Thank you very much Roy and Jeff for your help. I contacted dear David, the author of ncdf4 package, at first and he lead me here. Sorry for any inconvenience.
I wish you success in your work. Regards, On Fri, Jul 8, 2016, 04:28 Roy Mendelssohn - NOAA Federal < roy.mendelss...@noaa.gov> wrote: > I have moved this over to the netcdf-group mail list, which I think is the > more appropriate place at this point. You are copied, and hopefully > someone from ESRL will see it and provide the proper response. > > HTH, > > -Roy > > > On Jul 7, 2016, at 6:02 PM, Ismail SEZEN <sezenism...@gmail.com> wrote: > > > > Thank you Roy. If I use "round(uwind, digits = 2)”, all data will have 2 > decimal places after decimal point. It’s ok. But How do you know you should > round the number to 2 decimal digits? According to definitions of precision > and least_significant_digit, should I round to 2 decimal digits or 1 > decimal digit? > > > > For instance, If you check the header information of omega.2015.nc file > it says; > > > > $ ncdump -h omega.2015.nc > > > > ... > > omega:precision = 3s; > > omega:least_significant_digit = 3s; > > … > > > > So, I need to round values to 3 decimal places after point? > > > > and if you check the output of rhum.2015.nc; > > > > $ ncdump -h rhum.2015.nc > > ... > > rhum:precision = 2s ; > > rhum:least_significant_digit = 0s ; > > … > > > > Then I need to round values to 2 decimal places after point? > > > > Should I accomplish the rounding operation according to precision or > least_significant_digit attributes? I think someone put these attributes in > netcdf files for some reason. Also I belive, if required, this kind of an > operation must be done in related package but author said that it is > nothing to do with ncdf4 package. > > > > Please, forgive me for taking your time. > > > > > >> On 08 Jul 2016, at 03:21, Roy Mendelssohn - NOAA Federal < > roy.mendelss...@noaa.gov> wrote: > >> > >> After looking at the file, doing an extract say into the variable > uwind, if I do: > >> > >> str(uwind) > >> > >> I see what I expect, but if I just do: > >> > >> uwind > >> > >> > >> I see what you are seeing. Try: > >> > >> uwindnew <- round(uwind, digits = 2) > >> > >> > >> and see if that gives you the results you would expect. > >> > >> HTH, > >> > >> -Roy > >> > >>> On Jul 7, 2016, at 4:49 PM, Ismail SEZEN <sezenism...@gmail.com> > wrote: > >>> > >>> Thank you Roy. > >>> > >>> I use NCEP/NCAR Reanalysis 2 data [1]. More precisely, u-wind data of > the year 2015 [2]. I am also pretty sure that the variables like > scale_factor or add_offset should be precise like 0.01 or 187.65 but > somehow (I hope this is not an issue originated by me) they are not, > including data. Also let me note that I already contacted to author of > ncdf4 package and also sent an email to ESRL, too, but no luck yet. > >>> > >>> For a vectoral data, absolute and mutual u components of wind speed at > the poles must be equal. For instance, at “2015-01-01 00 GMT”, u-wind at > longitude=0 and latitude=90 is 9.1999979 m/s and u-wind at longitude=180 > and latitude=90 is -9.2000017 m/s. Minus sign comes from positive north > direction. Physically, their absolute values must be equal. > >>> > >>> 1- > http://www.esrl.noaa.gov/psd/data/gridded/data.ncep.reanalysis2.html > >>> 2- > ftp://ftp.cdc.noaa.gov/Datasets/ncep.reanalysis2.dailyavgs/pressure/uwnd.2015.nc > >>> > >>> > >>> > >>>> On 08 Jul 2016, at 02:27, Roy Mendelssohn - NOAA Federal < > roy.mendelss...@noaa.gov> wrote: > >>>> > >>>> Hi Ismail: > >>>> > >>>> Can you point me to a particular netcdf file you are working with. I > would like to play with it for awhile. I am pretty certain the scale > factor is 0.01 and what you are seeing in rounding error (or mor precisely > I should say problems with representations of floating point numbers), but > i would like to see if there is away around this. > >>>> > >>>> Thank, > >>>> > >>>> -Roy > >>>> > >>>>> On Jul 7, 2016, at 4:16 PM, Ismail SEZEN <sezenism...@gmail.com> > wrote: > >>>>> > >>>>> Thank you very much Jeff. I think I’m too far to be able to explain > myself. Perhaps, this is the wrong list for this question but I sent it in > hope there is someone has deep understanding of netcdf data and use R. Let > me tell the story simpler. Assume that you read a numeric vector of data > from a netcdf file: > >>>>> > >>>>> data <- c(9.1999979, 8.7999979, 7.9999979, 3.0999980, 6.1000018, > 10.1000017, 10.4000017, 9.2000017) > >>>>> > >>>>> you know that the values above are a model output and also you know > that, physically, first and last values must be equal but somehow they are > not. > >>>>> > >>>>> And now, you want to use “periodic” spline for the values above. > >>>>> > >>>>> spline(1:8, data, method = “periodic”) > >>>>> > >>>>> Voila! spline method throws a warning message: “spline: first and > last y values differ - using y[1] for both”. Then I go on digging and > discover 2 attributes in netcdf file: “precision = 2” and > “least_significant_digit = 1”. And I also found their definitions at [1]. > >>>>> > >>>>> precision -- number of places to right of decimal point that are > significant, based on packing used. Type is short. > >>>>> least_significant_digit -- power of ten of the smallest decimal > place in unpacked data that is a reliable value. Type is short. > >>>>> > >>>>> Please, do not condemn me, english is not my main language :). At > this point, as a scientist, what would you do according to explanations > above? I think I didn’t exactly understand the difference between precision > and least_significant_digit. One says “significant” and latter says > “reliable”. Should I round the numbers to 2 decimal places or 1 decimal > place after decimal point? > >>>>> > >>>>> Thanks, > >>>>> > >>>>> 1- > http://www.esrl.noaa.gov/psd/data/gridded/conventions/cdc_netcdf_standard.shtml > >>>>> > >>>>> > >>>>>> On 08 Jul 2016, at 01:29, Jeff Newmiller <jdnew...@dcn.davis.ca.us> > wrote: > >>>>>> > >>>>>> Correction: > >>>>>> > >>>>>> ?options (not par) > >>>>>> -- > >>>>>> Sent from my phone. Please excuse my brevity. > >>>>>> > >>>>>> On July 7, 2016 3:26:06 PM PDT, Jeff Newmiller < > jdnew...@dcn.davis.ca.us> wrote: > >>>>>>> Same as with any floating point numeric computation environment... > you > >>>>>>> don't. There is always uncertainty in any floating point number... > it > >>>>>>> is just larger in this data than you might be used to. > >>>>>>> > >>>>>>> Once you get to the stage where you want to output values, read up > on > >>>>>>> > >>>>>>> ?round > >>>>>>> ?par (digits) > >>>>>>> > >>>>>>> and don't worry about the incidental display of extra digits prior > to > >>>>>>> presentation (output). > >>>>>>> -- > >>>>>>> Sent from my phone. Please excuse my brevity. > >>>>>>> > >>>>>>> On July 7, 2016 12:50:54 AM PDT, Ismail SEZEN < > sezenism...@gmail.com> > >>>>>>> wrote: > >>>>>>>> Hello, > >>>>>>>> > >>>>>>>> I use ncdf4 and ncdf4.helpers packages to get wind data from > ncep/ncar > >>>>>>>> reanalysis ncetcdf files. But data is in the form of (9.199998, > >>>>>>>> 8.799998, 7.999998, 3.099998, -6.8000018, …). I’m aware of > precision > >>>>>>>> and least_significant_digit attributes of ncdf4 object [1]. For > uwnd > >>>>>>>> data, precision = 2 and least_significant_digits = 1. My doubt is > that > >>>>>>>> should I round data to 2 decimal places or 1 decimal place after > >>>>>>>> decimal point? > >>>>>>>> > >>>>>>>> Same issue is valid for some header info. > >>>>>>>> > >>>>>>>> Output of ncdf4 object: > >>>>>>>> > >>>>>>>> > >>>>>>>> Output of ncdump on terminal: > >>>>>>>> > >>>>>>>> > >>>>>>>> for instance, ncdump's scale factor is 0.01f but ncdf4 object’s > >>>>>>>> scale_factor is 0.00999999977648258. You can notice same issue for > >>>>>>>> actual_range and add_offset. Also a similar issue exist for the > data. > >>>>>>>> How can I truncate those extra unsignificant decimal places or > round > >>>>>>>> the numbers to significant decimal places? > >>>>>>>> > >>>>>>>> 1 - > >>>>>>>> > http://www.esrl.noaa.gov/psd/data/gridded/conventions/cdc_netcdf_standard.shtml > >>>>>>>> < > http://www.esrl.noaa.gov/psd/data/gridded/conventions/cdc_netcdf_standard.shtml > > > >>>>>>>> ______________________________________________ > >>>>>>>> R-help@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@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. > >>>>>> > >>>>> > >>>>> > >>>>> [[alternative HTML version deleted]] > >>>>> > >>>>> ______________________________________________ > >>>>> R-help@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. > >>>> > >>>> ********************** > >>>> "The contents of this message do not reflect any position of the U.S. > Government or NOAA." > >>>> ********************** > >>>> Roy Mendelssohn > >>>> Supervisory Operations Research Analyst > >>>> NOAA/NMFS > >>>> Environmental Research Division > >>>> Southwest Fisheries Science Center > >>>> ***Note new address and phone*** > >>>> 110 Shaffer Road > >>>> Santa Cruz, CA 95060 > >>>> Phone: (831)-420-3666 > >>>> Fax: (831) 420-3980 > >>>> e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/ > >>>> > >>>> "Old age and treachery will overcome youth and skill." > >>>> "From those who have been given much, much will be expected" > >>>> "the arc of the moral universe is long, but it bends toward justice" > -MLK Jr. > >>>> > >>> > >> > >> ********************** > >> "The contents of this message do not reflect any position of the U.S. > Government or NOAA." > >> ********************** > >> Roy Mendelssohn > >> Supervisory Operations Research Analyst > >> NOAA/NMFS > >> Environmental Research Division > >> Southwest Fisheries Science Center > >> ***Note new address and phone*** > >> 110 Shaffer Road > >> Santa Cruz, CA 95060 > >> Phone: (831)-420-3666 > >> Fax: (831) 420-3980 > >> e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/ > >> > >> "Old age and treachery will overcome youth and skill." > >> "From those who have been given much, much will be expected" > >> "the arc of the moral universe is long, but it bends toward justice" > -MLK Jr. > >> > > > > ********************** > "The contents of this message do not reflect any position of the U.S. > Government or NOAA." > ********************** > Roy Mendelssohn > Supervisory Operations Research Analyst > NOAA/NMFS > Environmental Research Division > Southwest Fisheries Science Center > ***Note new address and phone*** > 110 Shaffer Road > Santa Cruz, CA 95060 > Phone: (831)-420-3666 > Fax: (831) 420-3980 > e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/ > > "Old age and treachery will overcome youth and skill." > "From those who have been given much, much will be expected" > "the arc of the moral universe is long, but it bends toward justice" -MLK > Jr. > > [[alternative HTML version deleted]] ______________________________________________ R-help@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.
