API-Reference.md

@@ -28,27 +28,24 @@ Functions ordered alphabetically.
 
 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 the data frame 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 the data frame based on `yr`, `mo`, `dy`, `hr`. <br> Invalid values are set to missing. For these reports the code generates a date variable with a 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 the 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 match. Priority values are based on those from [ICOADS.](https://icoads.noaa.gov/e-doc/imma/R3.0-imma1.pdf)
-[`add_ID_class.R `](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/add_ID_class.R)   | Adds an specific `id` class to the report. Based on the [ICOADS docs](https://icoads.noaa.gov/e-doc/imma/R3.0-imma1.pdf) and earlier source documentation, the `id`'s have been classified as to their "`id` type" (logbook number, ship number, etc.) and validity. Where an [ITU](https://en.wikipedia.org/wiki/ITU_prefix) callsign is found, the country for that callsign is also identified.
+[`add_ID_class.R `](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/add_ID_class.R)   | Adds an specific `id` class to the report. Based on the [ICOADS doc.](https://icoads.noaa.gov/e-doc/imma/R3.0-imma1.pdf) and other earlier sources, the `id`'s have been classified as to their "`id` type" (logbook number, ship number, etc.) and validity. Where an [ITU](https://en.wikipedia.org/wiki/ITU_prefix) callsign is found, the country for that callsign is also identified.
 [`add_shipnames.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/add_shipnames.R)   | Adds ship names according to `dck` numbers.  
-[`assess_match.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/assess_match.R)   | Finds maximum differences between reports across variables of interest (`sst`,`slp`,`at`,`dpt`,`wbt`,`rh`,`w`,`d`,`ww`,`n`,`vv`,`wh`,`nh`,`w1`). Flags delayed mode report(s) with an older [IMMT](https://icoads.noaa.gov/immt5.html) number as worst duplicate(s).
+[`assess_match.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/assess_match.R)   | Finds maximum differences between reports across variables of interest (`sst, slp, at, dpt, wbt, rh, w, d, ww, n, vv, wh, nh, w1`). <br> Flags delayed mode report(s) with an older [IMMT](https://icoads.noaa.gov/immt5.html) number as worst duplicate(s).
 `find_gap_func.R`   | -------
-[`fix_usmm_705to707cors_func.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/fix_usmm_705to707cors_func.R)   | Called in `add_shipnames.R` but never used should it be delete from the repository?  
-[`flag_id_dups.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/flag_id_dups.R)   |  Adds a flag to reports that fail the ship track check. This are flagged as a worst duplicate.
+`fix_usmm_705to707cors_func.R`  | Called in `add_shipnames.R` but never used should it be delete from the repository?  
+[`flag_id_dups.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/flag_id_dups.R)   |  Adds a flag to reports that fail the [IMMA](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/wikis/how-to-install#imma-toolbox) ship track check. Such reports are flagged as the worst duplicate.
 `get_gap_pos.R`   | -----
 [`get_groups.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/get_groups.R) | Assigns a group number to a specific type of `dck` or `dck`'s. The group is appended to the record `id` to avoid mixing data with the same `id` from different types of data (e.g. Japanese data, UK Navy).
-[`get_id_class.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/get_id_class.R)   | Used in `add_ID_class.R `. Assigns an `id` class to callsigns listed in metadata of Pub 47??). 
+[`get_id_class.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/get_id_class.R)   | Used in `add_ID_class.R `. Assigns an `id` class to callsigns listed in metadata of Pub 47 (**Not sure**).
 `get_isolated.R`   | Contains function [gcd.slc](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/get_isolated.R#L10): Calculates the geodesic distance between two points specified by radian latitude/longitude using the spherical law of cosines ([slc](https://en.wikipedia.org/wiki/Spherical_law_of_cosines)).
 [`get_itu_country.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/get_itu_country.R)  | Gets the ITU call sign prefixes associated with a country.
-[`get_matchedids.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/get_matchedids.R)   | Uses the output from [`new_get_pairs.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/new_get_pairs.R). The function matches `id`'s between reports that have been paired as duplicate. ?? 
-`get_mismatch.R`  | I don't understand too much the difference between this and the function below.
-[`get_prec.R`]()   |  Adds a precision variable to each data frame. 
-
-
-Finds the mismatch between reports that have been flag as potential duplicates, by comparing key variables (`sst`,`slp`,`at`,`dpt`,`w`,`d`,`n`,`ww`,`w1`,`vv`) within a [tolerance limit](Workflow/quality-control) 
-`get_speed.R`   | 
-`id_group_func.R`   | 
+`get_matchedids.R`   | ------
+`get_mismatch.R`  | -------
+[`get_prec.R`]()   | Get's the `dck`/`sid` [precision of measurement](Workflow/quality-control) for selected variables (`sst`,`slp`,`at`,`dpt`,`w`,`d`,`n`,`ww`,`w1`,`vv`)
+`get_speed.R` Do we need this?  | Also contains function [gcd.slc](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/get_isolated.R#L10): Calculates the geodesic distance between two points specified by radian latitude/longitude using the spherical law of cosines ([slc](https://en.wikipedia.org/wiki/Spherical_law_of_cosines)).
+[`id_group_func.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/id_group_func.R)   | Makes sure that all `id`s grouped in [`get_groups.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rutils/get_groups.R) are properly associated.
 `liz_merge.R`   | 
 `new_add_match_id.R`   | 
 `new_homog_ids.R`   |