[R] error with the expand.grid command
Ben Tupper
btupper @end|ng |rom b|ge|ow@org
Thu Aug 9 14:32:50 CEST 2018
Hello,
You will have much better success if you subscribe and post to the R-sig-geo mailing list rather than the R-help mailing list. You can subscribe to that list here... https://www.r-project.org/mail.html <https://www.r-project.org/mail.html>
If you are open to other suggestions, here are a couple of other tips to help you get help.
Change your email client to send plain text rather than richly formatted messages. Using richly formatted text will often result in a garbled message and always results in this little gem you can see a the bottom of your message...
> [[alternative HTML version deleted]]
More specifically to your problem, there isn't anyway for others to help you since we could not access your data (like the NCDF file) and variables (like lon, lat, time, tt and ttt). Anything you can do to make the issue super easy for someone to help means you are more likely to get the help you seek. There are some really nice tutorials on how to ask a question on a help list that will most likely score you the help you seek. Here's an example... https://www.r-project.org/posting-guide.html <https://www.r-project.org/posting-guide.html> but there are more out there on the world wild web.
Best of luck and see you over on R-sig-geo!
Ben
> On Aug 9, 2018, at 2:20 AM, Mayur Tade <mayur.tade using gmail.com> wrote:
>
> hello sir...
> i am trying to extract the chlorophyll data of particular lat and lon from
> the world chlorophyll data from the netcdf file in R. as i am new to R i am
> facing the problem related to it when i am trying expand.grid command it is
> showing me this message.....message is followed.....its my kind request
> please help me with the same
> ttt<-expand.grid(lon,lat,time)
> Error in paste0(nmc[i], "=", if (is.numeric(x)) format(x) else x) :
> cannot coerce type 'closure' to vector of type 'character'
>
> here is the print of my netcdf file for you kind information.....follow...
>
>> print(tt)
> File E:\chlorophyll data research student..mayur
> t..KUFOS\1997\ESACCI-OC-L3S-CHLOR_A-MERGED-1M_MONTHLY_4km_
> GEO_PML_OCx-199709-fv3.1.nc
> <http://esacci-oc-l3s-chlor_a-merged-1m_monthly_4km_geo_pml_ocx-199709-fv3.1.nc/>
> (NC_FORMAT_NETCDF4_CLASSIC):
>
> 9 variables (excluding dimension variables):
> float MERIS_nobs_sum[lon,lat,time]
> _FillValue: 0
> long_name: Count of the number of observations from the MERIS
> sensor contributing to this bin cell
> number_of_files_composited: 19
> float MODISA_nobs_sum[lon,lat,time]
> _FillValue: 0
> long_name: Count of the number of observations from the MODIS
> (Aqua) sensor contributing to this bin cell
> number_of_files_composited: 19
> float SeaWiFS_nobs_sum[lon,lat,time]
> _FillValue: 0
> long_name: Count of the number of observations from the SeaWiFS
> (GAC and LAC) sensor contributing to this bin cell
> number_of_files_composited: 19
> float VIIRS_nobs_sum[lon,lat,time]
> _FillValue: 0
> long_name: Count of the number of observations from the VIIRS
> sensor contributing to this bin cell
> number_of_files_composited: 19
> float chlor_a[lon,lat,time]
> _FillValue: 9.96920996838687e+36
> long_name: Chlorophyll-a concentration in seawater (not
> log-transformed), generated by SeaDAS using a blended combination of OCI
> (OC4v6 + Hu's CI), OC3 and OC5, depending on water class memberships
> units: milligram m-3
> ancillary_variables: chlor_a_log10_rmsd chlor_a_log10_bias
> grid_mapping: crs
> standard_name: mass_concentration_of_chlorophyll_a_in_sea_water
> units_nonstandard: mg m^-3
> parameter_vocab_uri:
> http://vocab.nerc.ac.uk/collection/P04/current/
> float chlor_a_log10_bias[lon,lat,time]
> _FillValue: 9.96920996838687e+36
> long_name: Bias of log10-transformed chlorophyll-a concentration
> in seawater.
> grid_mapping: crs
> rel: uncertainty
> comment: Uncertainty lookups derived from file:
> /data/datasets/CCI/v3.1-production/stage09b-uncertainty_tables/chlor_a/
> cci_chla_bias.dat
> ref: http://www.esa-oceancolour-cci.org/?q=webfm_send/581
> float chlor_a_log10_rmsd[lon,lat,time]
> _FillValue: 9.96920996838687e+36
> long_name: Root-mean-square-difference of log10-transformed
> chlorophyll-a concentration in seawater.
> grid_mapping: crs
> rel: uncertainty
> comment: Uncertainty lookups derived from file:
> /data/datasets/CCI/v3.1-production/stage09b-uncertainty_tables/chlor_a/
> cci_chla_rmsd.dat
> ref: http://www.esa-oceancolour-cci.org/?q=webfm_send/581
> int crs[time]
> grid_mapping_name: latitude_longitude
> float total_nobs_sum[lon,lat,time]
> _FillValue: 0
> long_name: Count of the total number of observations
> contributing to this bin cell
> number_of_files_composited: 19
>
> 3 dimensions:
> time Size:1
> axis: T
> standard_name: time
> units: days since 1970-01-01 00:00:00
> lat Size:4320
> units: degrees_north
> long_name: latitude
> standard_name: latitude
> valid_min: -89.9791641235352
> valid_max: 89.9791641235352
> axis: Y
> lon Size:8640
> units: degrees_east
> long_name: longitude
> standard_name: longitude
> valid_min: -179.97917175293
> valid_max: 179.97917175293
> axis: X
>
> 47 global attributes:
> Metadata_Conventions: Unidata Dataset Discovery v1.0
> cdm_data_type: Grid
> comment: See summary attribute
> creator_email: help using esa-oceancolour-cci.org
> creator_name: Plymouth Marine Laboratory
> creator_url: http://esa-oceancolour-cci.org
> geospatial_lat_max: 90
> geospatial_lat_min: -90
> geospatial_lat_resolution: .04166666666666666666
> geospatial_lat_units: decimal degrees north
> geospatial_lon_max: 180
> geospatial_lon_min: -180
> geospatial_lon_resolution: .04166666666666666666
> geospatial_lon_units: decimal degrees east
> geospatial_vertical_max: 0
> geospatial_vertical_min: 0
> institution: Plymouth Marine Laboratory
> keywords: satellite,observation,ocean,ocean colour
> keywords_vocabulary: none
> license: ESA CCI Data Policy: free and open access. When
> referencing, please use: Ocean Colour Climate Change Initiative dataset,
> Version <Version Number>, European Space Agency, available online at
> http://www.esa-oceancolour-cci.org. We would also appreciate being notified
> of publications so that we can list them on the project website at
> http://www.esa-oceancolour-cci.org/?q=publications
> naming_authority: uk.ac.pml
> number_of_optical_water_types: 14
> platform: Orbview-2,Aqua,Envisat,Suomi-NPP
> processing_level: Level-3
> project: Climate Change Initiative - European Space Agency
> references: http://www.esa-oceancolour-cci.org/
> sensor: SeaWiFS,MODIS,MERIS,VIIRS
> source: NASA SeaWiFS L2 R2014.0 LAC and GAC, MODIS-Aqua L1A, MERIS
> L1B 3rd reprocessing inc OCL corrections, NASA VIIRS L2 R2014.0.1 (data
> identical to R2014.0.2)
> spatial_resolution: 4km nominal at equator
> standard_name_vocabulary: NetCDF Climate and Forecast (CF) Metadata
> Conventions Version 1.6
> title: ESA CCI Ocean Colour Product
> number_of_files_composited: 19
> creation_date: Tue Aug 23 09:00:23 2016
> date_created: Tue Aug 23 09:00:23 2016
> time_coverage_resolution: P1M
> time_coverage_duration: P1M
> start_date: 01-SEP-1997 00:00:00.000000
> stop_date: 30-SEP-1997 23:59:00.000000
> time_coverage_start: 199709010000Z
> time_coverage_end: 199709302359Z
> netcdf_file_type: NETCDF4_CLASSIC
> history: Source data were:
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970904-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970904-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970906-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970906-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970909-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970909-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970910-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970910-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970915-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970915-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970916-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970916-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970918-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970918-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970919-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970919-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970920-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970920-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970921-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970921-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970922-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970922-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970923-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970923-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970924-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970924-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970925-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970925-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970926-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970926-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970927-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970927-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970928-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970928-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970929-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970929-fv3.1.nc/>
> ,
> ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1D_DAILY_4km_GEO_PML_
> OCx_QAA-19970930-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1d_daily_4km_geo_pml_ocx_qaa-19970930-fv3.1.nc/>
> ;
> netcdf_compositor_cci composites Rrs_412, Rrs_443, Rrs_490, Rrs_510,
> Rrs_555, Rrs_670, water_class1, water_class2, water_class3, water_class4,
> water_class5, water_class6, water_class7, water_class8, water_class9,
> water_class10, water_class11, water_class12, water_class13, water_class14,
> atot_412, atot_443, atot_490, atot_510, atot_555, atot_670, aph_412,
> aph_443, aph_490, aph_510, aph_555, aph_670, adg_412, adg_443, adg_490,
> adg_510, adg_555, adg_670, bbp_412, bbp_443, bbp_490, bbp_510, bbp_555,
> bbp_670, chlor_a, kd_490, chlor_a_log10_bias, Rrs_412_bias, Rrs_443_bias,
> Rrs_490_bias, Rrs_510_bias, Rrs_555_bias, Rrs_670_bias, aph_412_bias,
> aph_443_bias, aph_490_bias, aph_510_bias, aph_555_bias, aph_670_bias,
> adg_412_bias, adg_443_bias, adg_490_bias, adg_510_bias, adg_555_bias,
> adg_670_bias, kd_490_bias with --mean, chlor_a_log10_rmsd, Rrs_412_rmsd,
> Rrs_443_rmsd, Rrs_490_rmsd, Rrs_510_rmsd, Rrs_555_rmsd, Rrs_670_rmsd,
> aph_412_rmsd, aph_443_rmsd, aph_490_rmsd, aph_510_rmsd, aph_555_rmsd,
> aph_670_rmsd, adg_412_rmsd, adg_443_rmsd, adg_490_rmsd, adg_510_rmsd,
> adg_555_rmsd, adg_670_rmsd, kd_490_rmsd with --root-mean-square, and
> SeaWiFS_nobs, MODISA_nobs, MERIS_nobs, VIIRS_nobs, total_nobs - with --total
> 1471940520 Subsetted from
> standardised_geo/ESACCI-OC-L3S-OC_PRODUCTS-MERGED-1M_
> MONTHLY_4km_GEO_PML_OCx_QAA-199709-fv3.1.nc
> <http://esacci-oc-l3s-oc_products-merged-1m_monthly_4km_geo_pml_ocx_qaa-199709-fv3.1.nc/>
> to only include variables
> MERIS_nobs_sum,MODISA_nobs_sum,SeaWiFS_nobs_sum,VIIRS_
> nobs_sum,chlor_a,chlor_a_log10_bias,chlor_a_log10_rmsd,
> crs,lat,lon,time,total_nobs_sum
> Conventions: CF-1.6
> product_version: 3.1
> summary: Data products generated by the Ocean Colour component of
> the European Space Agency Climate Change Initiative project. These files are
> daily composites of merged sensor (MERIS, MODIS Aqua, SeaWiFS LAC & GAC,
> VIIRS) products. MODIS Aqua and MERIS were band-shifted and bias-corrected
> to SeaWiFS bands and values using a temporally and spatially varying scheme
> based on the overlap years of 2003-2007. VIIRS was band-shifted and
> bias-corrected in a second stage against the MODIS Rrs that had already been
> corrected to SeaWiFS levels, for the overlap period 2012-2013. VIIRS and
> SeaWiFS Rrs were derived from standard NASA L2 products; MERIS and MODIS
> from a combination of NASA's l2gen (for basic sensor geometry corrections,
> etc) and HYGEOS Polymer v3.5 (for atmospheric correction). The Rrs were
> binned to a sinusoidal 4km level-3 grid, and later to 4km geographic
> projection, by Brockmann Consult's BEAM. Derived products were generally
> computed with the standard SeaDAS algorithms. QAA IOPs were derived using
> the standard SeaDAS algorithm but with a modified backscattering table to
> match that used in the bandshifting. The final chlorophyll is a combination
> of OC4, Hu's CI and OC5, depending on the water class memberships.
> Uncertainty estimates were added using the fuzzy water classifier and
> uncertainty estimation algorithm of Tim Moore as documented in Jackson et al
> (2017).
> tracking_id: 659b397a-953c-4814-a3e2-460d6218fcfa
> id:
> ESACCI-OC-L3S-CHLOR_A-MERGED-1M_MONTHLY_4km_GEO_PML_OCx-199709-fv3.1.nc
> <http://esacci-oc-l3s-chlor_a-merged-1m_monthly_4km_geo_pml_ocx-199709-fv3.1.nc/>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help using 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.
>
Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org
Ecological Forecasting: https://eco.bigelow.org/
[[alternative HTML version deleted]]
More information about the R-help
mailing list