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Workflow · Changes

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trying markdown authored May 15, 2020 by bearecinos's avatar bearecinos
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Workflow.md
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...@@ -31,28 +31,4 @@ specialist ship data sources, such as research vessels ...@@ -31,28 +31,4 @@ specialist ship data sources, such as research vessels
identification and linking of IDs between each pair of duplicate reports. identification and linking of IDs between each pair of duplicate reports.
3. Preformed [quality control](quality-control) on the data to point out the best duplicate. 3. Preformed [quality control](quality-control) on the data to point out the best duplicate.
```mermaid [![](https://mermaid.ink/img/eyJjb2RlIjoiZ3JhcGggVEJcbkExW3JzY3JpcHRzXVxuXG4gaWQxWyhJQ09BRFMgdjMuMCldIC0tPiB8c3BsaXRfYnlfdHlwZS5SfGlkMltTZXBhcmF0ZSByZWNvcmRzIGFjY29yZGluZyA8YnI-IHRvIHRoZSBkaWZmZXJlbnQgcGxhdGZvcm0gdHlwZXMuXVxuIGlkMiAtLT4gfHNpbXBsZV9kdXAuUnxpZDNbRmlyc3QgZHVwbGljYXRlIGlkZW50aWZpY2F0aW9uIGJldHdlZW4gPGJyPiBzaGlwIGRhdGEgYW5kIHRoZSBkaWZmZXJlbnQgcGxhdGZvcm0gdHlwZXMuIDxicj4gQ29uc2lkZXJzIHRoZSByZWNvcmRzIGFzIGR1cGxpY2F0ZXMgaWYgdGhleSA8YnI-IHNob3cgbWF0Y2hpbmcgZGF0ZSwgdGltZSAmIHBvc2l0aW9uLl0gXG4gaWQzIC0tPiB8c2hpcDJwbGF0LlJ8aWQ0W0V4Y2x1ZGUgbm9uLXNoaXAgZGF0YS5dIFxuIGlkNCAtLT4gaWQ1WyhJQ09BRFMgU0hJUCBkYXRhKV1cbiBpZDUgLS0-IHxwcm9jZXNzX2lkcy5SfGlkNltIb21vZ2VuaXplIGFuZCByZS1mb3JtYXQgPGJyPiBzaGlwIElEcyBmcm9tIGRpZmZlcmVudCBkZWNrcy4gPGJyPiBMaW5rcyBtZXRhZGF0YSBmcm9tIFB1YiA0NyAmIGxvZ2Jvb2tzIDxicj4gdG8gZm9ybWVkIGEgcGxhdXNpYmxlIHNoaXAgdHJhY2suXVxuIGlkNiAtLT4gIHxwcm9jZXNzX3NoaXBkYXRhLlJ8aWQ3W1Byb2Nlc3Mgc2hpcCBkYXRhOiA8YnI-IGNvcnJlY3Rpb24gb2YgZGF0ZXMgJiB0aW1lcy5dIFxuIGlkNyAtLT4gfG5ld19nZXRfcGFpcnMuUnxpZDhbU2Vjb25kIGR1cGxpY2F0ZSBpZGVudGlmaWNhdGlvbi4gPGJyPiBQYWlycyB0aGUgcmVwb3J0cyBhcyBkdXBsaWNhdGUgaWYgPGJyPiB0aGV5IGhhdmUgYXNzb2NpYXRlZCBzaGlwIElEcy4gPGJyPiBSZXBvcnRzIHRoYXQgZmFpbCB0aGUgdHJhY2sgY2hlY2sgPGJyPiBhcmUgZmxhZ2dlZCBhcyB0aGUgd29yc3QuXSBcbiBpZDggLS0-IHxuZXdfZ2V0X2R1cHMuUnxpZDlbQ291bnQgdGhlIG51bWJlciBvZiBkdXBsaWNhdGVzIGFuZCBmbGFnIHRoZSBiZXN0Ll1cbiBpZDkgLS0-IHxuZXdfbWVyZ2VfaWRzX3llYXIuUnxpZDEwW0xpbmtzIG9mIElEJ3MgaW50byBjbGFzc2VzLl1cbiBpZDEwIC0tPiB8Y2xlYW5fZGF0YS5SfGlkMTFbQ2xlYW5zIG9mIHNoaXAgZGF0YS5dIFxuIGlkMTEgLS0-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)](https://mermaid-js.github.io/mermaid-live-editor/#/edit/eyJjb2RlIjoiZ3JhcGggVEJcbkExW3JzY3JpcHRzXVxuXG4gaWQxWyhJQ09BRFMgdjMuMCldIC0tPiB8c3BsaXRfYnlfdHlwZS5SfGlkMltTZXBhcmF0ZSByZWNvcmRzIGFjY29yZGluZyA8YnI-IHRvIHRoZSBkaWZmZXJlbnQgcGxhdGZvcm0gdHlwZXMuXVxuIGlkMiAtLT4gfHNpbXBsZV9kdXAuUnxpZDNbRmlyc3QgZHVwbGljYXRlIGlkZW50aWZpY2F0aW9uIGJldHdlZW4gPGJyPiBzaGlwIGRhdGEgYW5kIHRoZSBkaWZmZXJlbnQgcGxhdGZvcm0gdHlwZXMuIDxicj4gQ29uc2lkZXJzIHRoZSByZWNvcmRzIGFzIGR1cGxpY2F0ZXMgaWYgdGhleSA8YnI-IHNob3cgbWF0Y2hpbmcgZGF0ZSwgdGltZSAmIHBvc2l0aW9uLl0gXG4gaWQzIC0tPiB8c2hpcDJwbGF0LlJ8aWQ0W0V4Y2x1ZGUgbm9uLXNoaXAgZGF0YS5dIFxuIGlkNCAtLT4gaWQ1WyhJQ09BRFMgU0hJUCBkYXRhKV1cbiBpZDUgLS0-IHxwcm9jZXNzX2lkcy5SfGlkNltIb21vZ2VuaXplIGFuZCByZS1mb3JtYXQgPGJyPiBzaGlwIElEcyBmcm9tIGRpZmZlcmVudCBkZWNrcy4gPGJyPiBMaW5rcyBtZXRhZGF0YSBmcm9tIFB1YiA0NyAmIGxvZ2Jvb2tzIDxicj4gdG8gZm9ybWVkIGEgcGxhdXNpYmxlIHNoaXAgdHJhY2suXVxuIGlkNiAtLT4gIHxwcm9jZXNzX3NoaXBkYXRhLlJ8aWQ3W1Byb2Nlc3Mgc2hpcCBkYXRhOiA8YnI-IGNvcnJlY3Rpb24gb2YgZGF0ZXMgJiB0aW1lcy5dIFxuIGlkNyAtLT4gfG5ld19nZXRfcGFpcnMuUnxpZDhbU2Vjb25kIGR1cGxpY2F0ZSBpZGVudGlmaWNhdGlvbi4gPGJyPiBQYWlycyB0aGUgcmVwb3J0cyBhcyBkdXBsaWNhdGUgaWYgPGJyPiB0aGV5IGhhdmUgYXNzb2NpYXRlZCBzaGlwIElEcy4gPGJyPiBSZXBvcnRzIHRoYXQgZmFpbCB0aGUgdHJhY2sgY2hlY2sgPGJyPiBhcmUgZmxhZ2dlZCBhcyB0aGUgd29yc3QuXSBcbiBpZDggLS0-IHxuZXdfZ2V0X2R1cHMuUnxpZDlbQ291bnQgdGhlIG51bWJlciBvZiBkdXBsaWNhdGVzIGFuZCBmbGFnIHRoZSBiZXN0Ll1cbiBpZDkgLS0-IHxuZXdfbWVyZ2VfaWRzX3llYXIuUnxpZDEwW0xpbmtzIG9mIElEJ3MgaW50byBjbGFzc2VzLl1cbiBpZDEwIC0tPiB8Y2xlYW5fZGF0YS5SfGlkMTFbQ2xlYW5zIG9mIHNoaXAgZGF0YS5dIFxuIGlkMTEgLS0-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)
graph TB \ No newline at end of file
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[Count the number of duplicates and flag the best.]
id9 --> |new_merge_ids_year.R|id10[Links of ID's into classes.]
id10 --> |clean_data.R|id11[Cleans 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
classDef scripts fill:#8C929D,stroke:#333,stroke-width:1px
classDef rest fill:#e8eaf6,stroke:#333,stroke-width:1px
class id2,id3,id4 pre-processing;
class A1,id1,id5,id13 scripts;
class id6,id7,id8,id9,id10,id11,id12 rest
```
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