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Here we provide an overview of the key elements of our framework including describing the contact function that links economic activities to contacts, the SIRD (Susceptible-Infectious-Recovered-Dead) model, the dynamic economic model governing choices, and calibration. The core of our approach is a dynamic optimization model of individual behavior coupled with an SIRD model of infectious disease spread. Additional details are found in the SI.Contact functionWe model daily contacts as a function of economic activities (labor supply, measured in hours, and consumption demand, measured in dollars) creating a detailed mapping between contacts and economic activities. For example, all else equal, if a susceptible individual reduces their labor supply from 8 to 4 h, they reduce their daily contacts at work from 7.5 to 3.75. Epidemiological data is central to calibrating this mapping between epidemiology and economic behavior. Intuitively, the calibration involves calculating the mean number of disease-transmitting contacts occurring at the start of the epidemic and linking it to the number of dollars spent on consumption and hours of labor supplied before the recession begins.We use an SIRD transmission framework to simulate SARS-CoV-2 transmission for a population of 331 million interacting agents. This is supported by several studies (e.g.,77,78) that identify infectiousness prior to symptom onset. We consider three health types m ∈ {S, I, R} for individuals, corresponding to epidemiological compartments of susceptible (S), infectious (I), and recovered (R). Individuals of health type m engage in various economic activities ({A}_{i}^{m}), with i denoting the activities modeled. One of the ({A}_{i}^{m}) is assumed to represent unavoidable other non-economic activities, such as sleeping and commuting, which occur during the hours of the day not used for economic activities (see SI 2.3.1). Disease dynamics are driven by contacts between susceptible and infectious types, where the number of susceptible-infectious contacts per person is given by the following linear equation:$${{{{{{{{mathscr{C}}}}}}}}}^{SI}({{{{{{{bf{A}}}}}}}})=mathop{sum}limits_{i}{rho }_{i}{A}_{i}^{S}{A}_{i}^{I}$$
(1)
while similar in several respects to prior epi-econ models15,16,74, a methodological contribution is that ρi converts hours worked and dollars spent into contacts. For example, ρc has units of contacts per squared dollar spent at consumption activities, while ρl has units of contacts per squared hour worked.We also consider robustness to different functional forms in Fig. 6F, G as a reduced-form way to consider multiple consumption and labor activities with heterogeneous contact rates. Formally:$${{{{{{{{mathscr{C}}}}}}}}}^{SI}({{{{{{{bf{A}}}}}}}})=mathop{sum}limits_{i}{rho }_{i}{({A}_{i}^{S}{A}_{i}^{I})}^{alpha },$$
(2)
where α  > 1 (convex) corresponds to a contact function where higher-contact activities are easiest to reduce or individuals with more contacts are easier to isolate. α  More

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.This is a summary of: Qiao, L. et al. Soil quality both increases crop production and improves resilience to climate change. Nat. Clim. Change https://doi.org/10.1038/s41558-022-01376-8 (2022). More

Fisheries overexploitation is a problem in all oceans and seas globally. Authorities and administrations in charge of assigning quotas have very little fine-grained information on the fish captures, and instead use large-scale, coarse data to assess the health level of fisheries. Thus, being able to cross-match fish species and sizes, to the sea regions they were captured from, can be helpful in this regard, providing finer-grained information.Previous attempts at assembling datasets for fish detection and classification exist, ranging from fish detection or counting in underwater images and video streams1,2,3, to counting on belts on trawler ships4, to classification in laboratory conditions5,6, or in underwater preprocessed images of single fish7,8,9, or single fish in free-form pictures10, as well as simultaneous detection and classification of several fish11,12. However, none of the works found in the literature addresses the topic of simultaneous instance segmentation and species classification, along with fish size estimation, in a fish market environment, as is the aim of this paper. Instance segmentation refers to the extraction of pixel-level masks for each individual object (in this case fish specimens), rather than bounding boxes (object detection), or class label masks (e.g. a single mask for all fish specimens of the same species, also referred to as semantic segmentation). Moreover, works in the literature use pictures taken in laboratory conditions (with a single fish per image, shown from the side), or in underwater conditions. Only French et al.4 uses pictures of fish catches on a belt, for counting purposes. Table 1 shows a summary of the datasets identified in the literature, along with their characteristics, including how the proposed dataset compares.Table 1 Summary of previous datasets found in the literature, and comparison to proposed dataset.Full size tableThe DeepFish project (website: http://deepfish.dtic.ua.es/) is aimed at providing fish species classification and size estimation for fish specimens arriving at fish markets, both for the automation of fish sales, and the retrieval of fine-grained information about the health of fisheries. For a period of six months (April to September 2021), images have been captured at the fish market in El Campello (Alicante, Spain). Images of market trays show a variety of fish species, including targeted as well as accidental captures from the ‘Cabo de la Huerta’, an important site for protection and preservation of marine habitats and biodiversity as defined by the European Comission Habitats Directive (92/43/EEC). From the pictures, a total of 59 different species are identified with 12 species having more than 100 specimens and 25 with more than 10 specimens, as shown in Table 2. There is a high imbalance of species captured due to the natural variation in fish species populations according to seasonality and other ecological factors (rarity of the species, i.e. total population count, etc). Due to some species showing sexual dimorphism (i.e. Symphodus tinca), this species is split into two separate class labels, leading to a different number of species, and class labels (59 species, but 60 class labels). The dataset presents a high temporal imbalance too. As shown in Fig. 1, the capture of new fish tray images was not evenly distributed during the six month study period. Several factors contributed to this: wholesale fish market operating days (e.g. no weekend data, holidays and stop periods, etc.), fish species variability (one of the aims was to be able to capture at least 100 specimens from several species, and seasonality meant some could not be available for capture in later months), as well as the time availability of research group members to attend the fish arrival, tray preparation and auctioning in the evenings.Table 2 Distribution of fish species in the dataset.Full size tableFig. 1Temporal distribution of fish tray images captured. It can be observed that April (04) and May (05) were much more active than the rest of months. This is due to several contributing factors.Full size imageThe resulting DeepFish dataset introduced here contains annotated images from 1,291 fish market trays, with a total of 7,339 specimens (individual fish instances) which were labelled (species and mask) using a specially-adapted version of the Django labeller instance segmentation labelling tool13. Subsequently, another JSON file is generated, following the Microsoft Common Objects in Context (MS COCO) dataset format14, which can be directly fed to a neural network. This is done via a script that is also provided15. Figure 2 shows the distribution of individuals for the selected species within the dataset. Furthermore, Fig. 3 shows examples of the trays, with instance segmentation (ground truth silhouette, i.e. as an interpolation from human-provided points) along with species labelling (different colour shading).Fig. 2Graphical view of the distribution of fish species in the DeepFish dataset for species above 10 specimens. Note, Symphodus tinca is considered separately due to sexual dimorphism (211 male; 335 female samples).Full size imageFig. 3Examples of ground truth fish instance masks with class labelling, showing the 12 species (13 labels) with more than 100 specimens (in bold in Table 2).Full size imageFrom the point of view of research, this data is important for the classification of fish species, instance segmentation, as well as specimen size estimation (e.g. as a regression problem, or otherwise). From an end-results perspective, data automatically labelled with fish instance segmentation accompanied by species name and estimated size is useful to different stakeholders, namely: fishing authorities (to understand how much of each species is being caught per zone), maritime conservation (to calculate depletion of fisheries), but also managers of the markets themselves, as well as clients (digitized sales, e-commerce), etc.The usage of the provided data can be manifold, as it can be used for several problems, namely: object detection and classification, which involves finding objects (in this case fish specimens) providing a bounding box, and a class for each of these boxes; additionally, the data can also be used for semantic segmentation, which can provide a pixel-wise segmentation of the image providing labels (in this case species labels) to different pixel regions of the image; furthermore, also instance segmentation is possible, in which not just a single label for all instances of the same species is provided, but each specimen is provided with a mask (specimen segmentation), as well as a label (species). Furthermore, several measurements of each fish are provided, which can also be used to estimate their size, since they have been shown to be correlated with each other16. These are estimated from the calculated homography (given the tray size is known), given the burden of measuring each fish due to the large amount of specimens in the dataset. More

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