Agile stock assessment

Stock assessment determines the status of fishery stock to support management decision making. Considering the iterations between exploratory calculations and the need to compare outputs to elicit better model settings, we should focus on not only the accuracy of abundance estimation and the tolerance of uncertainty but also the efficiency of the project workflow. Although in Japan, a stock assessment model was introduced written in the R language in 2012, the workflow did not sufficiently adjust, creating problems because the current workflow is contrary to the principles of effective value creation. To make our project sustainable, we propose adopting the agile methodology, an iterative development method used by software developers, for stock assessment. Therefore, we wrote an example report as a package document in the R language. Developed under a continuous integration environment, the report remains up to date, with every modification on component files. This method enabled our work to be efficient and transparent by allowing and documenting scenario branching, error corrections, and annual updates. We show that the iterative development cycle benefit us by allowing us to focus on the essential business problem of the assessment project.

ing their tacit knowledge to written programs because they see computer  Although we can set up a CI document system independent of pro-95 gramming language, We think R language and its general document system  nario branching, debugging after discussion, and managing annual updates. 115 We implemented our project following the basic directory structure of the 116 R package (Fig. 3). An Rmarkdown file report. Rmd was created under 117 directory vignettes/. The report can be built by the function build() 118 of package devtools. In the following section, we express the call of some_ 119 function() of the R package some_package as some_package::some_function( GitHub as an issue tracking system.

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In the following sections, we explain our work within each iteration. Here,

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we use the term "iteration" to express the following set of work steps done  In the first iteration, we will show how scenario branching can be handled 159 in a continuous documentation workflow. The first example issue of our 160 project is "What will happen to stock abundance if the assumption on recent 161 selectivity is modified?"

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To recompare the scenarios after bugfix, we reverted (Table 1)     cloud computer that uploaded the report in html format to online storage.

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This keeps our document up to date with the source code and data.

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In the present paper, we followed the standard development procedure   The value of a project must be distinguished from its product; it is the 301 customer satisfaction provided by the product. Taking the car industry as 302 an example, the value is not the car itself but the pleasurable experience 303 brought by driving the car. The value that stock assessment provides to 304 management is a smooth decision-making process, which is provided by the 305 product: a comprehensible assessment report. All of our work contributes 306 to customer value because we arranged the value stream, the focus of the 307 second principle.

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The value stream is all the actions that are needed to provide value to the 309 customer. At the beginning of the first iteration, we built a CI documentation  and it helps to avoid miscommunication because everyone sees exactly the 379 same behavior in the rendered report on the cloud server. is repeatable because it is executable by any person. As a result, making the 387 procedure visible helps find errors as well.

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We have tacit expectations for not only our procedure but also our data. 389 We can make our expectations visible by writing tests that allow us to focus 390 on unusual data as well, such as unbelievably low or high amounts. The 391 accumulation of explicit knowledge leads to the building of a knowledge base, 392 which will have strong appeal in the case of peer review of stock assessment.

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The standardization of the method eliminates project-specific rules and 394 methodologies. We developed our program as an R package, which standard-395 izes our program and makes it comprehensible among the R user community.

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Standardization distinguishes essential differences in business knowledge be-  In this article, we defined our user as management. We confess that this 402 definition was so arbitrary that we premised the development of a report

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For successful value creation, we must realize who our true end-user is.

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Stock assessment is part of a stratified business activity: fishery scientists 409 give management an assessment report to support smooth decision making; quires a cultural shift for projects away from using the GUI word processor, 442 the investment will pay off because stock assessment is a continuous project.

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The method can be applied to all projects, not only stock assessment but 444 also other research activities.