API-Reference.md

@@ -10,18 +10,20 @@ Scripts here follow the same order as in the [Workflow diagram](https://git.noc.
 
 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)   |  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. More information in [Processing of `id`'s](Workflow/processing-of-ids).
+[`read_imma1.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/read_imma1.R) | Reads ICOADS Release3 IMMA1 files to Rda format.  
+[`split_by_type.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/split_by_type.R) | This script splits up the Rda versions of ICOADS R3 Total files by platform type (ship, moored buoy etc.) adding or correcting the PT flag when necessary. The separation of records into the different platform types 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)`. The script finds reports in the ship files output that are also contained in the files output from platforms, coastal data, moored buoys or drifters. 
+[`ship2plat.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/ship2plat.R)   | Assesses potential matches and identify reports that are "not ship". Uses additional information from WMO Publication 47 to flag non-ship data. [Kent. *et al.,* (2007)](https://doi.org/10.1175/JTECH1949.1). These reports are then written to directory MFILES_NOTSHIP to be excluded from further SHIP processing.
+[`process_ids.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/process_ids.R)   |  The script adds various ID info and flags to the ICOADS shipdata. 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. More information in [Processing of `id`'s](Workflow/processing-of-ids). 
 [`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 [**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. --.
+[`remove_output_files.R`](https://git.noc.ac.uk/brecinosrivas/icoads-r-hostace/-/blob/master/rscripts/remove_output_files.R)   |  Clean of `output_data/output_files` before re-running.
 
-**Utils**
+**icoads.utils package description**
 ---------
 
 The following functions are in alphabetical order.