "2021-02-08 09:15:48 GMT" "2021-02-08 09:15:49 GMT"
> # [3] "2021-02-08 09:15:50 GMT" "2021-02-08 09:15:51 GMT"
> # [5] "2021-02-08 09:15:52 GMT" "2021-02-08 09:15:53 GMT"
>
> So the version in lattice (which was supposed to be a temporary
> stopgap till R 2.12 was released) has not kept up. I will fix.
>
> Does the output above look OK to you?
It is ok for me except the fact that I would like to see on the x-axis
labels the fractional seconds, at least the milliseconds.
> Best,
> -Deepayan
>
>
>> # 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
>>
>>
>>
>>
>>
>>
>> --
>> L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
>> https://www.avast.com/antivirus
>>
>> ______________________________________________
>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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.
--
L'absence de virus dans ce courrier électronique a été vérifiée par le logiciel antivirus Avast.
https://www.avast.com/antivirus
More information about the R-help
mailing list