This repository houses data, code, documentation, and report files for the Caribbean Ecosystem Status Report created by the NOAA Fisheries Southeast Fisheries Science Center. We are currently working on the 2024 ESR. This is the CURRENT version of the report. The repository https://github.com/Gulf-IEA/Caribbean-ESR.git is now a DEPRECIATED repository. Once the report is finalized a note will be added to this ReadME.
This report is being built as a quarto book using the NMFS Open Science NOAA quarto book template.
The list of indicators included in the 2024 ESR can be found in this table. This table also includes information about data sources, indicator status, and automation level. Eventually all of this information will be migrated to an indicator catalog. The catalog is still a work in progress.
There are several folders in this repository.
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indicator_data --> houses all the non-confidential data needed to create each indicator. Confidential data are stored elsewhere. Scripts with confidential data (mainly fisheries-dependent indicators) will not run without access to the data files.
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indicator_processing --> houses all the code (R scripts) for creating each indicator. The CalculateAllIndicators.R file runs all of the R scripts for all indicators. This should be run anytime the report needs to be updated. This folder also contains the PlotAllIndicators.R file, which creates all of the time series plots for the ESR and saves them to the indicator_plots folder. This should be run after running CalculateAllIndicators.R whenever the report needs to be updated. The remaining R scripts in this file are used for indicator synthesis.
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indicator_objects --> houses all of the .RData outputs from the R scripts used to create each indicator. These are objects all in a standardized format with each indicator variable and a time column as well as label information.
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indicator_plots --> houses all the output plots from the PlotAllIndicators.R script as well as any additional plots that are created separately to be used in the report.
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content --> houses the quarto files needed to create the ESR report.
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additional folders and files are associated with building the quarto book.
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