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@cnrdh
cnrdh / samplelog-errors.json
Created February 9, 2018 11:20
Samplelog datetime & positition errors
(node:5073) ExperimentalWarning: The ESM module loader is experimental.
About to convert 15 CSV file(s) with SamplelogCsvTransformer
data/input/2010/alkekonge_2010_samplelog.csv
data/input/2010/ice_2010_samplelog.csv
data/input/2011/ice_2011_samplelog.csv
data/input/2011/mosj_2011_samplelog.csv
data/input/2012/ice_2012_samplelog.csv
data/input/2012/mosj_2012_samplelog.csv
data/input/2012/polarnight_2012_samplelog.csv
data/input/2013/mosj_ice_2013_samplelog.csv
@cnrdh
cnrdh / metadata.json
Last active February 15, 2018 11:06
Argos-fox-DS/DIAG-metadata
[
{
"id": "bdac05e2c27e7a8d621b8035a389264cc2c5e878",
"technology": "argos",
"collection": "tracking",
"type": "diag",
"programs": [
"11660"
],
"platforms": [
@cnrdh
cnrdh / coccolithophore-occurrence-with-sample-event.csv
Last active October 25, 2018 09:23
Coccolithophore taxonomy data (2009-2015)
We can make this file beautiful and searchable if this error is corrected: It looks like row 3 should actually have 55 columns, instead of 22. in line 2.
taxon,qualifier,density,sample,comment,verbatimTaxon,samplesizeunit,samplesize,event,depth.0,depth.1,type,subtype,depth_from,depth_to,time,longitude,latitude,station,vessel,expedition,gear,depth_bottom,warn.0,filtered_volume,sample_type,responsible,__h16,__h17,__h18,__h19,__h20,ice_core_number,distance_from_core_bottom_cm_from,distance_from_core_bottom_cm_to,op,length,__h15,program,cast_number,animal_group,floe,location,ice_core_type,ice_thickness_cm,snow_thickness_cm,freeboard_cm,total_melted_volume_ml,salinity,__h31,__h32,contact_person,dilution_factor,ice_thickness_m,error.0
Prymnesiophyceae,indet.,11250.79903,MER09-01-13,,Coccolithophora,L,1,20f0d444-4c32-5493-b18d-2523c2e11cad,50,50,taxonomy,phytoplankton,50,50,2009-06-15T09:45:00Z,7.77,78.8,V6,G.O. Sars,MERCLIM-2009,Niskin bottle,1130,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
Algirosphaera robusta,,3214.51401,MER09-01-13,,,L,1,20f0d444-4c32-5493-b18d-2523c2e11cad,50,50,taxonomy,phytoplankton,50,50,2009-06-15T09:45:00Z,7.77,78.8,V6,G.O. Sars,MERCLIM-2009,Niskin bo
@cnrdh
cnrdh / 20km-grid.geojson
Last active September 4, 2018 11:11
Marine species grid densities
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@cnrdh
cnrdh / dwcSamplingEventMapFromImrActivity.mjs
Last active November 1, 2018 12:32
Sampling events from HI toktlogger
import wellknown from 'wellknown'; //https://www.npmjs.com/package/wellknown
// @param Object a: activity from IMR toktlogger
// @return Map
export function dwcSamplingEventMapFromImrActivity(a) {
const startCoordinates = a.startPosition.coordinates;
const endCoordinates = a.endPosition.coordinates;
const multiPoint = { type: 'MultiPoint', coordinates: [startCoordinates, endCoordinates]};
@cnrdh
cnrdh / marine-db-sampling-grid.geojson
Last active September 4, 2018 11:18
Marine database sampling density (10 km grid)
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@cnrdh
cnrdh / non-matching-taxa.ndjson
Last active October 25, 2018 17:42
Species in [functional-groups] not in taxon-db
"Achnanthes longipes"
"Actinocyclus"
"Actinocyclus tenuissimus"
"Ceratium fusus"
"Chaetoceros convulutus"
"Coccolithophora"
"Coscinodiscus centralis"
"Coxiella pseudoannulata"
"Cylindrotheca gracilis"
"Dinoflagellata"
@cnrdh
cnrdh / aw-nonmatches.txt
Last active October 17, 2018 19:59
AW list of phyto
"Actinocyclus"
"Alexandrium minimum"
"Arcocellulus cornucervis "
"Asteromphalus hyalinus "
"Athecate dinoflagellate"
"Bacteriosira bathyomphala"
"Biflagellatae"
"Calyptrosphaera sphaeroidea "
"Centriceae"
"Ceratoneis closterium "
@cnrdh
cnrdh / readme.md
Last active October 23, 2018 09:21
Argos CSV

Argos CSV variants

CSV exported from Argos web page

headers: (37) ["_120_db", "alarm", "altitude", "best_level", "comp", "delta_freq", "ellipse_orientation", "error_radius", "format_name", "frequency", "gdop", "heading", "lat_sol_1", "lat_sol_2", "latitude", "loc_date", "loc_idx", "loc_quality", "long_1", "long_2", "longitude", "low_voltage_flag", "msg", "msg_date", "nopc", "pass_dur__s", "platform", "platform_id_no", "prg_no", "raw_data", "saltwater_failsafe_flag", "sat", "semi_major_axis", "semi_minor_axis", "speed", "temperature", "underwater_percentage"]

Platform ID No.,Platform,Prg No.,Pass dur. (s),Msg Date,Sat.,Alarm,Format name,Loc. date,Longitude,Latitude,Altitude,Heading,Speed,Loc. quality,Frequency,Long. 1,Lat. sol. 1,Long. 2,Lat. sol. 2,Loc. idx,Nopc,Comp.,Msg,> - 120 DB,Best level,Delta freq.,Error radius,Semi-major axis,Semi-minor axis,Ellipse orientation,GDOP,Raw data,LOW VOLTAGE FLAG,SALTWATER FAILSAFE FLAG,TEMPERATURE,UNDERWATER PERCENTAGE
153814,,18660,0,2018-10-01 01:28:08,NK,N
@cnrdh
cnrdh / match.txt
Created November 16, 2018 13:05
Known species
ndjson-join --left 'd.scientificName' ~/nedlasta/alien.ndjson data/input/taxonomy/taxonomy-db.ndjson | ndjson-map 'match=!(null==d[1]), [d[0].scientificName,match, d[0], d[1]]' | grep true
["Oithona similis",true,{"Division":"crustaceans","Genus":"Oithona","Species":"similis","scientificName":"Oithona similis","":"","Endemic":"","Cosmopolitic":"","Natural dispersion":"","Alien":"","Invasive":""},{"scientificName":"Oithona similis","taxonRank":"species","synonym":"false","taxonomicStatus":"accepted","scientificNameAuthorship":"Claus, 1866","modified":"2018-02-01T17:59:34.278+0000","kingdom":"Animalia","phylum":"Arthropoda","class":"Hexanauplia","order":"Cyclopoida","family":"Oithonidae","genus":"Oithona","taxonID":"https://api.gbif.org/v1/species/5166639","references":"","taxonRemarks":"","type":"Taxon"}]
["Thalassiosira",true,{"Division":"diatoms","Genus":"Thalassiosira","Species":"sp.","scientificName":"Thalassiosira","":"","Endemic":"","Cosmopolitic":"","Natural dispersion":"","Alien":"","Invasive":""},{"sc