Input files

In this section we describe input files used by Echopop, grouped by data type. The tables below describe the required data columns. All other columns are ignored by Echopop. All input files are in Excel format.

EchoPro column names

There may be some inconsistencies in the columns used by files in EchoPro for previous years. All column names described below are based on the files associated with the 2019 survey.

Biological data

Length

The “length” spreadsheet/dataframe includes data from station 1, in which fish are lengthed individually but neither aged nor weighed. The fish lengths are aggregated by length bins and reported as counts for each bin, rather than reported individually as in the “specimen” spreadsheet/dataframe below.

Echopop column	EchoPro column	Data type	Units	Description
haul_num	Haul	integer float		Haul number. Rows with empty values are removed
species_id	Species_Code	integer float string		Species identification code (ID) Rows with empty values are removed
sex	Sex	integer		Sex of the animal Male: 1/”m”/”male”, Female: 2/”f”/”female”, Unsexed: 3/”u”/”unsexed” Missing values are replaced with “unsexed”
length	Length	float	cm (0.0, ∞)	Animal fork length Missing values are replaced with NaN
length_count	Frequency	integer	count [0, ∞)	Number of animals with the corresponding binned fork length Missing values are replaced with 0

Specimen

The “specimen” spreadsheet/dataframe includes data from station 2, in which each individual fish is weighed and aged.

Echopop column	EchoPro column	Data type	Units	Description
haul_num	Haul	integer		Haul number. Rows with empty values are removed
species_id	Species_Code	integer		Species identification code (ID) Rows with empty values are removed
sex	Sex	integer		Sex of the animal Male: 1/”m”/”male”, Female: 2/”f”/”female”, Unsexed: 3/”u”/”unsexed” Missing values are replaced with “unsexed”
length	Length	float	cm (0.0, ∞)	Animal fork length Missing values are replaced with NaN
weight	Weight	float	kg (0.0, ∞)	Specimen weight Missing values are replaced with NaN
age	Age	float integer	years [0.0, ∞)	Age of the animal Missing values are replaced with NaN

Catch

The “catch” spreadsheet/dataframe includes the total weight for unaged fish for the entire haul.

Echopop column	EchoPro column	Data type	Units	Description
haul_num	Haul	integer		Haul number Rows with empty values are removed
species_id	Species_Code	integer		Species identification code (ID) Rows with empty values are removed
haul_weight	Weight_In_Haul	float	kg [0.0, ∞)	Haul weight Rows with empty values are removed

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.

Echopop column	EchoPro column	Data type	Units	Description
stratum_num	Strata index	integer		Index/grouping representing the stratum identifier based on either length (KS) or latitude (INPFC) Rows with empty values are removed
haul_num	Haul	integer		Haul number Rows with empty values are removed
fraction_hake	wt	float	proportion [0.0-1.0]	Fraction of the haul weight that is hake Missing values are replaced with 0.0

Geostrata

File that defines the geographic definition of strata.

Echopop column	EchoPro column	Data type	Units	Description
stratum_num	Strata index	integer		Index/grouping representing the stratum identifier based on either length (KS) or latitude (INPFC) Rows with empty values are removed
northlimit_latitude	Latitude (upper limit)	float	decimal degrees [-90.0, 90.0]	Northern limit of stratum Rows with empty values are removed

NASC

No age-1 fish

NASC (Nautical Area Scattering Coefficient) values that do not include age-1 values. Values are defined along transects at cells with an approximately 0.5 nmi spacing,

Echopop column	EchoPro column	Data type	Units	Description
transect_num	Transect	integer float		Transect number Rows with empty values are removed
distance_s	VL start	float	nmi [0.0, ∞)	Vessel log cumulative distance at start of transect interval Missing values are replaced with NaN
distance_e	VL end	float	nmi [0.0, ∞)	Vessel log cumulative distance at end of transect interval Missing values are replaced with NaN
latitude	Latitude	float	decimal degrees [-90.0, 90.0]	Transect interval center latitude Missing values are replaced with NaN
longitude	Longitude	float	decimal degrees [-180.0, 180.0]	Transect interval center longitude Missing values are replaced with NaN
transect_spacing	Spacing	float	nmi [0.0, ∞)	Distance (spacing) between transects Missing values are replaced with the user-defined value for max_transect_spacing in the initialization_config.yml configuration file
NASC	NASC	float	m2 nmi-2 [0.0, ∞)	Nautical area scattering strength (\(\textit{NASC}\)) Missing values are replaced with 0.0
haul_num	Haul	integer float		Assigned haul number A value of 0 is used for transect intervals where no haul was present or used Rows with empty values are removed

All aged fish

NASC values that include all ages. The file structure is the same as for the files excluding age-1 fish.

Kriging

Mesh

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

Echopop column	EchoPro column	Data type	Units	Description
centroid_latitude	Latitude of centroid	float	decimal degrees [-90.0, 90.0]	Mesh cell centroid latitude Rows with empty values are removed
centroid_longitude	Longitude of centroid	float	decimal degrees [-180.0, 180.0]	Mesh cell centroid longitude Rows with empty values are removed
fraction_cell_in_polygon	Cell portion	float	proportion [0.0-1.0]	Fraction of mesh cell that is within the interpolation polygon that delineates the mesh Missing values are replaced with 0.0

Smoothed shelf-break contour

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

Echopop column	EchoPro column	Data type	Units	Description
latitude	Latitude	float	decimal degrees [-90.0, 90.0]	Isobath latitude Rows with empty values are removed
longitude	Longitude	float	decimal degrees [-180.0, 180.0]	Isobath longitude Rows with empty values are removed

Kriging and variogram parameters

This file comprises two columns: 1) the parameter names and 2) their associated values.

Echopop parameter	EchoPro parameter	Data type	Valid range	Description
correlation_range	vario.lscl	float	[0.0, ∞)	The relative length scale, or range at which the correlation between points becomes approximately constant
sill	vario.sill	float	[0.0, ∞)	The total variance where the change autocorrelation reaches (or nears) 0.0
nugget	vario.nugt	float	[0.0, ∞)	The \(y\)-intercept of the variogram representing the short-scale (i.e. smaller than the lag resolution) variance
decay_power	vario.pwr	float	[0.0, ∞)	The exponent used for variogram models with exponentiated spatial decay terms
hole_effect_range	vario.hole	float	[0.0, ∞)	Length scale or range of the hole effect
lag_resolution	vario.res	float	(0.0, ∞)	The (scaled) distance between lags
anisotropy	vario.ratio	float	(0.0, ∞)	The directional aspect ratio of anisotropy
search_radius	krig.srad	float	(0.0, ∞)	The adaptive search radius used for kriging
kmin	kmin	integer	(0, ∞)	The minimum number of nearest kriging points
kmax	kmax	integer	(kmin, ∞)	The maximum number of nearest kriging points