From the comments, the time is in some sort of MDJ seconds, so you can covert it into a time index with Gabor's hint:
library(zoo)
z <- read.zoo("myfile.dat", sep = ",",
FUN = function(x){as.POSIXct(x,origin='1858-11-17',tz='UTC')})
Where 1858-11-17 is the MJD epoch per http://en.wikipedia.org/wiki/Julian_day
Alternately you could specifiy the origin and add the seconds-since:
z <- read.zoo("myfile.dat", sep = ",",
FUN = function(x){as.POSIXct('1858-11-17',tz='UTC')+x})
Then it seems you want the data aggregated by various granularity in time:
plot(aggregate(z,cut(time(z),breaks='year' ),mean))
plot(aggregate(z,cut(time(z),breaks='quarter'),mean))
plot(aggregate(z,cut(time(z),breaks='month' ),mean))
plot(aggregate(z,cut(time(z),breaks='day' ),mean))
plot(aggregate(z,cut(time(z),breaks='hour' ),mean))
plot(aggregate(z,cut(time(z),breaks='6 min' ),mean))
plot(aggregate(z,cut(time(z),breaks='min' ),mean))
plot(aggregate(z,cut(time(z),breaks='10 sec' ),mean))
plot(aggregate(z,cut(time(z),breaks='sec' ),mean))