ZooplanktonMeanSizeTotalStock

Brief intro to the indicator

The HELCOM core indicator Zooplankton mean size and total stock (MSTS) is used to assess the status of pelagic habitat in the HELCOM Holistic Assessment of the Baltic Sea. The indicator report with information on indicator concept and results can be found on the HELCOM website, here.

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Indicator data

The indicator use data collected as part of the HELCOM COMBINE monitoring program. Data are reported to the COMBINE database maintained by ICES. The indicator calculation script here use data extracts from the COMBINE database, as well as it allows to use aggregated data (yearly means) as input.

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Input files

1. 'MSTS_addPar.txt'

Column name	Variable type	Description
HELCOM_subbasin	Character	name of a subbasin (assessment unit) of the Baltic Sea as defined in HELCOM
RefFISH	Character	reference period defined based on expert opinion and Weight-At-Age or other herring/sprat feeding condition indices. year_from:year_to
RefCHL	Character	reference period defined based on expert opinion and chlorophyll-a, Secchi depth or other eutrophication proxy. year_from:year_to
Hist_data_source	Character	data source to be used (note: 'input' or 'COMBINE') for calculation of the threshold values (and supplementary parameters: lambda, ref-mean, ref-sd). input - if yearly means are to be used for reference period; COMBINE - if data extract from ICES is to be used for reference period
defGES_TZB[mg_m-3]	Numeric	defined threshold value for Total Stock (total zooplankton biomass) parameter
defGES_MS[ug_ind-1]	Numeric	defined threshold value for MEan Size parameter
Per_start[month]	Numeric	reference period defined based on expert opinion and chlorophyll-a, Secchi depth or other eutrophication proxy
Per_end[month]	Numeric	reference period defined based on expert opinion and chlorophyll-a, Secchi depth or other eutrophication proxy
Depth_minLimit[m]	Numeric	data covering layer to the defined depth or deeper are included in the calculation
Depth_maxLimit[m]	Numeric	data covering layer not deeper than defined are included in the calculations

2. 'MSTS_hist_data.txt'

Provides information on assessment units idetified as 'input' in Hist_data_source column in 'MSTS_addPar.txt'. No missing data are allowed in timeseries. If NA's are present an estimate must be provided before running the script!

Column name	Variable type	Description
year	Numeric	year
HELCOM_subbasin	Character	name of a subbasin (assessment unit) of the Baltic Sea as defined in HELCOM
ICES_area	Character	name of a subbasin of the Baltic Sea as defined in ICES
RefFISH	Logical	reference period defined based on expert opinion and Weight-At-Age or other herring/sprat feeding condition indices (1 - used as a reference year; 0 - not used as a reference year)
RefCHL	Logical	reference period defined based on expert opinion and chlorophyll-a, Secchi depth or other eutrophication proxy (1 - used as a reference year; 0 - not used as a reference year)
TZB	Numeric	Total zooplankton biomass (Total Stock proxy), annual mean for period relevant in MSTS-assessment, see 'MSTS_addPar.txt' Per_start[month], Per_end[month]
MS	Numeric	Mean Size of zooplankton, annual mean for period relevant in MSTS-asessment, see 'MSTS_addPar.txt' Per_start[month], Per_end[month]

3. 'MSTS_ZPspecies.txt'

Redundant if only MSTS-relevant species are included in data, i.e., without predatory cladocerans and meroplankton). Includes all variations of zp taxa reported to ICES.

Column name	Variable type	Description
SPECI	Character	Taxon code as reported to ICES
SPECI_name	Character	Taxon name as reported to ICES
AphiaID	Numeric	AphiaID as defined in WoRMS
WoRMS_name	Character	Taxon name as defined in WoRMS
AphiaID_accepted	Numeric	AphiaID for the accepted taxon name as defined in WoRMS
WoRMS_accepted_name	Numeric	Accepted taxon name as defined in WoRMS
MSTS_use	Logical	describing whether taxon is used for MSTS-assessment, only herbivorous holoplankton are included (1 - yes; 0- no)

4. 'MSTS_statn.txt'

Information relevant for data aggregation (if necesaray). It defines stations (STATN) to be included in the MSTS calculations.

Column name	Variable type	Description
HELCOM_subbasin	Character	name of a subbasin (assessment unit) of the Baltic Sea as defined in HELCOM
STATN	Character	station name as reported to ICES DOME
MSTS_calc	Logical	describing whether Station is used for calculations of MSTS threshold values (1 - yes; 0- no)
Layer_considered	Character	describing the type of water layer considered in MSTS for the specific Station data (C - whole water column, from top to bottom; TXX - top XX meters of the water column
BotDepth_considered[m]	Numeric	bottom depth of the water layer considered for MSTS in meters

5. ICES example file 'ICES_HELCOM_zp.txt'

An example data from https://data.ices.dk/view-map describing zooplankton biological community. Example data are limited to represent four HELCOM subbasins: Bothnian Bay, Bothnian Sea, Gulf of Riga, Western Gotland Basin.

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Output files

• Tabular outputs

  1. Aggregated data: abundance and wet weight per sample covering the defined depth layer

  2. Fin Assessment Data:

  • MSTS assessment data 'MSTS_assessment_df_[date].txt'. Holds yearly data per HELCOM subbasin (assessment unit) on untransformed and transformed TZB and MS, z-scores, lowerCusum, Alarm column (1 for sub-GES; 0 for GES)

  • MSTS assessment confidence values 'MSTS_confidence_[date].txt'. n_ObPerYear - number of datapoins (samples) per year included in the assessment (temporal confidence); n_STATNobserved - number of different stations included in the assessment (spatial confidence).

  • GES values calculated/used in the assessment 'MSTS_GES_[date].txt'.

• Graphical outputs

  1. Trend plot with Kendall's statistics for TZB and MS

  2. Trend plot for lower CuSum

  3. MSTS plot

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