API-Reference.md

@@ -11,20 +11,20 @@ Script | Description
 [`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.
+[`process_ids.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/process_ids.R)   |  Reformat of ship `id`'s coming 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) 
+[`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 [**r-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. --.
+[`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 `](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_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`   |