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Laurent Rhelp

2021-Feb-22 16:16 UTC

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

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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logiciel antivirus Avast.
https://www.avast.com/antivirus

Gabor Grothendieck

2021-Feb-22 16:56 UTC

head link

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

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 at 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
>
>
>
>
>
>
> --
> L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le
logiciel antivirus Avast.
> https://www.avast.com/antivirus
>
> ______________________________________________
> R-help at 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.


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

Deepayan Sarkar

2021-Feb-22 17:01 UTC

head link

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

On Mon, Feb 22, 2021 at 9:56 PM Laurent Rhelp <LaurentRHelp at 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?

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 ?lectronique a ?t? v?rifi?e par le
logiciel antivirus Avast.
> https://www.avast.com/antivirus
>
> ______________________________________________
> R-help at 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.

R help - Feb 2021 - xyplot.zoo trouble with the index when I use microseconds (type POSIXct)

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

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

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