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Last edited by Beatriz Recinos
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Workflow

Data input

The following data is required by the scripts of this repository:

  • ICOADS v3.0. Freeman. et al., (2017).
  • Metadata from WMO Publication 47. Kent. et al., (2007)
  • CLIWOC logbook IDs. (needs a link)
  • Inventory of ship names in the US Maury Collection
  • generate_id (needs description)
  • Precision criteria file. An estimate of the precision of each key variable (e.g. sst, lat, lon) per dck, yr and or sid. This precision criteria is require in order to set tolerances when comparing variables from ICOADS (See the list of ICOADS variables used in this repository). Comparison of variables allows for a match between reports in the duplicate identification procedure.
  • Json files containing ITU callsign prefixes associated with a country.
  • seq IDS. (needs description)

Processing stages

The following diagram is a summary of the data processing workflow follow by the shell scripts defined in scr. Each block represents a main task done by one script inrscripts. The corresponding .R file name is highlight in grey between each stage (For more information on eah .R script, please see the API-reference)

Orange blocks represent pre-processing tasks done to the ICOADS data, in order to:

  1. Select data taken only by commercial ships, excluding specialist ship data sources, such as research vessels (For more information see the selection criteria).
  2. Preprocessing of ID's to improve duplicate identification and linking of id's between each pair of duplicate reports.
  3. Preformed quality control on the data to point out the best duplicate.

The rest of the blocks represent processing scripts that concentrate in the duplicates identification and matching of reports ID's.

graph TB
A1[rscripts]

 id1[(ICOADS v3.0)] --> |split_by_type.R|id2[Separate records according <br> to the different platform types.]
 id2 --> |simple_dup.R|id3[First duplicate identification between <br> ship data and the different platform types. <br> Considers the records as duplicates if they <br> show matching date, time & position.] 
 id3 --> |ship2plat.R|id4[Exclude non-ship data.] 
 id4 --> id5[(ICOADS SHIP data)]
 id5 --> |process_ids.R|id6[Homogenize and re-format <br> ship IDs from different decks. <br> Links metadata from Pub 47 & logbooks <br> to formed a plausible ship track.]
 id6 -->  |process_shipdata.R|id7[Process ship data: <br> correction of dates & times.] 
 id7 --> |new_get_pairs.R|id8[Second duplicate identification. <br> Pairs the reports as duplicate if <br> they have associated ship IDs. <br> Reports that fail the track check <br> are flagged as the worst.] 
 id8 --> |new_get_dups.R|id9[Counts the number of duplicates and flags the best.]
 id9 --> |new_merge_ids_year.R|id10[Links ID's into classes.]
 id10 --> |clean_data.R|id11[Clean of ship data.] 
 id11 --> |clean2track.R|id12[Forms ship tracks for linked IDs.] 
 id12 --> id13[(Output data)]

classDef pre-processing fill:#fcc679,stroke:#333,stroke-width:1px,font-size:16px,font-weight:100,text-align:center
classDef scripts fill:#8C929D,stroke:#333,stroke-width:1px,font-size:16px,font-weight:100,text-align:center
classDef rest fill:#e8eaf6,stroke:#333,stroke-width:1px,font-size:16px,font-weight:100,text-align:center
class id2,id3,id4 pre-processing;
class A1,id1,id5,id13 scripts;
class id6,id7,id8,id9,id10,id11,id12 rest

Output data