ERDDAP gives a simple, consistent way to download subsets of gridded and tabular scientific datasets in common file formats and make graphs and maps. This ERDDAP installation has oceanographic data (for example, data from satellites and buoys).
Find out more about ERDDAP at http://coastwatch.pfeg.noaa.gov/erddap/index.html.
library('rnoaa')
erddap_table('erdCalCOFIfshsiz')
#> <NOAA ERDDAP tabledap> erdCalCOFIfshsiz
#> Path: [/Users/sacmac/.rnoaa/erddap/f18cc75d8bf5ca831a96f42486a7bd5d.csv]
#> Last updated: [2014-12-19 15:47:55]
#> File size: [4.6 MB]
#> Dimensions: [20939 X 24]
#>
#> cruise ship ship_code order_occupied tow_type net_type
#> 2 199104 DAVID STARR JORDAN JD 1 MOCNESS_1m M1
#> 3 199104 DAVID STARR JORDAN JD 2 MOCNESS_1m M1
#> 4 199104 DAVID STARR JORDAN JD 2 MOCNESS_1m M1
#> 5 199104 DAVID STARR JORDAN JD 2 MOCNESS_1m M1
#> 6 199104 DAVID STARR JORDAN JD 4 MOCNESS_1m M1
#> 7 199104 DAVID STARR JORDAN JD 5 MOCNESS_1m M1
#> 8 199104 DAVID STARR JORDAN JD 6 MOCNESS_1m M1
#> 9 199104 DAVID STARR JORDAN JD 7 MOCNESS_1m M1
#> 10 199104 DAVID STARR JORDAN JD 11 MOCNESS_1m M1
#> 11 199104 DAVID STARR JORDAN JD 32 MOCNESS_1m M1
#> .. ... ... ... ... ... ...
#> Variables not shown: tow_number (int), net_location (chr),
#> standard_haul_factor (dbl), volume_sampled (chr), percent_sorted
#> (chr), sample_quality (dbl), latitude (chr), longitude (chr), line
#> (dbl), station (dbl), time (chr), scientific_name (chr), common_name
#> (chr), itis_tsn (int), calcofi_species_code (int), fish_size (chr),
#> fish_count (dbl), fish_1000m3 (chr)
erddap_table('erdCalCOFIfshsiz', 'time>=2001-07-07', 'time<=2001-07-08')
#> <NOAA ERDDAP tabledap> erdCalCOFIfshsiz
#> Path: [/Users/sacmac/.rnoaa/erddap/9e5119eb5c8ed63b9619be1367b0344c.csv]
#> Last updated: [2014-12-19 18:07:32]
#> File size: [0.05 MB]
#> Dimensions: [217 X 24]
#>
#> cruise ship ship_code order_occupied tow_type net_type
#> 2 200106 DAVID STARR JORDAN JD 43 MOCNESS_10m M2
#> 3 200106 DAVID STARR JORDAN JD 43 MOCNESS_10m M2
#> 4 200106 DAVID STARR JORDAN JD 43 MOCNESS_10m M2
#> 5 200106 DAVID STARR JORDAN JD 43 MOCNESS_10m M2
#> 6 200106 DAVID STARR JORDAN JD 43 MOCNESS_10m M2
#> 7 200106 DAVID STARR JORDAN JD 43 MOCNESS_10m M2
#> 8 200106 DAVID STARR JORDAN JD 43 MOCNESS_10m M2
#> 9 200106 DAVID STARR JORDAN JD 43 MOCNESS_10m M2
#> 10 200106 DAVID STARR JORDAN JD 43 MOCNESS_10m M2
#> 11 200106 DAVID STARR JORDAN JD 43 MOCNESS_10m M2
#> .. ... ... ... ... ... ...
#> Variables not shown: tow_number (int), net_location (chr),
#> standard_haul_factor (dbl), volume_sampled (chr), percent_sorted
#> (chr), sample_quality (dbl), latitude (chr), longitude (chr), line
#> (dbl), station (dbl), time (chr), scientific_name (chr), common_name
#> (chr), itis_tsn (int), calcofi_species_code (int), fish_size (chr),
#> fish_count (dbl), fish_1000m3 (chr)
erddap_table('erdCalCOFIfshsiz', fields=c('longitude','latitude','fish_size','itis_tsn'), 'time>=2001-07-07','time<=2001-07-10')
#> <NOAA ERDDAP tabledap> erdCalCOFIfshsiz
#> Path: [/Users/sacmac/.rnoaa/erddap/7b04d4ddfe4ad3540ec6213129fa050c.csv]
#> Last updated: [2014-12-19 18:07:47]
#> File size: [0.02 MB]
#> Dimensions: [558 X 4]
#>
#> longitude latitude fish_size itis_tsn
#> 2 -118.26 33.255 22.9 623745
#> 3 -118.26 33.255 22.9 623745
#> 4 -118.10667 32.738335 31.5 623625
#> 5 -118.10667 32.738335 48.3 623625
#> 6 -118.10667 32.738335 15.5 162221
#> 7 -118.10667 32.738335 16.3 162221
#> 8 -118.10667 32.738335 17.8 162221
#> 9 -118.10667 32.738335 18.2 162221
#> 10 -118.10667 32.738335 19.2 162221
#> 11 -118.10667 32.738335 20.0 162221
#> .. ... ... ... ...
erddap_table('erdCinpKfmBT', fields=c('latitude','longitude','Aplysia_californica_Mean_Density','Muricea_californica_Mean_Density'), 'time>=2007-06-24','time<=2007-07-01')
#> <NOAA ERDDAP tabledap> erdCinpKfmBT
#> Path: [/Users/sacmac/.rnoaa/erddap/681451f3fee8ee9e426012609975a89e.csv]
#> Last updated: [2014-12-19 18:08:22]
#> File size: [1.49 KB]
#> Dimensions: [37 X 4]
#>
#> latitude longitude Aplysia_californica_Mean_Density
#> 2 34.0 -119.416666666667 0.009722223
#> 3 34.0 -119.383333333333 0.0
#> 4 34.0 -119.366666666667 0.0
#> 5 34.0 -119.383333333333 0.16
#> 6 34.0 -119.416666666667 0.03
#> 7 34.0166666666667 -119.35 0.0
#> 8 34.0 -119.35 0.008333334
#> 9 33.0 -118.533333333333 NaN
#> 10 32.95 -118.533333333333 NaN
#> 11 32.8 -118.4 NaN
#> .. ... ... ...
#> Variables not shown: Muricea_californica_Mean_Density (chr)
Search for data
(out <- erddap_search(query='size'))
#> 6 results, showing first 20
#> title
#> 11 NOAA Global Coral Bleaching Monitoring Products
#> 12 Coawst 4 use, Best Time Series [time][eta_rho][xi_rho]
#> 13 Coawst 4 use, Best Time Series [time][eta_u][xi_u]
#> 14 Coawst 4 use, Best Time Series [time][eta_v][xi_v]
#> 15 Coawst 4 use, Best Time Series [time][s_rho][eta_rho][xi_rho]
#> 16 Coawst 4 use, Best Time Series [time][Nbed][eta_rho][xi_rho]
#> dataset_id
#> 11 NOAA_DHW
#> 12 whoi_ed12_89ce_9592
#> 13 whoi_61c3_0b5d_cd61
#> 14 whoi_62d0_9d64_c8ff
#> 15 whoi_7dd7_db97_4bbe
#> 16 whoi_a4fb_2c9c_16a7
Or, list datasets
tdp <- erddap_datasets('table')
Using a datasetid, search for information on a datasetid
id <- as.character(tdp$Dataset.ID[8])
erddap_info(id)$variables
#> variable_name data_type actual_range
#> 1 cndc float
#> 2 cndc_adjusted float
#> 3 cndc_adjusted_error float
#> 4 cndc_adjusted_qc float
#> 5 cndc_qc float
#> 6 doxy float
#> 7 doxy_adjusted float
#> 8 doxy_adjusted_error float
#> 9 doxy_adjusted_qc float
#> 10 doxy_qc float
#> 11 id int
#> 12 latitude float -90.0, 90.0
#> 13 longitude float 0.0, 360.0
#> 14 pres float
#> 15 pres_adjusted float
#> 16 pres_adjusted_error float
#> 17 pres_adjusted_qc float
#> 18 pres_qc float
#> 19 psal float
#> 20 psal_adjusted float
#> 21 psal_adjusted_error float
#> 22 psal_adjusted_qc float
#> 23 psal_qc float
#> 24 temp float
#> 25 temp_adjusted float
#> 26 temp_adjusted_error float
#> 27 temp_adjusted_qc float
#> 28 temp_doxy float
#> 29 temp_doxy_adjusted float
#> 30 temp_doxy_adjusted_error float
#> 31 temp_doxy_adjusted_qc float
#> 32 temp_doxy_qc float
#> 33 temp_qc float
#> 34 time double 8.1048066E8, NaN
Get data from the dataset
erddap_table(id, fields = c('latitude','longitude'))
#> <NOAA ERDDAP tabledap> apdrcArgoAll
#> Path: [/Users/sacmac/.rnoaa/erddap/7b238871e478bf43df2e1f703e6e85e5.csv]
#> Last updated: [2014-12-19 18:15:39]
#> File size: [0.07 MB]
#> Dimensions: [5000 X 2]
#>
#> latitude longitude
#> 2 49.868 215.335
#> 3 50.023 215.47
#> 4 50.115 215.676
#> 5 50.156 215.676
#> 6 50.132 215.601
#> 7 50.1 215.544
#> 8 50.158 215.582
#> 9 50.278 215.585
#> 10 50.417 215.702
#> 11 50.548 215.779
#> .. ... ...
Limit by time with date only
erddap_table(id, fields = c('latitude','longitude','time'), 'time>=2001-07-14', 'time<=2001-09-14')
#> <NOAA ERDDAP tabledap> apdrcArgoAll
#> Path: [/Users/sacmac/.rnoaa/erddap/d449b321be463619aab879c8ca2e40e7.csv]
#> Last updated: [2014-12-19 18:22:51]
#> File size: [0.05 MB]
#> Dimensions: [1490 X 3]
#>
#> latitude longitude time
#> 2 75.005 0.583 2001-07-14T04:29:00Z
#> 3 73.819 1.418 2001-07-14T01:01:59Z
#> 4 -24.702 106.08 2001-07-14T00:33:23Z
#> 5 -12.953 108.299 2001-07-14T04:23:12Z
#> 6 4.943 164.673 2001-07-14T18:36:46Z
#> 7 -4.769 189.924 2001-07-14T21:49:35Z
#> 8 11.312 195.319 2001-07-14T06:15:47Z
#> 9 48.906 229.489 2001-07-14T14:50:00Z
#> 10 -10.93 235.776 2001-07-14T08:47:12Z
#> 11 11.672 264.219 2001-07-14T05:31:14Z
#> .. ... ... ...
erddap_table('erdCalCOFIfshsiz', fields=c('longitude','latitude','fish_size','itis_tsn'), 'time>=2001-07-07','time<=2001-07-10', distinct=TRUE)
#> <NOAA ERDDAP tabledap> erdCalCOFIfshsiz
#> Path: [/Users/sacmac/.rnoaa/erddap/e05d5adb0fecd3bb2276c920e1bd2457.csv]
#> Last updated: [2014-12-19 18:16:09]
#> File size: [0.02 MB]
#> Dimensions: [518 X 4]
#>
#> longitude latitude fish_size itis_tsn
#> 2 -118.74333 32.873333 14.2 162584
#> 3 -118.74333 32.873333 15.0 162221
#> 4 -118.74333 32.873333 15.2 170085
#> 5 -118.74333 32.873333 17.2 162221
#> 6 -118.74333 32.873333 18.3 162221
#> 7 -118.74333 32.873333 18.7 170085
#> 8 -118.74333 32.873333 20.0 162664
#> 9 -118.74333 32.873333 20.2 162664
#> 10 -118.74333 32.873333 20.4 623745
#> 11 -118.74333 32.873333 23.1 623745
#> .. ... ... ... ...
In this example, values are the same, but sometimes they can be different given the units value passed
erddap_table('erdCinpKfmT', fields=c('longitude','latitude','time','temperature'), 'time>=2007-09-19', 'time<=2007-09-21', units='udunits')
#> <NOAA ERDDAP tabledap> erdCinpKfmT
#> Path: [/Users/sacmac/.rnoaa/erddap/d1aaf6eca896d080b1c2251f7a8cec17.csv]
#> Last updated: [2014-12-19 18:16:21]
#> File size: [2.18 KB]
#> Dimensions: [48 X 4]
#>
#> longitude latitude time temperature
#> 2 -120.1 33.883335 2007-09-19T00:13:00Z 16.22
#> 3 -120.1 33.883335 2007-09-19T01:13:00Z 16.38
#> 4 -120.1 33.883335 2007-09-19T02:13:00Z 16.38
#> 5 -120.1 33.883335 2007-09-19T03:13:00Z 16.38
#> 6 -120.1 33.883335 2007-09-19T04:13:00Z 14.48
#> 7 -120.1 33.883335 2007-09-19T05:13:00Z 13.86
#> 8 -120.1 33.883335 2007-09-19T06:13:00Z 13.55
#> 9 -120.1 33.883335 2007-09-19T07:13:00Z 13.24
#> 10 -120.1 33.883335 2007-09-19T08:13:00Z 13.09
#> 11 -120.1 33.883335 2007-09-19T09:13:00Z 12.78
#> .. ... ... ... ...
erddap_table('erdCinpKfmT', fields=c('longitude','latitude','time','temperature'), 'time>=2007-09-19', 'time<=2007-09-21', units='ucum')
#> <NOAA ERDDAP tabledap> erdCinpKfmT
#> Path: [/Users/sacmac/.rnoaa/erddap/a53175d2b882b8054906b46d4efe8218.csv]
#> Last updated: [2014-12-19 18:16:34]
#> File size: [2.17 KB]
#> Dimensions: [48 X 4]
#>
#> longitude latitude time temperature
#> 2 -120.1 33.883335 2007-09-19T00:13:00Z 16.22
#> 3 -120.1 33.883335 2007-09-19T01:13:00Z 16.38
#> 4 -120.1 33.883335 2007-09-19T02:13:00Z 16.38
#> 5 -120.1 33.883335 2007-09-19T03:13:00Z 16.38
#> 6 -120.1 33.883335 2007-09-19T04:13:00Z 14.48
#> 7 -120.1 33.883335 2007-09-19T05:13:00Z 13.86
#> 8 -120.1 33.883335 2007-09-19T06:13:00Z 13.55
#> 9 -120.1 33.883335 2007-09-19T07:13:00Z 13.24
#> 10 -120.1 33.883335 2007-09-19T08:13:00Z 13.09
#> 11 -120.1 33.883335 2007-09-19T09:13:00Z 12.78
#> .. ... ... ... ...
erddap_table('erdCinpKfmT', fields=c('longitude','latitude','time','temperature'), 'time>=2007-09-19', 'time<=2007-09-21', orderby='temperature')
#> <NOAA ERDDAP tabledap> erdCinpKfmT
#> Path: [/Users/sacmac/.rnoaa/erddap/9339183f5e454127988667d44e8fb0ca.csv]
#> Last updated: [2014-12-19 18:16:44]
#> File size: [2.18 KB]
#> Dimensions: [48 X 4]
#>
#> longitude latitude time temperature
#> 2 -120.1 33.883335 2007-09-20T12:13:00Z 12.0
#> 3 -120.1 33.883335 2007-09-20T13:13:00Z 12.0
#> 4 -120.1 33.883335 2007-09-20T14:13:00Z 12.0
#> 5 -120.1 33.883335 2007-09-20T11:13:00Z 12.16
#> 6 -120.1 33.883335 2007-09-20T15:13:00Z 12.16
#> 7 -120.1 33.883335 2007-09-20T10:13:00Z 12.31
#> 8 -120.1 33.883335 2007-09-20T16:13:00Z 12.31
#> 9 -120.1 33.883335 2007-09-20T17:13:00Z 12.62
#> 10 -120.1 33.883335 2007-09-19T09:13:00Z 12.78
#> 11 -120.1 33.883335 2007-09-20T09:13:00Z 12.78
#> .. ... ... ... ...
erddap_table('erdCinpKfmT', fields=c('longitude','latitude','time','temperature'), 'time>=2007-09-19', 'time<=2007-09-21', orderbymax='temperature')
#> <NOAA ERDDAP tabledap> erdCinpKfmT
#> Path: [/Users/sacmac/.rnoaa/erddap/e6e6116b3870afc9c093f6dab56ce6ba.csv]
#> Last updated: [2014-12-19 18:16:53]
#> File size: [0.12 KB]
#> Dimensions: [1 X 4]
#>
#> longitude latitude time temperature
#> 2 -120.1 33.883335 2007-09-19T03:13:00Z 16.38
erddap_table('erdCinpKfmT', fields=c('longitude','latitude','time','temperature'), 'time>=2007-09-19', 'time<=2007-09-21', orderbymin='temperature')
#> <NOAA ERDDAP tabledap> erdCinpKfmT
#> Path: [/Users/sacmac/.rnoaa/erddap/04557d97f6ecec410b114fc90da503d1.csv]
#> Last updated: [2014-12-19 18:17:12]
#> File size: [0.12 KB]
#> Dimensions: [1 X 4]
#>
#> longitude latitude time temperature
#> 2 -120.1 33.883335 2007-09-20T12:13:00Z 12.0
erddap_table('erdCinpKfmT', fields=c('longitude','latitude','time','temperature'), 'time>=2007-09-19', 'time<=2007-09-21', orderbyminmax='temperature')
#> <NOAA ERDDAP tabledap> erdCinpKfmT
#> Path: [/Users/sacmac/.rnoaa/erddap/4bd33e3b4de0d050b250fbccfd436ab7.csv]
#> Last updated: [2014-12-19 18:17:15]
#> File size: [0.16 KB]
#> Dimensions: [2 X 4]
#>
#> longitude latitude time temperature
#> 2 -120.1 33.883335 2007-09-20T12:13:00Z 12.0
#> 3 -120.1 33.883335 2007-09-19T03:13:00Z 16.38
erddap_table('erdCinpKfmT', fields=c('longitude','latitude','time','depth','temperature'), 'time>=2007-06-10', 'time<=2007-09-21', orderbymax=c('depth','temperature'))
#> <NOAA ERDDAP tabledap> erdCinpKfmT
#> Path: [/Users/sacmac/.rnoaa/erddap/e84ec03c5003845e4df2208ae39a975a.csv]
#> Last updated: [2014-12-19 18:17:24]
#> File size: [0.61 KB]
#> Dimensions: [11 X 5]
#>
#> longitude latitude time depth temperature
#> 2 -119.53333 34.033333 2007-08-07T02:40:00Z 5 20.54
#> 3 -119.36667 34.0 2007-07-05T03:42:00Z 6 19.72
#> 4 -119.35 34.0 2007-08-05T18:32:00Z 8 21.23
#> 5 -119.51667 34.033333 2007-08-06T04:02:00Z 9 20.47
#> 6 -120.13333 33.9 2007-08-04T22:34:00Z 10 19.35
#> 7 -119.38333 34.0 2007-08-02T15:38:00Z 11 20.86
#> 8 -120.183334 33.916668 2007-08-04T23:50:00Z 12 19.92
#> 9 -119.6 34.033333 2007-08-08T02:47:00Z 13 20.43
#> 10 -119.816666 33.933334 2007-07-17T02:21:00Z 15 18.47
#> 11 -119.416664 34.0 2007-07-10T23:25:00Z 16 19.14
#> .. ... ... ... ... ...
erddap_table('erdCalCOFIfshsiz', fields = c('latitude','longitude','scientific_name'), 'latitude>=34.8', 'latitude<=35', 'longitude>=-125', 'longitude<=-124')
#> <NOAA ERDDAP tabledap> erdCalCOFIfshsiz
#> Path: [/Users/sacmac/.rnoaa/erddap/8137b5814735d58e2d939b33a975c1a9.csv]
#> Last updated: [2014-12-19 15:48:00]
#> File size: [2.2 KB]
#> Dimensions: [56 X 3]
#>
#> latitude longitude scientific_name
#> 2 34.881668 -124.48 Cyclothone atraria
#> 3 34.881668 -124.48 Lipolagus ochotensis
#> 4 34.881668 -124.48 Bathylagoides wesethi
#> 5 34.881668 -124.48 Cyclothone acclinidens
#> 6 34.881668 -124.48 Cyclothone acclinidens
#> 7 34.881668 -124.48 Cyclothone signata
#> 8 34.881668 -124.48 Cyclothone signata
#> 9 34.881668 -124.48 Cyclothone signata
#> 10 34.881668 -124.48 Cyclothone signata
#> 11 34.881668 -124.48 Cyclothone signata
#> .. ... ... ...
out <- erddap_table('erdCalCOFIfshsiz', fields = c('latitude','longitude','scientific_name','itis_tsn'))
tsns <- unique(out$itis_tsn[1:100])
library("taxize")
classif <- classification(tsns, db = "itis")
head(rbind(classif)); tail(rbind(classif))
#> name rank id query db
#> 1 Animalia Kingdom 202423 172887 itis
#> 2 Bilateria Subkingdom 914154 172887 itis
#> 3 Deuterostomia Infrakingdom 914156 172887 itis
#> 4 Chordata Phylum 158852 172887 itis
#> 5 Vertebrata Subphylum 331030 172887 itis
#> 6 Gnathostomata Infraphylum 914179 172887 itis
#> name rank id query db
#> 161 Stomiiformes Order 553138 162167 itis
#> 162 Gonostomatoidei Suborder 553151 162167 itis
#> 163 Gonostomatidae Family 162163 162167 itis
#> 164 Cyclothone Genus 162164 162167 itis
#> 165 Cyclothone pallida Species 162167 162167 itis
#> 166 Bathylagus wesethi Species 162092 162092 itis