DOI: 10.17031/655c6fdc58a59
title: AtlantECO_CPR

description: Basic data: sample level data (each sample being 1 row, equating to approx. 10 nautical miles of tow, 3m3 of filtered seawater). For each taxa, values in cells indicate  abundance (according to standard CPR methodology, see Richardson et al. 2006, Prog in Oceanog 68. 27-74), values of 1.00E-10 indicate presence only, zero values are absence of taxon.

The archive contains 6 *.csv files:
	1. ‘CPR_Data_Phytoplankton_Daniele_19112023.csv’
	2. ‘CPR_List_Phytoplankton_Daniele_19112023.csv’
	3. ‘CPR_Data_SmallZooplankton_Daniele_19112023.csv’
	4. ‘CPR_List_SmallZooplankton_Daniele_19112023.csv’
	5. ‘CPR_Data_LargeZooplankton_Daniele_19112023.csv’
	6. ‘CPR_List_LargeZooplankton_Daniele_19112023.csv’

Architecture of each file:

• Individual measurements are stored in 3 files named "CPR_Data_*"
	"CPR_Data_Phytoplankton_Daniele_19112023.csv" contains measurements on all phytoplankton taxa.
	"CPR_Data_SmallZooplankton_Daniele_19112023.csv" contains measurements on all small zooplankton taxa (< 2 mm).
	"CPR_Data_LargeZooplankton_Daniele_19112023.csv" contains measurements on all phytoplankton taxa (> 2 mm).

• All files named "CPR_Data_*.csv" start with the same 6 columns containing all spatio-temporal information. 
	Columns are:
		1. SampleId: Unique sample identifier built as follow: XXXYY-Z with XXX number of the tow, YY name of the route, Z number of the sample.
		2. Latitude: in decimal degree North.
		3. Longitude: in decimal degree East.
		4. Midpoint_Date_UTC: String containing the temporal information for each sample. Time in UTC.
		5. Year: From 1958 to 2019.
		6. Month: from January to December.

	Note: Per request, the dataset is focused on the North Atlantic Ocean. 

• Following the spatio-temporal information, all files named "CPR_Data_*.csv" contains X number of column corresponding to the number of taxa selected.
Taxa name are coded using their unique identifier attributed by the CPR survey caleld "accepted_id". 
	Phytoplankton: 156 columns corresponding to 156 taxa.
	Small zooplankton (aka Traverse): 63 columns corresponding to 63 taxa.
	Large zooplankton (aka Eyecount): 140 columns corresponding to 140 taxa.

	Note: Even though the data are quantitative, the CPR procedure as a special value (here 10^-10) to represent the presence of a taxa.
		It is common practice to:
			-transform 10^-10 in 0 to deal with quantitative data
			-transform all non-zero values (including 10^-10) in 1 to deal with presence/absence data.

• Taxa names and associated information are stored in 3 files named "CPR_List_*.csv"
	"CPR_List_Phytoplankton_Daniele_19112023.csv" contains information on all phytoplankton taxa.
	"CPR_List_SmallZooplankton_Daniele_19112023.csv" contains information on all small zooplankton taxa (< 2 mm).
	"CPR_List_LargeZooplankton_Daniele_19112023.csv" contains information on all large zooplankton taxa (> 2 mm).

• All files named "CPR_List_*.csv" have 31 columns and a variable number of lines depending of the number of taxa selected.
 	Phytoplankton: 31 columns and 156 lines corresponding to 156 taxa.
	Small zooplankton (aka Traverse): 31 columns and 63 lines corresponding to 63 taxa.
	Large zooplankton (aka Eyecount): 31 columns and 140 linescorresponding to 140 taxa.

	Columns are:
		1. accepted_id = unique taxa id used by the CPR.
		2. Aphia_id = Aphia id (extracted from Worms website) corresponding to the ‘accepted_id’. 
			Note: two taxa can have the same aphia ids (e.g. adults and juveniles of the same taxa have different CPR ids, but same aphia ids).
		3. taxon_name = unique name used by the CPR survey.
		4. name_worms = name corresponding to the Aphia id.
			Note: two different taxa can have the same name-worms (e.g. adults and juveniles of the same taxa).
		5. DRI: Date of Routine Identification. Date before which a taxa was not identified.
			Not: Per request, only taxa with DRI <= 1993 were retained in this data extract.
		6. to 31. Taxonomy as extracted from WoRMS website, from Kingdom to Variety.