API-Reference.md

@@ -8,24 +8,24 @@ ____________
 
 Script | Description 
 -------- |:------------
-`split_by_type.R` | Separates records according to the different platform types. This is done following a [selection criteria](Workflow/data-selection).  
-`simple_dup.R`   | Duplicate record identification among ship data and the rest of the different platform types for which the records show a matching `date` , `time` and position `(lat, lon)`.
-`ship2plat.R`   | Excludes non-ship data. Uses additional information from WMO Publication 47 to flag non-ship data. [Kent. *et al.,* (2007)](https://doi.org/10.1175/JTECH1949.1)
-`process_ids.R`   |  Re-format of ship IDs that comes from different data sources (`SID`) to enable linking of data from the same ship (same ship name) across different `DCK`s. And to also enable linking to metadata information in WMO Publication No. 47.
-`process_shipdata.R`   | Corrects dates and times errors noticed in some `DCK`. Largely arise from confusion over historical definitions of the marine day and conversions between local time and UTC.
-`new_get_pairs.R`   | Duplicate record identification within the ship data. Pairs the reports as duplicate if they have associated ship `ID`s. The candidate pairs are then selected according to i) the number of matching elements (similar content of variables within a specific tolerance), ii) the `DCK`s, and iii) a comparison of the `ID`s.
-`new_get_dups.R`   | Counts the number of duplicated records and flags the best according to a [quality control criteria](Workflow/quality-control). Groups duplicated records by common `callsings`. 
-`new_merge_ids_year.R` | Links `ID`'s into classes. Ship tracks of the linked `ID`'s are then checked. Reports that fail the track check are flagged as the worst duplicate. Uses a shipping tracking alogrithm from [**imma**.](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/wikis/How-to-install#install-dependencies-with-conda-all-platforms) 
-`clean_data.R`   | ---. 
-`clean2track.R`   | Forms ship tracks for linked `ID`s. --.
+[`split_by_type.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/split_by_type.R) | Separates records according to the different platform types. This is done following a [selection criteria](Workflow/data-selection).  
+[`simple_dup.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/simple_dup.R)   | Duplicate record identification among ship data and the rest of the different platform types for which the records show a matching `date` , `time` and position `(lat, lon)`.
+[`ship2plat.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/ship2plat.R)   | Excludes non-ship data. Uses additional information from WMO Publication 47 to flag non-ship data. [Kent. *et al.,* (2007)](https://doi.org/10.1175/JTECH1949.1)
+[`process_ids.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/process_ids.R)   |  Re-format of ship IDs that comes from different data sources (`SID`) to enable linking of data from the same ship (same ship name) across different `DCK`s. And to also enable linking to metadata information in WMO Publication No. 47.
+[`process_shipdata.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/process_shipdata.R)   | Corrects dates and times errors noticed in some `DCK`. Largely arise from confusion over historical definitions of the marine day and conversions between local time and UTC.
+[`new_get_pairs.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/new_get_pairs.R)   | Duplicate record identification within the ship data. Pairs the reports as duplicate if they have associated ship `ID`s. The candidate pairs are then selected according to i) the number of matching elements (similar content of variables within a specific tolerance), ii) the `DCK`s, and iii) a comparison of the `ID`s.
+[`new_get_dups.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/new_get_dups.R)   | Counts the number of duplicated records and flags the best according to a [quality control criteria](Workflow/quality-control). Groups duplicated records by common `callsings`. 
+[`new_merge_ids_year.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/new_merge_ids_year.R) | Links `ID`'s into classes. Ship tracks of the linked `ID`'s are then checked. Reports that fail the track check are flagged as the worst duplicate. Uses a shipping tracking alogrithm from [**imma**.](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/wikis/How-to-install#install-dependencies-with-conda-all-platforms) 
+[`clean_data.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/clean_data.R)   | ---. 
+[`clean2track.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/clean2track.R)   | Forms ship tracks for linked `ID`s. --.
 
 **Utils**
 ____________
 
 Function | Description 
 -------- |:------------
-`add_date2.R ` |   
-`add_dck_priority.R `   | 
+[`add_date2.R `](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/add_date2.R) |  Adds a date variable to a file (YY_MM.Rda) based on yr, mo, dy, hr. Invalid values are set to missing. It generates a date variable with missing hour set to local noon and adds a **date.flag.** <br><br> `0 = valid date & time`<br> `1 = invalid date or time (time not missing)` <br> `2 = valid date, hr missing, 12 local added`
+[`add_dck_priority.R `](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/add_dck_priority.R)  | Function use to identify duplicates. During the identification procedure priorities are assigned to data from each`dck` (See [source](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/add_dck_priority.R)), data expected to be of best quality is assigned a priority of 1, data with larger priority numbers will be flagged as the worst duplicate if identified as potential matches. Priority values are based on those from [ICOADS.](https://icoads.noaa.gov/) 
 `add_ID_class.R `   | 
 `add_shipnames.R`   | 
 `assess_match.R`   | 
@@ -50,6 +50,8 @@ Function | Description
 `write_dup_func.R`  | 
 
 **ICOADS variables used**
+
+Visit the [ICOADS main website](https://icoads.noaa.gov/) or check th [IMMA report](https://icoads.noaa.gov/e-doc/imma/R3.0-imma1.pdf)
 ________________
 Code | Description 
 -----: |:------------
@@ -85,54 +87,54 @@ Code | Description
 `mds`    | metadata source
 `mo`     | month UTC
 `n`      | cloud amount
-`ne`     |
-`nh`     |
-`nhe`    |
-`nid`    |
-`oav`    |
-`oaz`    |
-`ocv`    |
-`ocz`    |
-`onv`    |
-`onz`    |
-`oov`    |
-`ooz`    |
-`ophv`   |
-`ophz`   |
-`opv`    |
-`opz`    |
-`osiv`   |
-`osiz`   |
-`osv`    |
-`osz`    |
-`pt`     |
-`qci`    |
-`rh`     |
-`ri`     |
-`rrr`    |
-`rs`     |
-`sa`     |
-`sbi`    |
-`si`     |
-`sid`    |
-`sim`    |
-`slp`    |
-`sme`    |
-`smf`    |
-`smv`    |
-`sst`    |
-`sx`     |
-`uh`     |
-`uid`    |
-`um`     |
-`vs`     |
-`vv`     |
-`w`      |
-`w1`     |
-`wbt`    |
-`wh`     |
-`wmi`    |
-`ww`     |
-`wwe`    |
-`wx`     |
-`yr`     |
+`ne`     | total cloud amount
+`nh`     | amt. of lowest clouds
+`nhe`    | lower cloud amount
+`nid`    | national source indic.1
+`oav`    | alkalinity value
+`oaz`    | alkalinity depth
+`ocv`    | total chlorophyll value
+`ocz`    | total chlorophyll depth
+`onv`    | nitrate value
+`onz`    | nitrate depth
+`oov`    | dissolved oxygen
+`ooz`    | dissolved oxygen depth
+`ophv`   | pH value
+`ophz`   | pH depth
+`opv`    | phosphate value
+`opz`    | phosphate depth
+`osiv`   | silicate value
+`osiz`   | silicate depth
+`osv`    | salinity value
+`osz`    | salinity depth
+`pt`     | platform type
+`qci`    | quality control indic.
+`rh`     | relative humidity
+`ri`     | relative lunar illuminance
+`rrr`    | amount of precip
+`rs`     | rate of Is (ice accretion on ship)
+`sa`     | solar altitude
+`sbi`    | sky-brightness indicator
+`si`     | SST meas. method ? or indic. for SST meas.
+`sid`    | source ID
+`sim`    | SST measurement method
+`slp`    | air pressure
+`sme`    | source meta. element
+`smf`    | source metadata file
+`smv`    | source format version
+`sst`    | sea surface temperature
+`sx`     | swell period indicator
+`uh`     | NOL high amount
+`uid`    | unique report ID
+`um`     | NOL middle amount
+`vs`     | ship's average speed
+`vv`     | visibility
+`w`      | wind speed
+`w1`     | past weather
+`wbt`    | wet-bulb temperature
+`wh`     | wave height
+`wmi`    | indic. for wave measurement
+`ww`     | present weather
+`wwe`    | present weather
+`wx`     | wave period indicator
+`yr`     | year UTC
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