API-Reference.md

@@ -28,22 +28,25 @@ 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 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/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)   | 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) call sign is found, the country for that call sign is also identified.
+[`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_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_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)   | Find maximum difference across given variables. 
-`find_gap_func.R`   | It appears to fill in gaps in data but it is unclear what it does from the code and from the document: C3S_D311a_Lot2.dup_doc_v3.pdf.
-[`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 repo?  
+[`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).
+`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.
-`get_gap_pos.R`   | It appears to fill in gaps in data positon but it is unclear what it does from the code and from the document: C3S_D311a_Lot2.dup_doc_v3.pdf.
+`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_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`   | 
-`get_mismatch.R`   | 
-`get_prec.R`   | 
+[`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`   | 
 `liz_merge.R`   |