Re: [R] Error in as.xts
Hello, I can see several things that are not right or may go wrong. (Without an actual dataset, this is just a series of hints.) 1. The read.csv statement. Like read.table, it creates a data.frame, which defaults to reading strings as factors, coded internally as integers. Sometimes there are problems, when using them and you are converting the dates/times to POSIXct. You can try to use read.csv option stringsAsFactors = FALSE and then do the conversions. These conversions would include converting 'species' and 'site' to factor, if you want them as factors. 2. Are there typos in your posted code example? 2.a) You read into data.frame 'd1' but then use d$date and d$TIME. 2.b) In 'd1' the column is named 'time', not 'TIME'. 3. Try to create the date/time and assign it to a variable, for instance, dtvar - as.POSIXct(...etc...) Now you can check length(dtvar) and NROW(d1) to see if they are equal. You can also see if the conversion was allright. This is a general rule: if there's an error in a complicated instruction, break it into smaller ones. Hope this helps, Rui Barradas Em 16-07-2012 03:10, Yolande Tra escreveu: Hi I got the following error using as.xts Error in xts(x, order.by = order.by, frequency = frequency, ...) : NROW(x) must match length(order.by) Here is how the data looks like d1 - read.csv(file.path(dataDir,AppendixA-FishCountsTable-2009.csv), as.is=T) d1[1:3,] dive_id date time species count sizesite depth level TRANSECT VIS_M 1 62 10/12/2009 12:44 E. lateralis 2 15 Hopkins15 B 1 4 2 62 10/12/2009 12:44 E. lateralis 1 22 Hopkins15 B 1 4 3 62 10/12/2009 12:44 E. lateralis 1 25 Hopkins15 B 1 4 diveData_2009 - as.xts( d1,order.by=as.POSIXct(strptime(paste(d$date, d$TIME ), %d/%m/%Y %H:%M) )) Error in xts(x, order.by = order.by, frequency = frequency, ...) : NROW(x) must match length(order.by) I could not figure out how to correct it Thank you for your help Yolande [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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@r-project.org mailing list 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.
Re: [R] Error in as.xts
Hello,
I'm glad it helped.
Your attachment came in corrupted. It's better to save the file as csv
or tab or space separated values text file. Use write.table or write.csv
to save the data. Even if there's a transmission problem, most of it
will be intact, just delete a row or so.
Rui Barradas
Em 16-07-2012 15:27, Yolande Tra escreveu:
Hello,
Can I ask you another question? Attached is the file created from
as.xts. After submitting the following code, I got an error. Please
help. Thanks.
diveCond - data.frame(matrix(0, nrow=61, ncol=17))
names(diveCond) - c(dive_id, timestamp, visability, r_wvht,
r_dpd, r_apt, r_mwd, r_wtmp, l_salinity, l_o2, l_hs,
l_tp, l_wdir, l_along, l_cross, l_mab, l_depth)
dive_id - 0
for(i in unique(as.character(index(diveData_2008{
dive_id - dive_id+1
diveCond$dive_id[dive_id] - dive_id
diveCond$timestamp[dive_id] - as.character(i)
diveCond$visability[dive_id] - as.numeric(diveData_2008[i][1,11])
}
Error in if (length(c(year, month, day, hour, min, sec)) == 6 c(year,:
missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In as_numeric() : NAs introduced by coercion
2: In as_numeric() : NAs introduced by coercion
Thanks,
Yolande
On Mon, Jul 16, 2012 at 2:51 AM, Rui Barradas ruipbarra...@sapo.pt
mailto:ruipbarra...@sapo.pt wrote:
Hello,
I can see several things that are not right or may go wrong.
(Without an actual dataset, this is just a series of hints.)
1. The read.csv statement. Like read.table, it creates a data.frame,
which defaults to reading strings as factors, coded internally as
integers. Sometimes there are problems, when using them and you are
converting the dates/times to POSIXct. You can try to use read.csv
option
stringsAsFactors = FALSE
and then do the conversions. These conversions would include
converting 'species' and 'site' to factor, if you want them as factors.
2. Are there typos in your posted code example?
2.a) You read into data.frame 'd1' but then use d$date and d$TIME.
2.b) In 'd1' the column is named 'time', not 'TIME'.
3. Try to create the date/time and assign it to a variable, for
instance,
dtvar - as.POSIXct(...etc...)
Now you can check length(dtvar) and NROW(d1) to see if they are
equal. You can also see if the conversion was allright. This is a
general rule: if there's an error in a complicated instruction,
break it into smaller ones.
Hope this helps,
Rui Barradas
Em 16-07-2012 03:10, Yolande Tra escreveu:
Hi
I got the following error using as.xts
Error in xts(x, order.by http://order.by/ = order.by
http://order.by/, frequency = frequency, ...) :
NROW(x) must match length(order.by http://order.by/)
Here is how the data looks like
d1 -
read.csv(file.path(dataDir,__AppendixA-FishCountsTable-__2009.csv),
as.is http://as.is/=T)
d1[1:3,]
dive_id date time species count sizesite
depth level
TRANSECT VIS_M
1 62 10/12/2009 12:44 E. lateralis 2 15 Hopkins15
B
1 4
2 62 10/12/2009 12:44 E. lateralis 1 22 Hopkins15
B
1 4
3 62 10/12/2009 12:44 E. lateralis 1 25 Hopkins15
B
1 4
diveData_2009 - as.xts( d1,order.by
http://order.by/=as.POSIXct(__strptime(paste(d$date,
d$TIME ), %d/%m/%Y %H:%M) ))
Error in xts(x, order.by http://order.by/ = order.by
http://order.by/, frequency = frequency, ...) :
NROW(x) must match length(order.by http://order.by/)
I could not figure out how to correct it
Thank you for your help
Yolande
[[alternative HTML version deleted]]
R-help@r-project.org mailto:R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/__listinfo/r-help
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/__posting-guide.html
http://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in as.xts
Hello,
I couldn't reproduce your error, with the csv file, your code run at the
first try. Here is exactly what I've done
dat - read.csv(diveData_2008.csv, header=TRUE, stringsAsFactors=FALSE)
# This 'DateTime' will be used again later.
DateTime - with(dat, paste(date, time))
DateTime - as.POSIXct(DateTime, format=%m/%d/%Y %H:%M)
# Create the xts object, slightly different, [ not as.xts() ]
diveData_2008 - xts(dat ,order.by=DateTime)
# Your code
diveCond - data.frame(matrix(0, nrow=61, ncol=17))
names(diveCond) - c(dive_id, timestamp, visability, r_wvht,
r_dpd, r_apt, r_mwd, r_wtmp, l_salinity, l_o2,
l_hs, l_tp, l_wdir, l_along, l_cross, l_mab,
l_depth)
dive_id - 0
for(i in unique(as.character(index(diveData_2008{
dive_id - dive_id+1
diveCond$dive_id[dive_id] - dive_id
diveCond$timestamp[dive_id] - as.character(i)
diveCond$visability[dive_id] - as.numeric(diveData_2008[i][1,11])
}
# See ?aggregate and note that the function is
# is FUN = `[`with further args 1 (the dots '...')
# to extract the first row in each sub-df
aggr - aggregate(TRANSECT ~ index(diveData_2008), data = diveData_2008,
`[`, 1)
names(aggr)[1] - timestamp
merge(data.frame(timestamp=unique(DateTime)), aggr, all.x=TRUE)
The output of this merge() is similar to your diveCond, but with much
less columns, it only has the columns with values different from zero.
The aggregate alone wouldn't include the NA value, only the ones with
an actual timestamp.
Anyway, there was no error in the creation of diveCond. This leads me to
the final note. If something is going wrong break the instructions nto
smaller simpler ones. See, for instance, how I've broken the DateTime
variable, without putting everything in the as.POSIXct, just the end
value after paste. Though the possible error wasn't there, it's allways
better to debug simpler code, EVEN if at the cost of making longer, with
more lines.
Hope this helps,
Rui Barradas
Em 16-07-2012 15:27, Yolande Tra escreveu:
Hello,
Can I ask you another question? Attached is the file created from
as.xts. After submitting the following code, I got an error. Please
help. Thanks.
diveCond - data.frame(matrix(0, nrow=61, ncol=17))
names(diveCond) - c(dive_id, timestamp, visability, r_wvht,
r_dpd, r_apt, r_mwd, r_wtmp, l_salinity, l_o2, l_hs,
l_tp, l_wdir, l_along, l_cross, l_mab, l_depth)
dive_id - 0
for(i in unique(as.character(index(diveData_2008{
dive_id - dive_id+1
diveCond$dive_id[dive_id] - dive_id
diveCond$timestamp[dive_id] - as.character(i)
diveCond$visability[dive_id] - as.numeric(diveData_2008[i][1,11])
}
Error in if (length(c(year, month, day, hour, min, sec)) == 6 c(year,:
missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In as_numeric() : NAs introduced by coercion
2: In as_numeric() : NAs introduced by coercion
Thanks,
Yolande
On Mon, Jul 16, 2012 at 2:51 AM, Rui Barradas ruipbarra...@sapo.pt
mailto:ruipbarra...@sapo.pt wrote:
Hello,
I can see several things that are not right or may go wrong.
(Without an actual dataset, this is just a series of hints.)
1. The read.csv statement. Like read.table, it creates a data.frame,
which defaults to reading strings as factors, coded internally as
integers. Sometimes there are problems, when using them and you are
converting the dates/times to POSIXct. You can try to use read.csv
option
stringsAsFactors = FALSE
and then do the conversions. These conversions would include
converting 'species' and 'site' to factor, if you want them as factors.
2. Are there typos in your posted code example?
2.a) You read into data.frame 'd1' but then use d$date and d$TIME.
2.b) In 'd1' the column is named 'time', not 'TIME'.
3. Try to create the date/time and assign it to a variable, for
instance,
dtvar - as.POSIXct(...etc...)
Now you can check length(dtvar) and NROW(d1) to see if they are
equal. You can also see if the conversion was allright. This is a
general rule: if there's an error in a complicated instruction,
break it into smaller ones.
Hope this helps,
Rui Barradas
Em 16-07-2012 03:10, Yolande Tra escreveu:
Hi
I got the following error using as.xts
Error in xts(x, order.by http://order.by/ = order.by
http://order.by/, frequency = frequency, ...) :
NROW(x) must match length(order.by http://order.by/)
Here is how the data looks like
d1 -
read.csv(file.path(dataDir,__AppendixA-FishCountsTable-__2009.csv),
as.is http://as.is/=T)
d1[1:3,]
dive_id date time species count sizesite
depth level
TRANSECT VIS_M
1 62 10/12/2009 12:44 E. lateralis 2 15 Hopkins15
B
1 4
2 62 10/12/2009 12:44 E. lateralis 1 22 Hopkins15
B
Re: [R] Error in as.xts
Hello,
You'll never get a df with 97 rows with that dataset. Just look.
(The last dive_id is 97 but it starts at 62, not at 1.)
dat - read.csv(diveData_2009.csv, header=TRUE, stringsAsFactors=FALSE)
#
DateTime - with(dat, paste(date, time))
DateTime - as.POSIXct(DateTime, format=%m/%d/%Y %H:%M)
diveData_2009 - xts(dat ,order.by=DateTime)
# Result shall not have 97 rows
uinx_2009 - unique(as.character(index(diveData_2009)))
length(uinx_2009) # 27
uid_2009 - unique(diveData_2009$dive_id)
length(uid_2009) # 36
# A solution
fun - function(x){
dd - with(x, paste(date[1], time[1]))
dd - as.POSIXct(dd, format = %m/%d/%Y %H:%M)
id - x$dive_id[1]
tt - x$TRANSECT[1]
data.frame(dive_id=id, timestamp=dd, TRANSECT=tt)
}
bb - by(dat, dat$dive_id, FUN = fun)
diveCond_2009 - do.call(rbind, bb)
Then add columns to this result:
diveCond_2009$r_wvht - 0
Etc.
Rui Barradas
Em 16-07-2012 19:46, Yolande Tra escreveu:
Yes the error happens for the 2009 file (attached). The dive_id in
diveCond stops at dive_id=88 even though the last dive_id in 2009 file
is dive_id=97
diveCond - data.frame(matrix(0, nrow=97, ncol=17))
names(diveCond) - c(dive_id, timestamp, visability, r_wvht,
r_dpd, r_apt, r_mwd, r_wtmp, l_salinity, l_o2, l_hs,
l_tp, l_wdir, l_along, l_cross, l_mab, l_depth)
dive_id - 0
for(i in unique(as.character(index(diveData_2008{
dive_id - dive_id+1
diveCond$dive_id[dive_id] - dive_id
diveCond$timestamp[dive_id] - as.character(i)
diveCond$visability[dive_id] - as.numeric(diveData_2008[i][1,11])
}
for(i in unique(as.character(index(diveData_2009{
dive_id - dive_id+1
diveCond$dive_id[dive_id] - dive_id
diveCond$timestamp[dive_id] - as.character(i)
diveCond$visability[dive_id] - as.numeric(diveData_2009[i][1,11])
}
On Mon, Jul 16, 2012 at 2:32 PM, Rui Barradas ruipbarra...@sapo.pt
mailto:ruipbarra...@sapo.pt wrote:
Hello,
I couldn't reproduce your error, with the csv file, your code run at
the first try. Here is exactly what I've done
dat - read.csv(diveData_2008.csv, header=TRUE,
stringsAsFactors=FALSE)
# This 'DateTime' will be used again later.
DateTime - with(dat, paste(date, time))
DateTime - as.POSIXct(DateTime, format=%m/%d/%Y %H:%M)
# Create the xts object, slightly different, [ not as.xts() ]
diveData_2008 - xts(dat ,order.by http://order.by/=DateTime)
# Your code
diveCond - data.frame(matrix(0, nrow=61, ncol=17))
names(diveCond) - c(dive_id, timestamp, visability, r_wvht,
r_dpd, r_apt, r_mwd, r_wtmp, l_salinity, l_o2,
l_hs, l_tp, l_wdir, l_along, l_cross, l_mab,
l_depth)
dive_id - 0
for(i in unique(as.character(index(__diveData_2008{
dive_id - dive_id+1
diveCond$dive_id[dive_id] - dive_id
diveCond$timestamp[dive_id] - as.character(i)
diveCond$visability[dive_id] -
as.numeric(diveData_2008[i][1,__11])
}
# See ?aggregate and note that the function is
# is FUN = `[`with further args 1 (the dots '...')
# to extract the first row in each sub-df
aggr - aggregate(TRANSECT ~ index(diveData_2008), data =
diveData_2008, `[`, 1)
names(aggr)[1] - timestamp
merge(data.frame(timestamp=__unique(DateTime)), aggr, all.x=TRUE)
The output of this merge() is similar to your diveCond, but with
much less columns, it only has the columns with values different
from zero.
The aggregate alone wouldn't include the NA value, only the ones
with an actual timestamp.
Anyway, there was no error in the creation of diveCond. This leads
me to the final note. If something is going wrong break the
instructions nto smaller simpler ones. See, for instance, how I've
broken the DateTime variable, without putting everything in the
as.POSIXct, just the end value after paste. Though the possible
error wasn't there, it's allways better to debug simpler code, EVEN
if at the cost of making longer, with more lines.
Hope this helps,
Rui Barradas
Em 16-07-2012 15:27, Yolande Tra escreveu:
Hello,
Can I ask you another question? Attached is the file created from
as.xts. After submitting the following code, I got an error. Please
help. Thanks.
diveCond - data.frame(matrix(0, nrow=61, ncol=17))
names(diveCond) - c(dive_id, timestamp, visability, r_wvht,
r_dpd, r_apt, r_mwd, r_wtmp, l_salinity, l_o2, l_hs,
l_tp, l_wdir, l_along, l_cross, l_mab, l_depth)
dive_id - 0
for(i in unique(as.character(index(__diveData_2008{
dive_id - dive_id+1
diveCond$dive_id[dive_id] - dive_id
diveCond$timestamp[dive_id] - as.character(i)
diveCond$visability[dive_id] - as.numeric(diveData_2008[i][1,__11])
}
Error in if (length(c(year, month, day, hour, min, sec)) == 6
c(year,:
missing value where
[R] Error in as.xts
Hi I got the following error using as.xts Error in xts(x, order.by = order.by, frequency = frequency, ...) : NROW(x) must match length(order.by) Here is how the data looks like d1 - read.csv(file.path(dataDir,AppendixA-FishCountsTable-2009.csv), as.is=T) d1[1:3,] dive_id date time species count sizesite depth level TRANSECT VIS_M 1 62 10/12/2009 12:44 E. lateralis 2 15 Hopkins15 B 1 4 2 62 10/12/2009 12:44 E. lateralis 1 22 Hopkins15 B 1 4 3 62 10/12/2009 12:44 E. lateralis 1 25 Hopkins15 B 1 4 diveData_2009 - as.xts( d1,order.by=as.POSIXct(strptime(paste(d$date, d$TIME ), %d/%m/%Y %H:%M) )) Error in xts(x, order.by = order.by, frequency = frequency, ...) : NROW(x) must match length(order.by) I could not figure out how to correct it Thank you for your help Yolande [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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.
