Input files

Input files used in an Echopop run, grouped by data type. The tables below describe the data columns required by Echopop; other columns will be ignored. All input files are in Excel format. File paths, names, and Excel tab names are specified in the survey year configuration file (e.g., survey_year_2019_config.yml).

Biological data are always separated into US vs Canada files. All other data files combine US and Canadian data.

To minimize duplication in the data file description tables below, additional definitions and information for some variables found in multiple files is provided here, especiallly for column names:

• haul_num: Haul number. Identifies the haul the collected data come from. A haul is usally described as a collection of trawls for a certain section of the survey.

• transect_num: Transect number.

• species_id: Species identification code (ID). Identifies what species is associated with the collected data. Pacific hake is 22500.

• N/P: Empty value Not Permitted.

• nmi: Nautical miles.

• Old name: Column name used previously in the Matlab EchoPro program

Biological (trawl) data

Current base directory used with the sample files: Biological

Data files from the US and Canada are found in subdirectories US and CAN, respectively.

Length

Current sample file (US data) relative to base directory: US/2019_biodata_length.xls, sheet biodata_length

Column name	Old name	Data type	Units	Empty value	Description
haul_num	Haul	integer		N/P	Haul number
species_id	Species_Code	integer		N/P	Species identification code (ID)
sex	Sex	integer		N/P	Sex of the animal. 1=Male, 2=Female, 3=Unknown/Not determined (“unsexed”)
length	Length	float	cm		Length of the animal
length_count	Frequency	float		empty (blank)	Number of animals in the haul, of a particular species, and of a certain sex and length. For example, we have 5 Hake from haul 1 that are males with length 20cm

Specimen

Current sample file (US data) relative to base directory: US/2019_biodata_specimen_AGES.xls, sheet biodata_specimen

Column name	Old name	Data type	Units	Empty value	Description
haul_num	Haul	integer		N/P	Haul number
species_id	Species_Code	integer		N/P	Species identification code (ID)
sex	Sex	integer		N/P	Sex of the animal. 1=Male, 2=Female, 3=Unknown/Not determined (“unsexed”)
length	Length	float	cm		Length of the animal
weight	Weight	float	kg	empty (blank)	Weight of the animal
age	Age	float	years	empty (blank)	Age of the animal

Catch

Current sample file (US data) relative to base directory: US/2019_biodata_catch.xls, sheet biodata_catch

Column name	Old name	Data type	Units	Empty value	Description
haul_num	Haul	integer		N/P	Haul number
species_id	Species_Code	integer		N/P	Species identification code (ID)
haul_weight	Weight_In_Haul	float	kg	N/P	Haul weight

Haul vs transect

File containing the mapping between hauls and transects. This is a new file that replaces the sole information that was being used from the gear file. Note that rows with empty transect_num must be omitted.

Current sample file (US data) relative to base directory: US/haul_to_transect_mapping_2019.xls, single sheet

Column name	Old name	Data type	Units	Empty value	Description
haul_num	Haul	integer		N/P	Haul number
transect_num	Transect	integer		N/P	Transect number

Stratification

Current base directory used with the sample files: Stratification

Strata may be based on age-length (KS, Kolmogorov-Smirnov test) or regional (INPFC, International North Pacific Fisheries Commission) stratifications. Each file contains two tabs, one for each strata type.

Strata

File that relates the stratification to the haul.

Current sample file (US data) relative to base directory: US_CAN strata 2019_final.xlsx, sheets Base KS and INPC

Column name	Old name	Data type	Units	Empty value	Description
stratum_num	Cluster name / INPFC	integer		N/P	Stratum number for KS or INPC strata (Base KS or INPC tab, respectively). For Base KS, 0 = Low sample size. The Old names listed are for the Base KS and INPFC tabs, respectively
haul_num	Haul	integer		N/P	Haul number
fraction_hake	wt	float	0-1	N/P	Fraction of the haul weight that is hake

Geo-strata

File that defines the geographic definition of strata.

Current sample file (US data) relative to base directory: Stratification_geographic_Lat_2019_final.xlsx, sheets stratification1 and INPC

Column name	Old name	Data type	Units	Empty value	Description
stratum_num	Strata index	integer		N/P	Stratum number for KS or INPC strata (stratification1 or INPC tab, respectively)
northlimit_latitude	Latitude (upper limit)	float	decimal degrees	N/P	Northern limit of stratum

NASC

Current base directory used with the sample files: Exports

No Age 1

NASC (Nautical Area Scattering Coefficient) values that do not include age1 values. Values are defined along transects at cells with an approximately 0.5 nmi spacing,

Current sample file (US data) relative to base directory: US_CAN_detailsa_2019_table2y+_ALL_final - updated.xlsx, single sheet

Column name	Old name	Data type	Units	Empty value	Description
transect_num	Transect	integer		N/P	Transect number
vessel_log_start	VL start	float	nmi	N/P	Vessel log cumulative distance at start of transect cell
vessel_log_end	VL end	float	nmi	N/P	Vessel log cumulative distance at end of transect cell
latitude	Latitude	float	decimal degrees	N/P	Transect cell center latitude
longitude	Longitude	float	decimal degrees	N/P	Transect cell center longitude
stratum_num	Stratum	integer		N/P	Base KS stratum number
transect_spacing	Spacing	float	nmi	N/P	Distance (spacing) between transects
NASC	NASC	float	m2 nmi-2	N/P	Nautical Area Scattering Coefficient
haul_num	Assigned haul	integer		N/P	Haul number. A value of 0 is used for transect cells where a haul was not present or used.

The following columns are currently not used in core computations. They are used in reports and in some plots (plots not implemented yet). The column names are the original names and have not been “sanitized”.

Column name	Old name	Data type	Units	Empty value	Description
Region ID	Region ID	int
Bottom depth	Bottom depth	float	meters?
Layer mean depth	Layer mean depth	float	meters?
Layer height	Layer height	float	meters?

All ages

NASC values that include all ages. The file structure is the same as for the “No Age 1” file.

Current sample file (US data) relative to base directory: US_CAN_detailsa_2019_table1y+_ALL_final - updated.xlsx, single sheet

Kriging

Current base directory used with the sample files: Kriging_files

Mesh

The “Mesh” file containing the centroids of the Kriging grid cells. Grid size is 2.5 nmi by 2.5 nmi.

Current sample file (US data) relative to base directory: Kriging_grid_files/krig_grid2_5nm_cut_centroids_2013.xlsx, sheet krigedgrid2_5nm_forChu

Column name	Old name	Data type	Units	Empty value	Description
centroid_latitude	Latitude of centroid	float	decimal degrees	N/P	Cell centroid latitude
centroid_longitude	Longitude of centroid	float	decimal degrees	N/P	Cell centroid longitude
fraction_cell_in_polygon	Cell portion	float	0-1	N/P	Fraction of mesh cell that is within the interpolation polygon that delineates the mesh

Smoothed shelf-break contour

Smoothed isobath contour used to transform the mesh points. A set of point locations delineating the 200 meter bathymetric contour that represents the shelf break.

Current sample file (US data) relative to base directory: Kriging_grid_files/transformation_isobath_coordinates.xlsx, sheet Smoothing_EasyKrig

Column name	Old name	Data type	Units	Empty value	Description
latitude	Latitude	float	decimal degrees	N/P	Point latitude
longitude	Longitude	float	decimal degrees	N/P	Point longitude