data/ - This directory holds any and all data that is direct requested from state/federal agencies or pulled from NOAA servers (ie. survey data). Data that gets output from other analyses (ie. a lot of the SS inputs) are stored somewhere else.
data/raw/ - Completely raw, unedited, data from various data sources. This folder is untracked and is safe to place confidential data in.
data/processed/ - Processed data from available data sources. This folder IS tracked, so no confidential data, only cleaned datasets ready for analysis. Every file in this directory should have an equivalent "raw" data file in data/raw.
data/for_ss/ - SS data files. These files should be able to be read directly into SS without further modification.
R/ - This directory should hold R scripts and analyses. These can take the form of either runnable .R scripts or .Rmd Rmarkdown documents/notebooks. Note that data outputs/plots should not be stored in this directory. This directory is further broken down into subdirectories based on data type ('bio/', 'comps/', 'discards/', 'landings/', and 'survey/'). Data type specific analyses and script should live in their relevant subdirectories rather than the root R/ directory.
R/utils/ - Any utility functions that may be of use across R analyses can go here. For example, plotting code, or helpful data cleaning functions.
R/Sensitivity_Anal/ - This directory holds all script developed for the sensitivity analyses. Among these scripts, the Create_New_Sensitivity_Analysis.R script serve as a basis as soon as you want to implement a new sensitivty analysis. For each sensitivty analysis, two R scripts are build: a script to developed the models of interest for this sensitivity and another one that is used to analyze and compare models.
model/ - This directory holds the stock synthesis model code.
model/ss_executables/ - This directory holds the executables for the two versions of SS considered in this assessment (3.24 and 3.30). For each version there is a subfolder that holds the available .exe of SS for different type of OS.
model/Sensitivity_Anal/ - This directory holds multiple sub-directory, each of one corresponds to a given sensitivity analysis. Each sub-directory will hold one or several folders corresponding to the model(s) developed for this sensitivty analysis.
outputs/ - Send all outputs (including plots and potential SS input files) generated by other analyses to this directory. There is no defined directory structure for this directory at this time, so be thoughtful as to directory and file names when you send outputs here.
| repository | use |
|---|---|
| nwfscSurvey | Analysis of the NWFSC trawl surveys |
| PacFIN.Utilities | Manipulate data from the PacFIN database for assessments |
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