GitLab

Note: still not complete! needs checking from liz

This page lists all available scripts, functions and variables from ICOADS used in this repository.

Workflow

Scripts here follow the same order as in the Workflow diagram.

Script	Description
read_imma1.R	Reads ICOADS Release3 IMMA1 files to Rda format.
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.
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	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). These reports are then written to directory MFILES_NOTSHIP to be excluded from further SHIP processing.
process_ships.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. 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.
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.
get_dups.R	Counts the number of duplicated records and flags the best according to a quality control criteria. Groups duplicated records by common callsigns.
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.
nrt_dup.R	---.
clean_data.R	---.
clean2track.R	Copies data with missing/generic id`'s after processing to directory TRACK_INPUT for use as input to Carella. et al., (2017).
remove_output_files.R	Clean of output_data/output_files before re-running.

icoads.utils package description

The following functions are in alphabetical order.

Function	Description
add_ID_class.R	Adds an specific id class to the report. Based on the ICOADS doc. 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 callsign is found, the country for that callsign is also identified.
add_date2.R	Adds a date variable to the data frame based on yr, mo, dy, hr. 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. 0 = valid date & time 1 = invalid date or time (time not missing) 2 = valid date, hr missing, 12 local added
add_dck_priority.R	Function use to identify duplicates. During the identification procedure priorities are assigned to the data from each dck (See source), 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.
add_match_id.R	Tests whether paired id's are allow to match according a matching criteria and by using the Damerau–Levenshtein (DL) distance formula.
add_shipnames.R	Adds ship names according to dck numbers.
find_gap_func.R	-------
flag_id_dups.R	Adds a flag to reports that fail the IMMA ship track check. Such reports are flagged as the worst duplicate.
get_gap_pos.R	-----
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	Used in add_ID_class.R. Assigns an id class to callsigns listed in metadata of Pub 47 (Not sure).
get_itu_country.R	Gets the ITU callsign prefix associated with a country.
get_matchedids.R	------
get_mis.R	Selects candidate pairs of duplicate reports according to i) the number of matching elements (similar content of variables within a specific tolerance).
get_prec.R	Get's the dck/sid precision of measurement for selected variables (sst,slp,at,dpt,w,d,n,ww,w1,vv)
get_pub47.R	function to process monthly files from Pub47.
get_speed.R	Contains several utility functions to convert between radians and degrees, calculate time and speed from coordinates and calculate the geodesic distance between two points specified by radian latitude/longitude using the spherical law of cosines (slc).
homog_ids.R	Uses standard linkages between id's to add id homogenisation information to each records.
id_group_func.R	Makes sure that all id's grouped in get_groups.R are properly associated.
liz_merge.R	Merges two data frames by specific columns.
print_id_match_info.R	Prints ICOADS duplicates information and id matching results.
read_rdsfiles.R	A collection of functions to read all different types of data files (e.g rds, .txt) used through out the code.
write_dup_func.R	Writes duplicate information in a pipe-delimited year-month output format. The report uid is followed by the report id then a flag with value 1 if the id has been changed, 0 if it remains the same. An example of the format is: ICOADS-30-0Y0HJK | 32024 | 0 ICOADS-30-0Y0HJL | 14 00117 | 1

ICOADS variables used

Visit the ICOADS main website or check th IMMA report.

Variable names are in alphabetical order.

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Code	Description
ah	high cloud amount
am	middle cloud amount
at	air temperature
c1	country recruited ship
c1m	recruiting country
cce	change code
che	high cloud type
cle	low cloud type
cme	middle cloud type
d	wind direction (true)
dck	deck
dpt	dew-point temperature
ds	ship course
dups	dup status
dy	day UTC
eoh	exposure of hygrometer
es	thickness of Is (ice accretion on ship)
he
hop	height of visual observation platform
hr	hour UTC1
id	identification/callsign
ii	ID indicator
immv	IMMT version (International Maritime Meteorological Tape)
ir	indic. for precip. data
irf	intermediate reject flag
is	ice accretion on ship
lat	latitude
lon	longitude
lz	2°×2° landlocked flag
mds	metadata source
mo	month UTC
n	cloud amount
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