README.Rmd

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# FishMIP 2.0: Ocean System Pathways Protocol

### [Contents]{.underline}

[Goal [2]](#goal)

[Experiments & Scenarios [3]](#experiments-scenarios)

[Input data [6]](#input-data)

[Climate forcing [6]](#climate-forcing)

[Fishing forcing [11]](#fishing-effort-forcing)

[Output data [14]](#output-data)

[Additional notes for Regional FishMIP Models
[16]](#additional-notes-for-regional-fishmip-models)

[Reporting model results [16]](#reporting-model-results)

## 

## Goal {#goal}

The goal of FishMIP 2.0's "Ocean System Pathways" (OSP) Protocol is to
project climate change impacts to ecosystems and fisheries under
different societal and fisheries management development scenarios. This
simulation round extends our previous climate impact projections to
include past and future fisheries development to enable us to identify
key risks and explore adaptation to climate change including
consequences for biodiversity, fisheries and food security.

The future scenarios we are using have been developed to complement and
be consistent with the [Shared Socioeconomic
Pathways](https://www.climateforesight.eu/seeds/shared-socioeconomic-pathways/),
but with socioeconomic drivers needed for fisheries and aquaculture.
These are labelled Ocean System Pathways (OSPs) ([Maury et al.
2024](https://essopenarchive.org/users/713515/articles/937359-the-ocean-system-pathways-osps-a-new-scenario-and-simulation-framework-to-investigate-the-future-of-the-world-fisheries)).

This protocol provides details on the experimental set-up and data
forcings required to run each of these scenarios, with and without
climate change.

Note that this protocol builds on the FishMIP's [Phase 1 ISIMIP
3b](https://github.com/Fish-MIP/FishMIP_2023_3b_Protocol/blob/main/FishMIP_Phase1_2020_CMIP6_runs_protocol_v1.0.pdf)
which focused primarily on results without fishing, for fast-track
inclusion in the IPCC 6th Assessment (Tittensor et al. 2021). The
historical component also contributes to FishMIP 2.0's ISIMIP 3a
protocol on ["Model Evaluation, Detection, and
Attribution"](https://github.com/Fish-MIP/FishMIP2.0_TrackA_ISIMIP3a)
(Blanchard et al. 2024, Frieler et al. 2023).

Timelines for simulations: TO BE DISCUSSED

| Scenarios                                     | Models           | Date      |
|-----------------------------------------------|------------------|-----------|
| OSP-Baseline (Table 1)                        | global, regional | 2025-2026 |
| OSP-Future (See Table 2)                      | global, regional | 2025-2026 |
| OSP-Fisheries and Food Security (See Table 3) | global, regional | TBD       |
| OSP-Nature Future Framework(See Table 4)      | global, regional | TBD       |

To aid with progress we will hold specific technical workshops to:

-   Ensure correct OSP integration inputs and access

-   Ensure fishing drivers work (separate global and regional breakaway
    groups)

-   Tool sharing & troubleshooting

-   Check model outputs/issues

In this document we describe the general experimental and scenario
set-up (Section 3). Further down in Section 4 we include the details of
the specific **input** variables that modellers can use to implement
scenarios. In Section 5 we describe the set of **outputs** to be
created. Finally in Sections 6-7 we provide further **notes** and
**instructions** on how to report and upload model results.

This protocol is a contribution to the wider Inter-Sectoral Model
Intercomparison Project (ISIMIP3a and ISIMIP3b) simulation rounds,
further details can be found here:

[https://protocol.isimip.org/#ISIMIP3b/marine-fishery_regional/marine-fishery_global](https://protocol.isimip.org/)

**For this simulation round, we are asking you to run XXXXXXXX**

## Experiments & Scenarios {#experiments-scenarios}

Each model experiment is a set of model simulations that has a
particular goal (e.g. model evaluation). A scenario is a particular
setting for forcing drivers that describes how each model run should be
set up in the experiment, including both the type of climate forcing
(CF) and the type of direct human forcing (DHF).

The OSP protocol is grouped into three simulation model experiments. The
below text is taken from [Maury et al.
2024.](https://essopenarchive.org/users/713515/articles/937359-the-ocean-system-pathways-osps-a-new-scenario-and-simulation-framework-to-investigate-the-future-of-the-world-fisheries)

**A. OSP-baseline:** This is designed to initialise and evaluate the
two-way feedback between socioeconomic demand scenarios, markets, and
fleets developed in a new simulation framework (Maury et al. 2024) to
model dynamic fishing effort and evaluate it against available data. It
also seeks to identify and disentangle the respective roles of climate
and socio-economic factors in the historical evolution of marine
ecosystems and fisheries. It includes components corresponding to the
**ISIMIP3a** (e.g. the Realistic-baseline) and the **ISIMIP3b** (e.g.
the Spin-up, Reference, Historical) protocols. Prior to the below
simulation runs, a 100-year **Spin-up** of the MEMs without fishing, and
using the pi-control climate forcing, is required.

-   A 1850-2100 **Reference** simulation (without fishing and without
    climate change), following the spin-up and using the pi-control
    climate forcing.

-   Three 1850-2014 **Historical** simulations:

    -   **Historical-a** with 1850-2014 historical climate forcing and
        fishing with 1850-2014 OSP drivers based on reconstructed and
        observed GDP and population. This simulation provides the 1957
        initial conditions for the Realistic-baseline simulation (see
        below).

    -   **Historical-b** with 1850-2014 historical climate forcing and
        **without fishing**.

    -   **Historical-c** without climate change (pi-control climate) and
        with fishing according to 1850-2014 OSP drivers based on
        reconstructed and observed GDP and population.

-   A 1958-2022 **Realistic-baseline** simulation with the
    reanalysis-driven 'realistic' climate forcing and fishing with
    1958-2022 OSP drivers based on observed GDP and population. This
    simulation branches off from the Historical-after 1957. 

The realistic-baseline simulation will be used to evaluate the
simulation framework against fishery catches (FAO, 2020, 2024a),
reconstructed fishing effort (Rousseau et al., 2024) and observed prices
(FAO, 2024b). 

To attribute climate effects, fishing effects and their potential
interactions (whether antagonistic or synergistic), a counterfactual
approach will be employed. The difference between the Historical-b and
the Reference simulation over the same time period will allow the
identification of historical climate effects on the ecosystem. The
difference between the Historical-c and the Reference simulation over
the same time period will allow the identification of historical fishing
effects on the ecosystem. The difference between the Historical-a
simulation and the sum of the climate and fishing effects (Hist-a minus
Historical-b minus Historical-c plus 2 Reference) will provide the
interactive effects of climate and fishing on the ecosystem. 

Further to this, the difference between the Historical-a and the
Historical-b simulations will enable the identification of fishing
impacts on the ecosystem experiencing climate change, and the difference
between the Historical-a and the Historical-c simulations will allow the
identification of climate change impacts on the coupled
social-ecological fishery system. 

##### Table 1: OSP-Baseline simulations. Control run and historical simulation experimental set-up. Note that each simulation is specified by the Climate forcing and Fishing forcing. Definitions of the specifiers (e.g. nat, picontrol etc.) that are used for ISIMIP filenaming are provided in Tables 3 and 4 below.

+------------+------------+------------+------------+------------+
| No.        | Simulation | Short      | T          | Priority   |
|            |            | d          | ime-period | level      |
|            |            | escription | and        |            |
|            |            |            | specifiers |            |
+============+============+============+============+============+
| 1          | **Pre-     | **         | 1850-2100  | 2          |
|            | industrial | Climate**: |            |            |
|            | control**  | No climate | picontrol  |            |
|            |            | change,    |            |            |
|            |            | fixed      | nat        |            |
|            |            | 1850s      |            |            |
|            |            | CO~`2`~    |            |            |
|            |            | levels     |            |            |
|            |            |            |            |            |
|            |            | **         |            |            |
|            |            | Fishing**: |            |            |
|            |            | No fishing |            |            |
+------------+------------+------------+------------+------------+
| 2          | **         | **         | 1850-2014  | 2          |
|            | Historical | Climate**: |            |            |
|            | fishing    | No climate | picontrol  |            |
|            | dynamics,  | change,    |            |            |
|            | no         | fixed      | histsoc    |            |
|            | climate**  | 1850s      |            |            |
|            |            | CO~`2`~    |            |            |
|            |            | levels     |            |            |
|            |            |            |            |            |
|            |            | **         |            |            |
|            |            | Fishing**: |            |            |
|            |            | Historical |            |            |
|            |            | fishing    |            |            |
|            |            | dynamics,  |            |            |
|            |            | forced by  |            |            |
|            |            | OSP        |            |            |
|            |            | drivers    |            |            |
+------------+------------+------------+------------+------------+
| 3          | **         | **         | 1850-2014  | 2          |
|            | Historical | Climate**: |            |            |
|            | climate    | Simul      | reanalyis  |            |
|            | only**     | ated**/rea |            |            |
|            |            | nalysis?** | nat        |            |
|            |            | historical |            |            |
|            |            | climate    |            |            |
|            |            | change     |            |            |
|            |            |            |            |            |
|            |            | **         |            |            |
|            |            | Fishing**: |            |            |
|            |            | No fishing |            |            |
+------------+------------+------------+------------+------------+
| 4          | **         | **         | 1850-2014  | 1          |
|            | Historical | Climate**: |            |            |
|            | climate    | Simulat    | reanalyis  |            |
|            | and        | ed**/rea   |            |            |
|            | fishing    | nalysis?** | histsoc    |            |
|            | dynamics** | historical |            |            |
|            |            | climate    |            |            |
|            |            | change     |            |            |
|            |            |            |            |            |
|            |            | **         |            |            |
|            |            | Fishing**: |            |            |
|            |            | Historical |            |            |
|            |            | fishing    |            |            |
|            |            | dynamics,  |            |            |
|            |            | forced by  |            |            |
|            |            | OSP        |            |            |
|            |            | drivers    |            |            |
+------------+------------+------------+------------+------------+
| 5          | Realistic  |            |            |            |
+------------+------------+------------+------------+------------+

#### Note on spin-up period (pre-1850)

| For fishing effort prior to 1850 hold fishing at 1850 levels. [need to DISCUSS above states no fishing, this is from 3a]
| 
| For the 'no fishing' runs (nat), the spin-up should not use any fishing effort.
| 

**B. OSP-future**: This second thread is dedicated to carrying out
scenario simulations from the perspective of the IPCC. The aim is to
estimate the impact of climate change and the socio-economic context on
marine ecosystems, fisheries and the benefits they provide to societies
worldwide. It contributes to ISIMIP3b, which focuses on assessing the
climate change impacts, and involves running:

[Scenario-a]{.underline}: The five OSP scenarios (2015-2100) with
fishing and SSP climate change, starting from the Historical-a
simulation. This simulation is designed to simulate the impacts of
climate change on fishery and food consumption in the different
socio-economic OSP contexts.

[Scenario-b]{.underline}: The five OSP scenarios (2015-2100) without
fishing but with SSP climate change, starting from the Historical-b
simulation. This simulation is designed to simulate the impacts of
different levels of future climate change on marine ecosystems.

[Scenario-c]{.underline}: The five OSP scenarios (2015-2100) with
fishing but no climate change (pi-control climate), starting from the
Historical-c simulation. This simulation is designed to highlight the
effects of the various socio-economic OSP contexts on fisheries.

Comparing the Scenario-a and Reference simulations during the same time
period will allow for the identification of the combined effects of
different climate change and socio-economic contexts. Comparing the
Scenario-b and Reference simulations will allow for the assessment of
climate impacts on the ecosystem at different levels of climate change.
Additionally, comparing Scenario-c and the Reference simulation will
enable the characterisation of the impact of distinct socio-economic
contexts on the social-ecological fishery system. The interactive
effects of climate and the socio-economic context on the
social-ecological fishery system can be determined by calculating the
difference between the Scenario-a simulation and the sum of the climate
and fishing effects (Scenario-a minus Scenario-b minus Scenario-c plus 2
Reference). 

Finally, the difference between the Scenario-a and the scenario-b
simulations will enable the identification of fishing impacts on the
ecosystem experiencing different levels of climate change, and the
difference between the Scenario-a and the Scenario-c simulations will
allow the identification of climate change impacts on the coupled
social-ecological fishery system. 

##### Table 2: OSP-Future simulation experimental set-up. Note that each simulation is specified by the Climate forcing and Fishing forcing. Definitions of the specifiers (e.g. nat, picontrol etc.) that are used for ISIMIP filenaming are provided in Tables 3 and 4 below.

+------------+------------+------------+------------+------------+
| No.        | Simulation | Short      | Time       | Phase      |
|            |            | d          | period and |            |
|            |            | escription | specifiers |            |
+============+============+============+============+============+
| 1-5        | **All SSPs | **         | 2015-2100  | 2          |
|            | (1-5), no  | Climate**: |            |            |
|            | climate    | No climate | picontrol  |            |
|            | change,    | change     |            |            |
|            | OSP1       |            | osp1soc    |            |
|            | fishing**  | **         |            |            |
|            |            | Fishing**: |            |            |
|            |            | OSP1-5     |            |            |
|            |            | future     |            |            |
|            |            | fisheries  |            |            |
|            |            | dynamics   |            |            |
|            |            | (following |            |            |
|            |            | on from    |            |            |
|            |            | historical |            |            |
|            |            | OSP)       |            |            |
+------------+------------+------------+------------+------------+
| 6-10       | **All SSPs | **         | 2015-2100  | 2          |
|            | with       | Climate**: | ssp        |            |
|            | climate    | SSP-RCP    | \<scen\>   |            |
|            | change     | climate    | nat        |            |
|            | (SSP1-2.6, | scenarios  |            |            |
|            | SSP5-8.5), | (e.g.      |            |            |
|            | no         | SSP1-2.6,  |            |            |
|            | fishing**  | SSP5-8.5)  |            |            |
|            | \|         |            |            |            |
|            |            | **         |            |            |
|            |            | Fishing**: |            |            |
|            |            | No fishing |            |            |
+------------+------------+------------+------------+------------+
| 11-15      | **All SSPs | **         | 2015-2100  | 2          |
|            | with       | Climate**: |            |            |
|            | climate    | SSP-RCP    | ssp        |            |
|            | change     | climate    | \<scen\>   |            |
|            | (SSP1-2.6, | scenario,  |            |            |
|            | SSP5-8.5)  | (e.g.      | o          |            |
|            | and OSP1-5 | SSP1-2.6,  | sp\<x\>soc |            |
|            | fishing**  | SSP5-8.5)  |            |            |
|            |            |            |            |            |
|            |            | **         |            |            |
|            |            | Fishing**: |            |            |
|            |            | OSP1-5     |            |            |
|            |            | future     |            |            |
|            |            | fisheries  |            |            |
|            |            | dynamics   |            |            |
|            |            | (matched   |            |            |
|            |            | to each    |            |            |
|            |            | SSP, e.g.  |            |            |
|            |            | SSP1RCP2.6 |            |            |
|            |            | would use  |            |            |
|            |            | OSP1)      |            |            |
+------------+------------+------------+------------+------------+

### The following additional policy-targeted experimental sensitivity runs will be updated in due course.

**C. OSP-management & food security:** This third thread is devoted to
scenario simulations from the FAO perspective. It aims to focus on the
effects of fishery management on food security, in the "conventional
trends" context of OSP2. It involves running:

The OSP2 scenario (2023-2100) with fishing, [no management,]{.underline}
and climate change (RCP4.5).

The OSP2 scenario (2023-2100) with fishing, [fully compliant MSY
management]{.underline}, and climate change (RCP4.5).

Comparing these two simulations with the OSP2 Scenario-a simulation
(with present-day management) will provide insights into the risks of
fishery management failure and the potential gains of fully compliant
MSY management on global food security.  

**D. OSP-Nature Future Framework:** This fourth thread is dedicated to
mapping the OSP scenario simulations to the IPBES perspective and the
NFF. The aim here is to compare three ways of envisioning the
"Sustainability First" OSP1 scenario, corresponding to the three
perspectives on Nature of the "Nature Futures Framework" from the IPBES
("Nature for Nature", "Nature as Culture", and "Nature for Society",
Pereira et al., 2020; Kim et al., 2023). While the definitive setup of
this set of simulations has not yet been fully determined, it would
involve running:

The OSP1 scenario (2023-2100) with fishing, [management transitioning to
50% of the ocean in fully protected MPAs]{.underline}, and moderate
climate change (SSP1-2.6). This simulation corresponds to the IPBES NFF
"Nature for Nature" pathway.

The OSP1 scenario (2023-2100) with fishing, [artisanal fisheries managed
at MSY and no industrial fisheries]{.underline}, and moderate climate
change (SSP1-2.6). This simulation corresponds to the IPBES NFF "Nature
as Culture" pathway.

The OSP1 scenario (2023-2100) with fishing, [the management of both
artisanal and industrial fisheries at Maximum Economic Yield
(MEY)]{.underline}, and moderate climate change (SSP1-2.6). This
simulation corresponds to the IPBES NFF "Nature for Society" pathway.

Comparing these three simulations will bring insights into the
performances of the three NFF strategies, in terms of food supply,
biodiversity conservation, employment and economic benefits generated in
the context of the OSP1 mild climate change. 

##### 

#### Scenario definitions

| Throughout the protocol we use 'specifiers' that are shortened names used to denote a particular scenario, variables, or other parameter in the filenames of model inputs and outputs. It is crucial that you also use the same specifiers in your output files.
| 
| **Correct formatting and naming of output files are essential for model intercomparison and analysis.**
| 
| Tables 2-4 describe the different scenarios for the model runs described in Table 1. These specifiers are used in the file names of the corresponding input files and should also be used for the names of the output files (see  [7](https://protocol.isimip.org/#reporting-model-results). Reporting model results).

##### Table 3: Climate scenario specifiers (climate-scenario).

+-------------------+----------------------------------------------------------+
| **Scenario        | **Description**                                          |
| specifier**       |                                                          |
|                   | Pre-industrial climate as simulated by the Earth System  |
| picontrol         | Models (ESMs)                                            |
+-------------------+----------------------------------------------------------+
| historical        | Historical climate as simulated by the ESMs, starting in |
|                   | 1950.                                                    |
+-------------------+----------------------------------------------------------+
| ssp126            | SSP1-2.6 climate as simulated by the ESMs                |
+-------------------+----------------------------------------------------------+
| ssp245            | SSP2-4.5 climate as simulated by the ESMs.               |
+-------------------+----------------------------------------------------------+
| ssp370            | SSP3-7.0 climate as simulated by the ESMs.               |
+-------------------+----------------------------------------------------------+
| ssp460            | SSP4-6.0 climate as simulated by the ESMs.               |
+-------------------+----------------------------------------------------------+
| ssp585            | SSP5-8.5 climate as simulated by the ESMs.               |
+-------------------+----------------------------------------------------------+

##### Table 4: Socio-economic scenario specifiers (soc-scenario).

+--------------+-------------------------------------------------------+
| **Scenario   | **Description**                                       |
| specifier**  |                                                       |
+:=============+:======================================================+
| **histsoc**  | Varying direct human influences in the historical     |
|              | period (1850-2014) (i.e. historical estimates of      |
|              | fishing drivers).                                     |
+--------------+-------------------------------------------------------+
| **2015soc**  | Fixed year-2015 direct human influences (i.e. fishing |
|              | effort).                                              |
+--------------+-------------------------------------------------------+
| **o          | Future fishing determined by SSP and OSP driver       |
| sp\<x\>soc** | forcings for OSP\<x\>, where \<x\> is 1-5.            |
+--------------+-------------------------------------------------------+
| **nat**      | No fishing (naturalized run).                         |
+--------------+-------------------------------------------------------+

**Please remember to use these same specifiers in your output files.
More on reporting data can be found at the end of this document.**

## Input data {#input-data}

**For modellers new to FishMIP:** to access all input data you first
need to set up an account with ISIMIP to access the DKRZ server. Please
follow the instructions here:
<https://www.isimip.org/dashboard/accessing-isimip-data-dkrz-server/>

### Climate forcing - UPDATE WITH DE-BIASED IPSL DATA {#climate-forcing}

##### Table 5: Climate forcing

+--------+--------+----------------------------------------+--------+
| Title  | Spec   | Institution                            | Or     |
|        | ifiers |                                        | iginal |
|        |        |                                        | reso   |
|        |        |                                        | lution |
+:=======+:=======+:=======================================+:=======+
| GF     | gf     | National Oceanic and Atmospheric       | 2      |
| DLESM4 | dlesm4 | Administration, Geophysical Fluid      | 88x180 |
|        |        | Dynamics Laboratory, Princeton, NJ     |        |
|        |        | 08540, USA                             |        |
+--------+--------+----------------------------------------+--------+
| IPSL   | ipslc  | Institut Pierre Simon Laplace, Paris   | 1      |
| CM6ALR | m6a-lr | 75252, France                          | 44x143 |
+--------+--------+----------------------------------------+--------+
| OT     |        |                                        |        |
| HERS?? |        |                                        |        |
+--------+--------+----------------------------------------+--------+

##### Table 6. Climate forcing variables and units for FishMIP 3a simulations. All variables are available on a 0.25 and 1 degree horizontal grid, monthly and annual resolutions. Note: Some variables are available as specific layers extracted from vertically resolved data. Their variable names have been suffixed with -bot (ocean bottom, e.g. o2-bot), -surf (surface values, e.g. pH-surf) or -vint (vertically integrated, e.g. phyc-vint), respectively, or prefixed with int (vertically integrated, e.g. intpp). Temperature is suffixed with b or s for bottom (e.g. tob) or surface (e.g. tos) layers, respectively.

+------------+------------+------------+------------+------------+
| Variable   | Specifier  | Unit       | Resolution | ESM        |
|            |            |            |            | datasets   |
+============+============+============+============+============+
| Mass       | **chl**    | kg m-3     | 0.25° , 1° | GFDL, IPSL |
| Con        |            |            | grid       |            |
| centration |            |            |            |            |
| of Total   |            |            |            |            |
| Phy        |            |            |            |            |
| toplankton |            |            |            |            |
| Expressed  |            |            |            |            |
| as         |            |            |            |            |
| C          |            |            |            |            |
| hlorophyll |            |            |            |            |
+------------+------------+------------+------------+------------+
| Sea Floor  | **deptho** | m          | 0.25° , 1° | GFDL, IPSL |
| Depth      |            |            | grid       |            |
+------------+------------+------------+------------+------------+
| Downward   | **exp      | mol m-2    | 0.25° , 1° | GFDL, IPSL |
| Flux of    | c-bot**    | s-1        | grid       |            |
| P          |            |            |            |            |
| articulate |            |            |            |            |
| Organic    |            |            |            |            |
| Carbon     |            |            |            |            |
+------------+------------+------------+------------+------------+
| P          | \*         | kg m-2     | 0.25° , 1° | GFDL, IPSL |
| articulate | intpoc\*\* |            | grid       |            |
| Organic    |            |            |            |            |
| Carbon     |            |            |            |            |
| Content    |            |            |            |            |
+------------+------------+------------+------------+------------+
| Primary    | **intpp**  | mol m-2    | 0.25° , 1° | GFDL, IPSL |
| Organic    |            | s-1        | grid       |            |
| Carbon     |            |            |            |            |
| Production |            |            |            |            |
| by All     |            |            |            |            |
| Types of   |            |            |            |            |
| Phy        |            |            |            |            |
| toplankton |            |            |            |            |
+------------+------------+------------+------------+------------+
| Net        | **intp     | mol m-2    | 0.25° , 1° | GFDL, IPSL |
| Primary    | pdiat**    | s-1        | grid       |            |
| Organic    |            |            |            |            |
| Carbon     |            |            |            |            |
| Production |            |            |            |            |
| by Diatoms |            |            |            |            |
+------------+------------+------------+------------+------------+
| Net        | **intp     | mol m-2    | 0.25° , 1° | GFDL, IPSL |
| Primary    | pdiaz**    | s-1        | grid       |            |
| Mole       |            |            |            |            |
| Pr         |            |            |            |            |
| oductivity |            |            |            |            |
| of Carbon  |            |            |            |            |
| by         |            |            |            |            |
| D          |            |            |            |            |
| iazotrophs |            |            |            |            |
+------------+------------+------------+------------+------------+
| Net        | **intp     | mol m-2    | 0.25° , 1° | GFDL, IPSL |
| Primary    | ppico**    | s-1        | grid       |            |
| Mole       |            |            |            |            |
| Pr         |            |            |            |            |
| oductivity |            |            |            |            |
| of Carbon  |            |            |            |            |
| by Picoph  |            |            |            |            |
| y          |            |            |            |            |
| toplankton |            |            |            |            |
+------------+------------+------------+------------+------------+
| Maximum    | **mlotst** | m          | 0.25° , 1° | GFDL, IPSL |
| Ocean      |            |            | grid       |            |
| Mixed      |            |            |            |            |
| Layer      |            |            |            |            |
| Thickness  |            |            |            |            |
| Defined by |            |            |            |            |
| Sigma T    |            |            |            |            |
+------------+------------+------------+------------+------------+
| Dissolved  | **o2,**    | mol m-3    | 0.25° , 1° | GFDL, IPSL |
| Oxygen     |            |            | grid       |            |
| Con        | **o        | mol m-2    |            |            |
| centration | 2-bot**    |            |            |            |
|            |            | mol m-2    |            |            |
|            | **o2       |            |            |            |
|            | -surf**    |            |            |            |
+------------+------------+------------+------------+------------+
| pH         | **ph**     | 1          | 0.25° , 1° | GFDL, IPSL |
|            |            |            | grid       |            |
|            | **ph-bot** | 1          |            |            |
|            |            |            |            |            |
|            | **ph       | 1          |            |            |
|            | -surf**    |            |            |            |
+------------+------------+------------+------------+------------+
| Phy        | **phyc**   | mol m-3    | 0.25° , 1° | GFDL, IPSL |
| toplankton |            |            | grid       |            |
| Carbon Co  | **phyc     | mol m-2    |            |            |
| n          | -vint**    |            |            |            |
| centration |            |            |            |            |
+------------+------------+------------+------------+------------+
| Mole       | *          | mol m-3    | 0.25° , 1° | GFDL, IPSL |
| Con        | *phydiat** |            | grid       |            |
| centration |            | mol m-2    |            |            |
| of Diatoms | **phydiat  |            |            |            |
| expressed  | -vint**    |            |            |            |
| as Carbon  |            |            |            |            |
| in sea     |            |            |            |            |
| water      |            |            |            |            |
+------------+------------+------------+------------+------------+
| Mole       | *          | mol m-3    | 0.25° , 1° | GFDL, IPSL |
| Con        | *phydiaz** |            | grid       |            |
| centration |            | mol m-2    |            |            |
| of         | **phydiaz  |            |            |            |
| D          | -vint**    |            |            |            |
| iazotrophs |            |            |            |            |
| Expressed  |            |            |            |            |
| as Carbon  |            |            |            |            |
| in Sea     |            |            |            |            |
| Water      |            |            |            |            |
+------------+------------+------------+------------+------------+
| Mole       | *          | mol m-3    | 0.25° , 1° | GFDL, IPSL |
| Con        | *phypico** |            | grid       |            |
| centration |            | mol m-2    |            |            |
| of         | **phypico  |            |            |            |
| Picoph     | -vint**    |            |            |            |
| ytoplankto |            |            |            |            |
| nExpressed |            |            |            |            |
| as Carbon  |            |            |            |            |
| in Sea     |            |            |            |            |
| Water      |            |            |            |            |
+------------+------------+------------+------------+------------+
| Sea Water  | **so**     | ‰          | 0.25° , 1° | GFDL, IPSL |
| Salinity   |            |            | grid       |            |
|            | **so-bot** | ‰          |            |            |
|            |            |            |            |            |
|            | **so       | %          |            |            |
|            | -surf**    |            |            |            |
+------------+------------+------------+------------+------------+
| Sea Water  | **thetao** | °C         | 0.25° , 1° | GFDL, IPSL |
| Potential  |            |            | grid       |            |
| T          |            |            |            |            |
| emperature |            |            |            |            |
+------------+------------+------------+------------+------------+
| Ocean      | **thk      | m          | 0.25° , 1° | GFDL, IPSL |
| Model Cell | cello**    |            | grid       |            |
| Thickness  |            |            |            |            |
+------------+------------+------------+------------+------------+
| Sea Water  | **tob**    | °C         | 0.25° , 1° | GFDL, IPSL |
| Potential  |            |            | grid       |            |
| T          |            |            |            |            |
| emperature |            |            |            |            |
| at Sea     |            |            |            |            |
| Floor      |            |            |            |            |
+------------+------------+------------+------------+------------+
| Sea        | **tos**    | °C         | 0.25° , 1° | GFDL, IPSL |
| Surface    |            |            | grid       |            |
| T          |            |            |            |            |
| emperature |            |            |            |            |
+------------+------------+------------+------------+------------+
| Sea Water  | **uo**     | m s-1      | 0.25° , 1° | GFDL, IPSL |
| X Velocity |            |            | grid       |            |
+------------+------------+------------+------------+------------+
| Sea Water  | **vo**     | m s-1      | 0.25° , 1° | GFDL, IPSL |
| Y Velocity |            |            | grid       |            |
+------------+------------+------------+------------+------------+
| Mole       | **zmeso**  | mol m-3    | 0.25° , 1° | GFDL, IPSL |
| Con        |            |            | grid       |            |
| centration | **zm       | mol m-2    |            |            |
| of Meso    | eso-vint** |            |            |            |
| z          |            |            |            |            |
| ooplankton |            |            |            |            |
| expressed  |            |            |            |            |
| as Carbon  |            |            |            |            |
| in sea     |            |            |            |            |
| water      |            |            |            |            |
+------------+------------+------------+------------+------------+
| Mole       | **zmicro** | mol m-3    | 0.25° , 1° | GFDL, IPSL |
| Con        |            |            | grid       |            |
| centration | **zmi      | mol m-2    |            |            |
| of         | cro-vint** |            |            |            |
| Microz     |            |            |            |            |
| ooplankton |            |            |            |            |
| expressed  |            |            |            |            |
| as Carbon  |            |            |            |            |
| in sea     |            |            |            |            |
| water      |            |            |            |            |
+------------+------------+------------+------------+------------+
| Z          | **zooc**   | mol m-3    | 0.25° , 1° | GFDL, IPSL |
| ooplankton |            |            | grid       |            |
| Carbon     | **z        | mol m-2    |            |            |
| Con        | ooc-vint** |            |            |            |
| centration |            |            |            |            |
+------------+------------+------------+------------+------------+
| Net        | **rsntds** | W m-2      | 0.25° , 1° | GFDL, IPSL |
| Downward   |            |            | grid       |            |
| Shortwave  |            |            |            |            |
| Radiation  |            |            |            |            |
| at Sea     |            |            |            |            |
| Water      |            |            |            |            |
| Surface    |            |            |            |            |
+------------+------------+------------+------------+------------+
| Sea Ice    | **siconc** | \%         | 0.25° , 1° | GFDL, IPSL |
| Area       |            |            | grid       |            |
| Fraction   |            |            |            |            |
+------------+------------+------------+------------+------------+

### Climate forcing file locations

The climate forcing input files can be found using the following
pattern:

``` linux
levante:/work/bb0820/ISIMIP/ISIMIP3b/InputData/climate/ocean/uncorrected/<glob
al or regional>/monthly/<climate-scenario>/<climate-forcing>/<climateforcing>_<ensemble-member>_<climate-scenario>_<climatevariable>_global_monthly_<start-year>_<end-year>.nc
```

The variables **deptho** and **thkcello** are fixed through time and can
be found in the "fixed/" folder (rather than monthly/).

#### Note on phytoplankton size structure inputs

Production and carbon data for large and small phytoplankton can be
derived from the variables in Table 1 by the following:

large = diatoms + diazotrophs

small = picophytoplankton

The GFDL model treats diazotrophs as large phytoplankton as part of
their food-web processes.

#### Note on regional model spatial extractions

For regional models, only specific grid cells will be needed from the
above global outputs. Please let us know if you require assistance to
extract results (e.g. using bounding boxes, masks or shapefiles). This
functionality is now partially available (bounding box) through the
ISIMIP web-based [data portal](https://data.isimip.org/).

A simple worked example on how to do this for specific regions in R is
provided here: <https://github.com/Fish-MIP/FishMIP_extracting-data>

### Fishing and socioeconomic drivers - NEEDS TO BE UPDATED - OSPs {#fishing-effort-forcing}

##### Table 7: Fishing effort data and variables.

+---------------+---------------+------------------+---------------+
| Specifier     | Included      | Time period      | Filename      |
|               | variables     | /Resolution      |               |
|               | (short names) |                  |               |
|               | and           |                  |               |
|               | definitions   |                  |               |
+===============+===============+==================+===============+
| histsoc       | NomActive =   | -   1850-2015    |               |
|               | Nominal       |                  |               |
|               | fishing       | -   Annual       |               |
|               | effort of the |                  |               |
|               | active fleet  |                  |               |
|               | d             |                  |               |
|               | is-aggregated |                  |               |
|               | by:           |                  |               |
|               |               |                  |               |
|               | -   eez       |                  |               |
|               | _country_name |                  |               |
|               |     = The     |                  |               |
|               |     exclusive |                  |               |
|               |     economic  |                  |               |
|               |     zone/high |                  |               |
|               |     seas name |                  |               |
|               |     in which  |                  |               |
|               |     fishing   |                  |               |
|               |     effort is |                  |               |
|               |     occurring |                  |               |
|               |               |                  |               |
|               | -   LME = A   |                  |               |
|               |     number    |                  |               |
|               |     code of   |                  |               |
|               |     the Large |                  |               |
|               |     Marine    |                  |               |
|               |     ecosystem |                  |               |
|               |     in which  |                  |               |
|               |     the       |                  |               |
|               |     Effort is |                  |               |
|               |     occurring |                  |               |
|               |               |                  |               |
|               | -   SAUP = A  |                  |               |
|               |     number    |                  |               |
|               |     code for  |                  |               |
|               |     the       |                  |               |
|               |     fishing   |                  |               |
|               |     country,  |                  |               |
|               |     following |                  |               |
|               |     Sea       |                  |               |
|               |     Around Us |                  |               |
|               |     numbering |                  |               |
|               |               |                  |               |
|               | -   Gear =    |                  |               |
|               |     the       |                  |               |
|               |     fishing   |                  |               |
|               |     gear      |                  |               |
|               |               |                  |               |
|               | -   FGroup =  |                  |               |
|               |     the       |                  |               |
|               |     targeted  |                  |               |
|               |               |                  |               |
|               |    functional |                  |               |
|               |     group     |                  |               |
|               |               |                  |               |
|               | -   Sector =  |                  |               |
|               |     the       |                  |               |
|               |     fishing   |                  |               |
|               |     sector    |                  |               |
|               |     defined   |                  |               |
|               |     by the    |                  |               |
|               |     law of    |                  |               |
|               |     the       |                  |               |
|               |     country   |                  |               |
+---------------+---------------+------------------+---------------+
| 2015soc       | Final year of | -   2015-2100    |               |
|               | values from   |                  |               |
|               | histsoc       | -   Annual       |               |
|               | repeated      |                  |               |
|               | until 2100    |                  |               |
+---------------+---------------+------------------+---------------+
| Historical    |               |                  |               |
| Population    |               |                  |               |
+---------------+---------------+------------------+---------------+
| Historical    |               |                  |               |
| GDP           |               |                  |               |
+---------------+---------------+------------------+---------------+
| SSP\<x\>      |               |                  |               |
| Population    |               |                  |               |
+---------------+---------------+------------------+---------------+
| SSP\<x\>GDP   |               |                  |               |
+---------------+---------------+------------------+---------------+
| MPAs          |               |                  |               |
+---------------+---------------+------------------+---------------+
| OS            |               |                  |               |
| P\<x\>Drivers |               |                  |               |
+---------------+---------------+------------------+---------------+

##### Table 8: Metadata for histsoc fishing effort variables.

+--------+--------+--------+----------------------------------------+
| Va     | Long   | Unit   | Description/notes                      |
| riable | name   |        |                                        |
| Name   |        |        |                                        |
+:=======+:=======+:=======+:=======================================+
| Year   | (End   | Number |                                        |
|        | of     | code   |                                        |
|        | the)   |        |                                        |
|        | year   |        |                                        |
|        | when   |        |                                        |
|        | the f  |        |                                        |
|        | ishing |        |                                        |
|        | effort |        |                                        |
|        | is occ |        |                                        |
|        | urring |        |                                        |
+--------+--------+--------+----------------------------------------+
| Sector | The f  | Name   | I = Industrial and A = artisanal,      |
|        | ishing | code   | where artisanal include powered and    |
|        | sector |        | unpowered artisanal fleets             |
|        | d      |        |                                        |
|        | efined |        |                                        |
|        | by the |        |                                        |
|        | law of |        |                                        |
|        | the c  |        |                                        |
|        | ountry |        |                                        |
+--------+--------+--------+----------------------------------------+
| LME    | Large  | Number | A number code of the Large Marine      |
|        | Marine | code   | ecosystem in which the Effort is       |
|        | Eco    |        | occurring                              |
|        | system |        |                                        |
|        | Number |        |                                        |
+--------+--------+--------+----------------------------------------+
| eez\_  | Exc    | Name   | The country-level exclusive economic   |
| countr | lusive | code   | zone (or high seas) name in which      |
| y_name | Ec     |        | fishing effort is occurring            |
|        | onomic |        |                                        |
|        | Zone   |        |                                        |
+--------+--------+--------+----------------------------------------+
| SAUP   | A      | Number | Ex supranational entities (USSR,       |
|        | number | code   | Yugoslavia) are disaggregated to their |
|        | code   |        | constituent countries. Serbian Fishing |
|        | for    |        | Effort included with Montenegro.       |
|        | the f  |        | Crimea included with Ukrainian.        |
|        | ishing |        |                                        |
|        | co     |        |                                        |
|        | untry, |        |                                        |
|        | fol    |        |                                        |
|        | lowing |        |                                        |
|        | Sea    |        |                                        |
|        | Around |        |                                        |
|        | Us num |        |                                        |
|        | bering |        |                                        |
+--------+--------+--------+----------------------------------------+
| Gear   | The f  | Name   | Gear names                             |
|        | ishing | code   |                                        |
|        | gear   |        |                                        |
+--------+--------+--------+----------------------------------------+
| FGroup | The ta | Name   | Functional groups are in accordance    |
|        | rgeted | code   | with those used by the Sea Around Us   |
|        | func   |        | Project                                |
|        | tional |        |                                        |
|        | group  |        |                                        |
+--------+--------+--------+----------------------------------------+
| Nom    | N      | Days   | NomActive (of the active fleet; i.e.,  |
| Active | ominal | at sea | total) = P (engine power of active the |
|        | f      | X kW   | fleet; i.e., total) x DAS (average     |
|        | ishing |        | days at sea of one vessel). Average    |
|        | effort |        | DAS for one vessel \~ 200 DAS/year.    |
|        | (i.e., |        | NomActive corresponds to the total     |
|        | not    |        | (reported, IUU, discards) catch. To    |
|        | inc    |        | find NomActive in DAS do (NomActive/P) |
|        | luding |        | X NV                                   |
|        | the t  |        |                                        |
|        | echnol |        |                                        |
|        | ogical |        |                                        |
|        | creep) |        |                                        |
|        | of the |        |                                        |
|        | active |        |                                        |
|        | fleet  |        |                                        |
+--------+--------+--------+----------------------------------------+

##### Table 9: Details for OSP relative change in drivers of fishing effort variables. HOW TO DESCRIBE HOW WE WILL VARY MANAGEMENT IN THE MODELS ACROSS OSPs??

| OSP  | Management                                 |
|------|--------------------------------------------|
| OSP1 | All stocks fished at Fmsy or B/B0 \> 0.5?? |
| OSP5 | Fmsy or B/B0??                             |

#### Implementation of OSPs

TO DO: We provide code examples showing how to implement the OSPs?

##### Table 8: Metadata for fishing effort variables.

#### Fishing effort data file locations

The monthly fishing effort forcing files for the spin-up and experiments
(Table 1) of this simulation protocol can be found on DKRZ here:

``` linux
levante:/work/bb0820/ISIMIP/ISIMIP3b/InputData/socioeconomic/fishing/histsoc/
```

#### Note on global model fishing effort forcing

For **global models**, the above spatially aggregated fishing effort can
be spatially allocated into 0.25 grid cells. This can be achieved using
different approaches such as a simple gravity model -- e.g. see [Coll et
al.
2020](https://www.frontiersin.org/articles/10.3389/fmars.2020.567877/full)
but details will depend on model structure.

We are developing a simplified worked example for global modellers to
explore and contribute to. This will be made available on github/FishMIP
in due course.

While we recommend using the above spatially aggregated effort, for
**global models** that cannot technically carry out spatial allocation
of effort, gridded total industrial and artisanal nominal active effort
have been provided in the same folder as the file above and are saved as
netcdf files. These can be allocated to functional groups (e.g.
according to relative biomass) depending on model structure.

#### Note on regional model fishing effort forcing

Downscaling of the above fishing effort to match regional model inputs
is likely to be needed. We request that regional modellers work together
in their specific regions to ensure we have clear and common
methodologies.

We are developing a worked example for regional modellers to explore and
contribute to for their region which will be made available on
github/FishMIP in due course.

#### Note on model calibration using fishing catch data and model evaluation requirements

Modellers are permitted to calibrate or tune their models using
historical fisheries catch data (that will also be used for model
evaluation) on the condition that **only years up to and including
2004** are used in model calibration/tuning.

Modelling groups **must** keep **detailed documentation** on how their
model was calibrated (e.g. input forcing, calibration data, time domain,
spatial domain, fish grouping (size, functional types, total),
optimization metric(s), weighting schemes, etc.) to be included in
manuscript methods. Written description of sources of calibration data
and methods used need to be provided with all simulation outputs. A
template will be provided for this documentation in due course.

The fisheries catch data .csv file that can be used for model
calibration is here:

``` linux
levante:/work/bb0820/ISIMIP/ISIMIP3a/InputData/socioeconomic/fishing/histsoc/calibration_catch_histsoc_1850_2004.csv.
```

The fisheries catch data are already aggregated into the functional
groups and spatial zones as the above effort forcing data. The original
reference including links to full database is [Watson & Tidd, 2018,
Marine Policy, 93:
171-177](https://www.sciencedirect.com/science/article/pii/S0308597X18300605).

### **Other static geographic information**:

Large marine ecosystem (LME) masks in four different spatial
resolutions. 0.1°, 0.25°, 0.5° and 1° are available here:

``` linux
/work/bb0820/ISIMIP/ISIMIP3a/InputData/geo_conditions/fishmip_regions/
```

Each region has its own variable within each file.

We have also provided conversion tables that can be used to look up LME
and SAUP names according to the numeric codes used in the catch and
effort files (e.g. LME 22 -- North Sea). These files (SAUPnames.csv and
LMEnames.csv) are also available here:

``` linux
/work/bb0820/ISIMIP/ISIMIP3a/InputData/geo_conditions/fishmip_regions/
```

## Output data - TO BE DISCUSSED {#output-data}

All spatially gridded outputs should be created as netcdf files. More
information on how to prepare these files can be found
[here](https://www.isimip.org/protocol/preparing-simulation-files).
Aspatial regional model results may be saved as .csv files.

In the output files, please label the time variable as "days since
1841-1-1 00:00:00" if the output covers the spin-up and transition
period (1841-1960) or "days since 1901-1-1 00:00:00" if the output
covers the experiment period (1961-2010).

##### Table 9: Mandatory output variables for Fisheries and Marine Ecosystem models (global and regional). See notes on additional optional model outputs below. Please use the value 1.e+20 for missing data within your output files. **All biomasses are in wet weight (not g C).**

+------------+------------+------------+------------+--------------+
| Variable   | Variable   | Unit       | Resolution | Comments     |
| long name  | spe cifier |            |            |              |
+============+============+============+============+==============+
| Total      | **tcb**    | g m-2      | 0.25° grid | All          |
| Consumer   |            |            |            | consumers    |
| Biomass    |            |            | monthly    | (trophic     |
| Density    |            |            |            | level \>1,   |
|            |            |            |            | vertebrates  |
|            |            |            |            | and in       |
|            |            |            |            | vertebrates) |
+------------+------------+------------+------------+--------------+
| Total      | **         | g m-2      | 0.25° grid | **Level      |
| Consumer   | tcblog10** |            |            | dimensio     |
| Biomass    |            |            | monthly    | ns:** (time, |
| Density in |            |            |            | bins, lat,   |
| log10      |            |            |            | lon).        |
| Weight     |            |            |            |              |
| Bins       |            |            |            | If the model |
|            |            |            |            | is size      |
|            |            |            |            | -structured, |
|            |            |            |            | please       |
|            |            |            |            | provide      |
|            |            |            |            | biomass in   |
|            |            |            |            | equal log 10 |
|            |            |            |            | g weight     |
|            |            |            |            | bins (1-10g, |
|            |            |            |            | 10-100g,     |
|            |            |            |            | 100g-1kg,    |
|            |            |            |            | 1-10kg,      |
|            |            |            |            | 10-100kg,    |
|            |            |            |            | \>100kg)     |
+------------+------------+------------+------------+--------------+
| Total      | **tpb**    | g m-2      | 0.25° grid | All pelagic  |
| Pelagic    |            |            |            | consumers    |
| Biomass    |            |            | m onthly   | (trophic     |
| Density    |            |            |            | level \>1,   |
|            |            |            |            | vertebrates  |
|            |            |            |            | and in       |
|            |            |            |            | vertebrates) |
+------------+------------+------------+------------+--------------+
| Total      | **tdb**    | g m-2      | 0.25° grid | All demersal |
| Demersal   |            |            |            | consumers    |
| Biomass    |            |            | m onthly   | (trophic     |
| Density    |            |            |            | level \>1,   |
|            |            |            |            | vertebrates  |
|            |            |            |            | and in       |
|            |            |            |            | vertebrates) |
+------------+------------+------------+------------+--------------+
| Total      | **tc**     | g m-2      | 0.25° grid | Catch at sea |
| Catch      |            |            |            | (all catch   |
| Density    |            |            | m onthly   | as a result  |
| (all       |            |            |            | of all       |
| commercial |            |            |            | effort       |
| functional |            |            |            | including    |
| groups /   |            |            |            | reported and |
| size       |            |            |            | IUU) summed  |
| classes)   |            |            |            | for both     |
|            |            |            |            | Industrial   |
|            |            |            |            | and          |
|            |            |            |            | Artisanal    |
|            |            |            |            | sector.      |
+------------+------------+------------+------------+--------------+
| Total      | **tic**    | g m-2      | 0.25° grid | Catch at sea |
| Industrial |            |            |            | (all catch   |
| Catch      |            |            | m onthly   | as a result  |
| Density    |            |            |            | of all       |
| (all       |            |            |            | effort       |
| commercial |            |            |            | including    |
| functional |            |            |            | reported and |
| groups /   |            |            |            | IUU) for     |
| size       |            |            |            | Industrial   |
| classes)   |            |            |            | sector only. |
+------------+------------+------------+------------+--------------+
| Total      | *          | g m-2      | 0.25° grid | **Level      |
| Catch      | *tclog10** |            |            | dimensio     |
| Density in |            |            | m onthly   | ns:** (time, |
| log10      |            |            |            | bins, lat,   |
| Weight     |            |            |            | lon).        |
| Bins       |            |            |            |              |
| across     |            |            |            | If the model |
| both       |            |            |            | is size      |
| sectors    |            |            |            | -structured, |
|            |            |            |            | please       |
|            |            |            |            | provide      |
|            |            |            |            | biomass in   |
|            |            |            |            | equal log 10 |
|            |            |            |            | g weight     |
|            |            |            |            | bins (1-10g, |
|            |            |            |            | 10-100g,     |
|            |            |            |            | 100g-1kg,    |
|            |            |            |            | 1-10kg,      |
|            |            |            |            | 10-100kg,    |
|            |            |            |            | \>100kg)     |
+------------+------------+------------+------------+--------------+
| Total      | **tpc**    | g m-2      | 0.25° grid | Catch at sea |
| Pelagic    |            |            |            | of all       |
| Density    |            |            | m onthly   | pelagic      |
| Catch      |            |            |            | consumers    |
| across     |            |            |            | (trophic     |
| Artisanal  |            |            |            | level \>1,   |
| and        |            |            |            | vertebrates  |
| Industrial |            |            |            | and in       |
| sectors    |            |            |            | vertebrates) |
+------------+------------+------------+------------+--------------+
| Total      | **tdc**    | g m-2      | 0.25° grid | Catch at sea |
| Demersal   |            |            |            | of all       |
| Catch      |            |            | m onthly   | demersal     |
| Density    |            |            |            | consumers    |
| across     |            |            |            | (trophic     |
| Artisanal  |            |            |            | level \>1,   |
| and        |            |            |            | vertebrates  |
| Industrial |            |            |            | and in       |
| sectors    |            |            |            | vertebrates) |
+------------+------------+------------+------------+--------------+
| **Optional |            |            |            |              |
| output     |            |            |            |              |
| from       |            |            |            |              |
| global and |            |            |            |              |
| regional   |            |            |            |              |
| models.    |            |            |            |              |
| All        |            |            |            |              |
| biomasses  |            |            |            |              |
| are in wet |            |            |            |              |
| weight,    |            |            |            |              |
| not g C.** |            |            |            |              |
+------------+------------+------------+------------+--------------+
| Biomass    | **bp30cm** | g m-2      | 0.25° grid | If a pelagic |
| Density of |            |            |            | species and  |
| Small      |            |            | monthly    | L infinity   |
| Pelagics   |            |            |            | is \<30 cm,  |
| \<30cm     |            |            |            | include in   |
|            |            |            |            | this         |
|            |            |            |            | variable     |
+------------+------------+------------+------------+--------------+
| Biomass    | **bp30to   | g m-2      | 0.25° grid | If a pelagic |
| Density of | 90cm**     |            |            | species and  |
| Medium     |            |            | monthly    | L infinity   |
| Pelagics   |            |            |            | is \>=30 cm  |
| \>=30cm    |            |            |            | and \<90cm,  |
| and \<90cm |            |            |            | include in   |
|            |            |            |            | this         |
|            |            |            |            | variable     |
+------------+------------+------------+------------+--------------+
| Biomass    | **bp90cm** | g m-2      | 0.25° grid | If a pelagic |
| Density of |            |            |            | species and  |
| Large      |            |            | monthly    | L infinity   |
| Pelagics   |            |            |            | is \>=90cm,  |
| \>=90cm    |            |            |            | include in   |
|            |            |            |            | this         |
|            |            |            |            | variable     |
+------------+------------+------------+------------+--------------+
| Biomass    | **bd30cm** | g m-2      | 0.25° grid | If a         |
| Density of |            |            |            | demersal     |
| Small      |            |            | m onthly   | species and  |
| Demersals  |            |            |            | L infinity   |
| \<30cm     |            |            |            | is \<30 cm,  |
|            |            |            |            | include in   |
|            |            |            |            | this         |
|            |            |            |            | variable     |
+------------+------------+------------+------------+--------------+
| Biomass    | **bd30to   | g m-2      | 0.25° grid | If a         |
| Density of | 90cm**     |            |            | demersal     |
| Medium     |            |            | m onthly   | species and  |
| Demersals  |            |            |            | L infinity   |
| \>=30cm    |            |            |            | is \>=30 cm  |
| and \<90cm |            |            |            | and \<90cm,  |
|            |            |            |            | include in   |
|            |            |            |            | this         |
|            |            |            |            | variable     |
+------------+------------+------------+------------+--------------+
| Biomass    | **bd90cm** | g m-2      | 0.25° grid | If a         |
| Density of |            |            |            | demersal     |
| Large      |            |            | m onthly   | species and  |
| Demersals  |            |            |            | L infinity   |
| \>=90cm    |            |            |            | is \>=90cm,  |
|            |            |            |            | include in   |
|            |            |            |            | this         |
|            |            |            |            | variable     |
+------------+------------+------------+------------+--------------+
| Catch      | **cp30cm** | g m-2      | 0.25° grid | Catch at sea |
| Density of |            |            |            | of pelagic   |
| Small      |            |            | m onthly   | species with |
| Pelagics   |            |            |            | L infinity   |
| \<30cm     |            |            |            | \<30 cm      |
+------------+------------+------------+------------+--------------+
| Catch      | **cp       | g m-2      | 0.25° grid | Catch at sea |
| Density of | 30to90cm** |            |            | of pelagic   |
| Medium     |            |            | m onthly   | species with |
| Pelagics   |            |            |            | L infinity   |
| \>=30cm    |            |            |            | \>=30 cm and |
| and \<90cm |            |            |            | \<90 cm      |
+------------+------------+------------+------------+--------------+
| Catch      | **cp90cm** | g m-2      | 0.25° grid | Catch at sea |
| Density of |            |            |            | of pelagic   |
| Large      |            |            | m onthly   | species with |
| Pelagics   |            |            |            | L infinity   |
| \>=90cm    |            |            |            | \>=90 cm     |
+------------+------------+------------+------------+--------------+
| Catch      | **cd30cm** | g m-2      | 0.25° grid | Catch at sea |
| Density of |            |            |            | of demersal  |
| Small      |            |            | m onthly   | species with |
| Demersals  |            |            |            | L infinity   |
| \<30cm     |            |            |            | \<30 cm      |
+------------+------------+------------+------------+--------------+
| Catch      | **cd       | g m-2      | 0.25° grid | Catch at sea |
| Density of | 30to90cm** |            |            | of demersal  |
| Medium     |            |            | m onthly   | species with |
| Demersals  |            |            |            | L infinity   |
| \>=30cm    |            |            |            | \>=30 cm and |
| and \<90cm |            |            |            | \<90 cm      |
+------------+------------+------------+------------+--------------+
| Catch      | **cd90cm** | g m-2      | 0.25° grid | Catch at sea |
| Density of |            |            |            | of demersal  |
| Large      |            |            | m onthly   | species with |
| Demersals  |            |            |            | L infinity   |
| \>=90cm    |            |            |            | \>=90 cm     |
+------------+------------+------------+------------+--------------+

## Additional notes for Regional FishMIP Models {#additional-notes-for-regional-fishmip-models}

More specific protocols for each regional model type will be developed
through our monthly online regional modeller sessions. Please contact
regional FishMIP coordinators for more information.

As a first step, regional modellers will need to provide shapefiles for
their respective model domains for us to help with spatial extraction of
the above global climate and fishing effort forcing inputs.

Region-specific climate forcing variables will be made available here:

``` linux
/work/bb0820/ISIMIP/ISIMIP3b/InputData/climate/ocean/<obsclim> or <ctrlclim>/regional/
```

A .csv file with fishing effort extracted for regional model ecosystems
is also available in the same folder as the global fishing effort data
(`../fishing/histsoc`), for regional models that have provided
shapefiles.

Regional modellers may wish to make their raw unaggregated output
available for more detailed analyses, including for example, a wider
range of functional groups/size classes/species and ecosystem
indicators. Please discuss this with FishMIP regional coordinators
before uploading files.

## Reporting model results {#reporting-model-results}

The specification on how to submit the data, as well as further
information and instructions are given on the ISIMIP website at:

<https://www.isimip.org/protocol/preparing-simulation-files>

**It is important that you comply precisely with the formatting
specified there**, to facilitate the analysis of your simulation results
in the ISIMIP framework. Incorrect formatting can seriously delay
analyses. The ISIMIP Team will be glad to assist with the preparation of
these files if necessary.

File names consist of a series of identifier, separated by underscores.
Things to note:

-   Report one variable per file.

-   In filenames, use lowercase letters only.

-   Use underscore (\_) to separate identifiers.

-   Variable names consist of a single word without hyphens or
    underscores.

-   Use hyphens (-) to separate strings within an identifier, e.g. in a
    model name.

-   Data model is NETCDF4_CLASSIC with minimum compression level of 5.

-   NetCDF file extension is .nc.

-   The relative time axis' reference date is days since 1841-1-1
    00:00:00 if the output covers the spin-up and transition period
    (1841-1960) or days since 1901-1-1 00:00:00 if the output covers the
    experiment period (1961-2010). We have provided .csv files to be
    used for the time dimension in creating NetCDF files based on the
    365 days calendar. Please see time_axix_spinup.csv and
    time_axis_experiment.csv in this repository. The script time_axis.r
    was used to create these files.

### Name pattern of output files:

Please name the files in the Fisheries and Marine Ecosystems sector
according to the following pattern:

**Global models**

``` linux
<model>_<climate-forcing>_<bias-adjustment>_<climate-scenario>_<soc-scenario>_<sens-scenario>_<variable>_<global>_<time-step>_<start-year>_<end-year>.nc
```

Example:

``` linux
boats_gfdl-mom6_cobalt2_none_obsclim_histsoc_default_tcb_global_monthly_1961_2010.nc
```

**Regional models**

``` linux
<model>_<climate-forcing>_<bias-adjustment>_<climate-scenario>_<soc-scenario>_<sens-scenario>_<variable>_<region>_<time-step>_<start-year>_<end-year>.nc
```

Example:

``` linux
osmose_gfdl-mom6_cobalt2_none_obsclim_histsoc_default_tcb_benguela_monthly_1961_2010.nc
```

Please see the climate-scenario, soc-scenario, sens-scenario and
variable identifiers given in the tables of this document.

### Path to outut files on DKRZ:

**Global models**

The output files covering the spin-up period (1841-1960) can be saved on
DKRZ here:

``` linux
/work/bb0820/ISIMIP/ISIMIP3a/UploadArea/marine-fishery_global/model_name/temp2
```

The output files covering the experiment period (1961-2010) can be saved
on DKRZ here

``` linux
/work/bb0820/ISIMIP/ISIMIP3a/UploadArea/marine-fishery_global/model_name/temp
```

**Regional models**

The output files covering the spin-up period (1841-1960) can be saved on
DKRZ here:

``` linux
/work/bb0820/ISIMIP/ISIMIP3a/UploadArea/marine-fishery_regional/model_name/temp2
```

The output files covering the experiment period (1961-2010) can be saved
on DKRZ here

``` linux
/work/bb0820/ISIMIP/ISIMIP3a/UploadArea/marine-fishery_regional/model_name/temp
```

Please contact FishMIP coordinators or ISIMIP data managers directly
([isimip-data\@pik‐potsdam.de](mailto:isimip-data@pik%E2%80%90potsdam.de))
if you have any questions or clarifications before submitting files or
if you do not find your model's path on DKRZ as described above.

**Please contact FishMIP coordinators** if you would like to participate
in this simulation round but have encountered issues with any aspect of
the protocol.

(For fishing): please provide all assumptions about catchability,
technological creep, and model calibration.

Please provide any conversion factors that you have used to convert
units.

### **Thank you for your contributions to FishMIP and ISIMIP!**

FishMIP is entirely community-driven, and we appreciate the effort of
all involved.