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read.zoo problem reading in date time

3 messages · stephen sefick, Charilaos Skiadas, Gabor Grothendieck

#
DateTime,Temp,SpCond,DOConc,Depth,pH,ORP,Turbidity+,Chlorophyll,Battery,Cond,DO%,Salinity,TDS
01/13/2006 17:01,10.87,84,9.36,0.664,7.3,132,28.8,3.1,11.5,0.062,84.6,0.04,0.055
01/13/2006 17:16,10.9,84,9.36,0.66,7.31,133,28.7,2.9,11.5,0.062,84.7,0.04,0.055
01/13/2006 17:31,10.92,84,9.36,0.655,7.3,132,28.4,2.6,11.4,0.062,84.8,0.04,0.055
01/13/2006 17:46,10.96,85,9.37,0.651,7.3,133,27.5,2.3,11.4,0.062,84.9,0.04,0.055
01/13/2006 18:01,10.96,85,9.35,0.644,7.33,132,28.2,2.9,11.4,0.062,84.7,0.04,0.055
01/13/2006 18:16,10.98,85,9.35,0.638,7.33,132,27.9,2.5,11.4,0.062,84.8,0.04,0.055
01/13/2006 18:31,11.01,85,9.35,0.635,7.31,131,26.4,3,11.5,0.062,84.8,0.04,0.055
01/13/2006 18:46,11.04,85,9.33,0.635,7.31,133,26.1,2.9,11.5,0.062,84.7,0.04,0.055
01/13/2006 19:01,11.04,85,9.33,0.632,7.33,133,26.3,2.9,11.4,0.062,84.7,0.04,0.055
01/13/2006 19:16,11.06,85,9.32,0.639,7.34,134,26,2.6,11.5,0.062,84.6,0.04,0.055
01/13/2006 19:31,11.11,85,9.37,0.656,7.35,136,25.6,2.1,11.4,0.062,85.2,0.04,0.055
01/13/2006 19:46,11.11,84,9.36,0.65,7.33,137,26.6,2.4,11.4,0.062,85.2,0.04,0.055
01/13/2006 20:01,11.18,84,9.41,0.649,7.35,138,27,2.8,11.4,0.062,85.7,0.04,0.055
01/13/2006 20:16,11.13,84,9.35,0.651,7.34,140,27.1,2.7,11.4,0.062,85,0.04,0.055
01/13/2006 20:31,11.12,84,9.33,0.656,7.32,142,26.7,2.9,11.4,0.062,84.8,0.04,0.055
01/13/2006 20:46,11.07,84,9.33,0.667,7.32,143,26.4,3.1,11.4,0.062,84.8,0.04,0.055
01/13/2006 21:01,11.05,84,9.35,0.67,7.31,145,26.6,2.7,11.4,0.062,84.9,0.04,0.055
01/13/2006 21:16,11.02,84,9.34,0.67,7.32,145,25.9,2.6,11.4,0.062,84.8,0.04,0.055
01/13/2006 21:31,11.01,84,9.35,0.673,7.32,146,26.3,3.1,11.4,0.062,84.8,0.04,0.055
01/13/2006 21:46,10.99,84,9.35,0.676,7.32,146,26.4,3.3,11.4,0.062,84.8,0.04,0.055
01/13/2006 22:01,10.96,84,9.34,0.673,7.32,146,26,2.6,11.5,0.062,84.7,0.04,0.055
01/13/2006 22:16,10.94,84,9.32,0.668,7.32,147,26.5,2.9,11.5,0.061,84.4,0.04,0.055
01/13/2006 22:31,10.93,84,9.3,0.666,7.31,148,25.8,2.4,11.4,0.062,84.3,0.04,0.055
01/13/2006 22:46,10.92,84,9.3,0.666,7.32,148,26,2.2,11.4,0.061,84.2,0.04,0.055
01/13/2006 23:01,10.91,84,9.27,0.666,7.32,148,26.5,2.9,11.5,0.062,83.9,0.04,0.055
01/13/2006 23:16,10.92,84,9.34,0.666,7.31,149,26.9,2.5,11.4,0.062,84.6,0.04,0.055
01/13/2006 23:31,10.93,84,9.31,0.667,7.33,148,25.8,2.8,11.4,0.062,84.3,0.04,0.055
01/13/2006 23:46,10.92,84,9.34,0.666,7.31,150,26.1,3.1,11.4,0.062,84.6,0.04,0.055
01/14/2006 00:01,10.95,84,9.28,0.667,7.3,144,26.4,2.5,11.5,0.062,84.1,0.04,0.055
01/14/2006 00:16,10.95,84,9.29,0.667,7.31,142,25.6,2.3,11.5,0.062,84.2,0.04,0.055
01/14/2006 00:31,10.94,84,9.29,0.669,7.3,142,25.6,2.4,11.4,0.062,84.2,0.04,0.055
01/14/2006 00:46,10.94,85,9.29,0.671,7.31,139,25.3,3.1,11.4,0.062,84.1,0.04,0.055
01/14/2006 01:01,10.95,85,9.26,0.672,7.3,141,25.3,2.6,11.3,0.062,83.9,0.04,0.055
01/14/2006 01:16,10.95,85,9.28,0.673,7.31,141,26,3.1,11.4,0.062,84,0.04,0.055
01/14/2006 01:31,10.96,85,9.27,0.673,7.34,139,25.4,2.1,11.4,0.062,84,0.04,0.055
01/14/2006 01:46,10.95,85,9.28,0.673,7.32,138,24.8,2.5,11.4,0.062,84.1,0.04,0.055
01/14/2006 02:01,10.93,85,9.27,0.673,7.31,137,25.1,2.2,11.4,0.062,84,0.04,0.055
01/14/2006 02:16,10.93,85,9.28,0.673,7.31,137,24.6,2,11.4,0.062,84.1,0.04,0.055
01/14/2006 02:31,10.94,85,9.29,0.671,7.35,133,24.8,2.8,11.4,0.062,84.2,0.04,0.055
01/14/2006 02:46,10.91,85,9.27,0.671,7.35,130,24.7,2.1,11.4,0.062,83.8,0.04,0.055
01/14/2006 03:01,10.92,85,9.28,0.67,7.32,131,24.5,2.6,11.4,0.062,84,0.04,0.055
01/14/2006 03:16,10.91,85,9.26,0.669,7.32,129,24.8,2.6,11.3,0.062,83.8,0.04,0.055
01/14/2006 03:31,10.9,85,9.28,0.671,7.32,129,24.5,2.5,11.4,0.062,84,0.04,0.055
01/14/2006 03:46,10.86,85,9.28,0.669,7.33,127,23.8,2.5,11.4,0.062,83.9,0.04,0.055
01/14/2006 04:01,10.87,85,9.27,0.669,7.33,128,24.3,2.7,11.4,0.062,83.9,0.04,0.055
01/14/2006 04:16,10.87,85,9.26,0.668,7.36,125,23.6,2.9,11.3,0.062,83.7,0.04,0.055
01/14/2006 04:31,10.8,85,9.28,0.667,7.34,123,23.6,2,11.3,0.062,83.8,0.04,0.056
01/14/2006 04:46,10.82,85,9.28,0.666,7.34,125,23.8,2.5,11.4,0.062,83.8,0.04,0.056
01/14/2006 05:01,10.82,85,9.26,0.665,7.33,124,24.3,2.3,11.3,0.062,83.7,0.04,0.056
01/14/2006 05:16,10.8,86,9.27,0.665,7.33,122,23.8,2.4,11.4,0.062,83.7,0.04,0.056
01/14/2006 05:31,10.78,86,9.28,0.667,7.35,122,24.1,3.1,11.3,0.062,83.7,0.04,0.056
01/14/2006 05:46,10.76,86,9.27,0.668,7.35,123,23.8,2.8,11.3,0.062,83.6,0.04,0.056
01/14/2006 06:01,10.77,86,9.26,0.668,7.34,116,24.2,2.6,11.3,0.062,83.5,0.04,0.056
x<-read.zoo("SC2.csv", sep="," , format="%m%m/%d%d/%y%y%y%y %h%h:%m%m")

        #Error in read.zoo("SC2.csv", sep = ",", format =
"%m%m/%d%d/%y%y%y%y %h%h:%m%m") :
        index contains NAs  Error message

what am I doing wrong SC2.csv is a comma seperated file.  The above
data is right out out of the csv file, which is more like 30,000 rows.
 There are some NA for all of the variables except DateTime for a week
here and a week there, but I can not find any missing dates.
thanks

stephen
#
On Mar 3, 2008, at 11:12 AM, stephen sefick wrote:

            
You need header=TRUE in there, since your dataset has a header.
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
#
One must specify that there is a header if there is one, each % item
should only
be listed once, and format is currently only used for "Date" class so
you want to
use the FUN= argument -- although in the development version of zoo format is
availailable more generally. Here are several ways to do this.  z1 is
created using
chron, z2 uses POSIXct and the z3 uses POSIXct and the new version of read.zoo
in the devel version of zoo.

library(zoo)
Lines <- "DateTime,Temp,SpCond,DOConc,Depth,pH,ORP,Turbidity+,Chlorophyll,Battery,Cond,DO%,Salinity,TDS
01/13/2006 17:01,10.87,84,9.36,0.664,7.3,132,28.8,3.1,11.5,0.062,84.6,0.04,0.055
01/13/2006 17:16,10.9,84,9.36,0.66,7.31,133,28.7,2.9,11.5,0.062,84.7,0.04,0.055
01/13/2006 17:31,10.92,84,9.36,0.655,7.3,132,28.4,2.6,11.4,0.062,84.8,0.04,0.055
01/13/2006 17:46,10.96,85,9.37,0.651,7.3,133,27.5,2.3,11.4,0.062,84.9,0.04,0.055
01/13/2006 18:01,10.96,85,9.35,0.644,7.33,132,28.2,2.9,11.4,0.062,84.7,0.04,0.055
01/13/2006 18:16,10.98,85,9.35,0.638,7.33,132,27.9,2.5,11.4,0.062,84.8,0.04,0.055
01/13/2006 18:31,11.01,85,9.35,0.635,7.31,131,26.4,3,11.5,0.062,84.8,0.04,0.055
01/13/2006 18:46,11.04,85,9.33,0.635,7.31,133,26.1,2.9,11.5,0.062,84.7,0.04,0.055
01/13/2006 19:01,11.04,85,9.33,0.632,7.33,133,26.3,2.9,11.4,0.062,84.7,0.04,0.055
01/13/2006 19:16,11.06,85,9.32,0.639,7.34,134,26,2.6,11.5,0.062,84.6,0.04,0.055
01/13/2006 19:31,11.11,85,9.37,0.656,7.35,136,25.6,2.1,11.4,0.062,85.2,0.04,0.055
01/13/2006 19:46,11.11,84,9.36,0.65,7.33,137,26.6,2.4,11.4,0.062,85.2,0.04,0.055
01/13/2006 20:01,11.18,84,9.41,0.649,7.35,138,27,2.8,11.4,0.062,85.7,0.04,0.055
01/13/2006 20:16,11.13,84,9.35,0.651,7.34,140,27.1,2.7,11.4,0.062,85,0.04,0.055
01/13/2006 20:31,11.12,84,9.33,0.656,7.32,142,26.7,2.9,11.4,0.062,84.8,0.04,0.055
01/13/2006 20:46,11.07,84,9.33,0.667,7.32,143,26.4,3.1,11.4,0.062,84.8,0.04,0.055
01/13/2006 21:01,11.05,84,9.35,0.67,7.31,145,26.6,2.7,11.4,0.062,84.9,0.04,0.055
01/13/2006 21:16,11.02,84,9.34,0.67,7.32,145,25.9,2.6,11.4,0.062,84.8,0.04,0.055
01/13/2006 21:31,11.01,84,9.35,0.673,7.32,146,26.3,3.1,11.4,0.062,84.8,0.04,0.055
01/13/2006 21:46,10.99,84,9.35,0.676,7.32,146,26.4,3.3,11.4,0.062,84.8,0.04,0.055
01/13/2006 22:01,10.96,84,9.34,0.673,7.32,146,26,2.6,11.5,0.062,84.7,0.04,0.055
01/13/2006 22:16,10.94,84,9.32,0.668,7.32,147,26.5,2.9,11.5,0.061,84.4,0.04,0.055
01/13/2006 22:31,10.93,84,9.3,0.666,7.31,148,25.8,2.4,11.4,0.062,84.3,0.04,0.055
01/13/2006 22:46,10.92,84,9.3,0.666,7.32,148,26,2.2,11.4,0.061,84.2,0.04,0.055
01/13/2006 23:01,10.91,84,9.27,0.666,7.32,148,26.5,2.9,11.5,0.062,83.9,0.04,0.055
01/13/2006 23:16,10.92,84,9.34,0.666,7.31,149,26.9,2.5,11.4,0.062,84.6,0.04,0.055
01/13/2006 23:31,10.93,84,9.31,0.667,7.33,148,25.8,2.8,11.4,0.062,84.3,0.04,0.055
01/13/2006 23:46,10.92,84,9.34,0.666,7.31,150,26.1,3.1,11.4,0.062,84.6,0.04,0.055
01/14/2006 00:01,10.95,84,9.28,0.667,7.3,144,26.4,2.5,11.5,0.062,84.1,0.04,0.055
01/14/2006 00:16,10.95,84,9.29,0.667,7.31,142,25.6,2.3,11.5,0.062,84.2,0.04,0.055
01/14/2006 00:31,10.94,84,9.29,0.669,7.3,142,25.6,2.4,11.4,0.062,84.2,0.04,0.055
01/14/2006 00:46,10.94,85,9.29,0.671,7.31,139,25.3,3.1,11.4,0.062,84.1,0.04,0.055
01/14/2006 01:01,10.95,85,9.26,0.672,7.3,141,25.3,2.6,11.3,0.062,83.9,0.04,0.055
01/14/2006 01:16,10.95,85,9.28,0.673,7.31,141,26,3.1,11.4,0.062,84,0.04,0.055
01/14/2006 01:31,10.96,85,9.27,0.673,7.34,139,25.4,2.1,11.4,0.062,84,0.04,0.055
01/14/2006 01:46,10.95,85,9.28,0.673,7.32,138,24.8,2.5,11.4,0.062,84.1,0.04,0.055
01/14/2006 02:01,10.93,85,9.27,0.673,7.31,137,25.1,2.2,11.4,0.062,84,0.04,0.055
01/14/2006 02:16,10.93,85,9.28,0.673,7.31,137,24.6,2,11.4,0.062,84.1,0.04,0.055
01/14/2006 02:31,10.94,85,9.29,0.671,7.35,133,24.8,2.8,11.4,0.062,84.2,0.04,0.055
01/14/2006 02:46,10.91,85,9.27,0.671,7.35,130,24.7,2.1,11.4,0.062,83.8,0.04,0.055
01/14/2006 03:01,10.92,85,9.28,0.67,7.32,131,24.5,2.6,11.4,0.062,84,0.04,0.055
01/14/2006 03:16,10.91,85,9.26,0.669,7.32,129,24.8,2.6,11.3,0.062,83.8,0.04,0.055
01/14/2006 03:31,10.9,85,9.28,0.671,7.32,129,24.5,2.5,11.4,0.062,84,0.04,0.055
01/14/2006 03:46,10.86,85,9.28,0.669,7.33,127,23.8,2.5,11.4,0.062,83.9,0.04,0.055
01/14/2006 04:01,10.87,85,9.27,0.669,7.33,128,24.3,2.7,11.4,0.062,83.9,0.04,0.055
01/14/2006 04:16,10.87,85,9.26,0.668,7.36,125,23.6,2.9,11.3,0.062,83.7,0.04,0.055
01/14/2006 04:31,10.8,85,9.28,0.667,7.34,123,23.6,2,11.3,0.062,83.8,0.04,0.056
01/14/2006 04:46,10.82,85,9.28,0.666,7.34,125,23.8,2.5,11.4,0.062,83.8,0.04,0.056
01/14/2006 05:01,10.82,85,9.26,0.665,7.33,124,24.3,2.3,11.3,0.062,83.7,0.04,0.056
01/14/2006 05:16,10.8,86,9.27,0.665,7.33,122,23.8,2.4,11.4,0.062,83.7,0.04,0.056
01/14/2006 05:31,10.78,86,9.28,0.667,7.35,122,24.1,3.1,11.3,0.062,83.7,0.04,0.056
01/14/2006 05:46,10.76,86,9.27,0.668,7.35,123,23.8,2.8,11.3,0.062,83.6,0.04,0.056
01/14/2006 06:01,10.77,86,9.26,0.668,7.34,116,24.2,2.6,11.3,0.062,83.5,0.04,0.056
"

# chron
library(chron)
fmt.chron <- function(x) {
    chron(sub(" .*", "", x), gsub(".* (.*)", "\\1:00", x))
}
z1 <- read.zoo(textConnection(Lines), sep = ",", header = TRUE, FUN = fmt.chron)

# POSIXct
fmt.POSIXct <- function(x) {
    as.POSIXct(strptime(x, "%m/%d/%Y %H:%M"))
}
z2 <- read.zoo(textConnection(Lines), sep = ",", header = TRUE, FUN =
fmt.POSIXct)

# POSIXct - using development version of zoo
# next line reads in devel version of read.zoo from R-Forge
source("http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/*checkout*/pkg/R/read.zoo.R?rev=445&root=zoo")
z3 <- read.zoo(textConnection(Lines), sep = ",", header = TRUE,
    format = "%m/%d/%Y %H:%M", tz = "")
On Mon, Mar 3, 2008 at 11:12 AM, stephen sefick <ssefick at gmail.com> wrote: