[R] error with the expand.grid command
MacQueen, Don
m@cqueen1 @end|ng |rom ||n|@gov
Thu Aug 9 18:45:32 CEST 2018
In my experience, error messages that reference a closure usually mean that you have supplied a function where you aren't supposed to.
In this case, I'd look and see if lon, lat, or time is a function (by accident, of course).
More specifically, right now in one of my R sessions, I get:
> class(time)
[1] "function"
> find('time')
[1] "package:stats"
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
Lab cell 925-724-7509
On 8/8/18, 11:20 PM, "R-help on behalf of Mayur Tade" <r-help-bounces using r-project.org on behalf of 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.
More information about the R-help
mailing list