Code snippets for easy re-use.

The goal of this repository is to store and share snippets of code that members of the FRAM team find useful. The following is an overview of the current code, which we hope will streamline finding and sharing useful code. This will be updated periodically, and the repository may contain snippets that are not documented here.

Command line code, in commandline/

• readme-maker.txt has directions for using windows commands to create a text file of the directory tree of the current directory. We have found this helpful when documenting complex projects for sharing/publication (for example: see "README.txt" of the data and code repository here: https://figshare.com/articles/dataset/Data_and_analysis_for_Plant_defense_synergies_and_antagonisms_affect_performance_of_specialist_herbivores_of_common_milkweed_/20421633)
• search-for-file-name.txt has an example for using windows command-line to carry out searching for specific filename using wildcards.
• search-sh.txt has an example for using windows command-line to carry out a seach of the CONTENTS of files. This can be particularly useful when trying to find the script that generated a file (presuming the file name wasn't programmatically generated, the script in question should contain the file name in it).

Visual Basic code, in VB/

Macros

• Scalars-Compute-MR.vb is the macro used in ChinRSScalers.*.xlsm, which populates the Columbia river marked fish rates from RMIS data.

R code, in R/

FRAM team tools

• SPSIterations.R is code from Derek Dapp that can automate the SPS iterations process for the Chinook TAMM.

Visualization tools

Making plots

• correlation_visualization.R has code to make a heatmap plot of correlations between variables of a dataframe, in a ggplot framework.
• correlation-paired-plot.R is a way to compare correlations between variables of a dataframe using base R.
• geom_pie2.R is a modified version of geom_pie from the scatterpie package. The scatterpie package can be used to add piechart layers onto maps, making it useful for some very specific types of plots. As of 2018 when Collin Edwards was using the package regularly, however, geom_pie only worked if the variables of the data frame used had specific names. geom_pie2() fixes this problem, making geom_pie behave consistently to other ggplot type functions.
• ggplot-template-area-periods.R provides example code to make a plot representing fishing in areas based on the start and end dates of fishing periods. Note that this can be used more generally for kind of data with start and end dates and multiple categories (e.g. fisheries).
• von-bertalanffy-fram.R provides code to plot the parameterized growth function for Chinook, including the average size at time step for ages 2-5.

Support

• color-blind-palette.R contains a simple vector of colorblind friendly colors that may be more visually appealing than the discrete values provided in the viridis package. (The viridis package has hugely helpful tools for making figures color-blind friendly, and seems particularly well suited for continuous color gradients). Colorblind friendliness of ggplot objects can easily be tested with colorBlindness::cvdPlot(). The colorBlindness package also has many good color palettes for discrete colors. See https://cran.r-project.org/web/packages/colorBlindness/vignettes/colorBlindness.html.
• color-wdfw-pallete.R contains the WDFW colors (based on the 2023 WDFW style guide) in vector form. Useful reference when using color_scale_manual or other color-determining functions.
• doy_2md.R has a few functions to simplify translating day of year into a month/year. While this could be useful in data manipulation, there are likely better tools for this, depending on the task (check out the lubridate package!). However, doy_2md() can be helpful when creating custom date axes.
• ggplot-axis-relabeling.R has a series of functions to streamline making custom axis labels based on transformations of the data. The main use case we see is plotting proportion data with appropriate percent axis ticks, such as when working with exploitation rate.
• ggtheme-larger.R and ggtheme-fram.R define ggplot themes that serve as good baselines when making figures for general consumption. ggtheme-larger.R is deprecated, and we are only leaving as a reference point for now. We recommend ggtheme-fram.R as a starting point.
• adjust-points.R contains a function that programmatically shifts overlapping points by a small amount to make colors/symbols easy to see.

FRAM / TAMM tools

• Update_Age_2_Recruit_Scalar_2024.R is a script to update age 2 recruit scalars (scalers). Note that the current iteration of this script likely requires 32 bit R to run.
• fram-flag-reporter.R has a prototype function to aggregate the different flags used for fisheries and stock in a FRAM database and spit out a summary report. Tis is likely superceded by current or future work in the framrsquared package.

Data manipulation

• check-mismatch.R takes two vectors and reports mismatches in a readable format. This is especially useful when joining data from different sources, as it simplifies checking for different spellings or abbreviations.
• data-frame-comparison.R has code to compare two data frames to look for mismatches. This can be very helpful for QA/QC (e.g., comparing the output of a new method to the output of an old method, when the results should be the same).
• data-frame-duplicates.R has code to identify duplicate rows within a dataframe, with a lot of flexibility of which columns to include when looking for duplicates.
• fishery-renamer.R has a function that translates the fishery names used in FRAM and TAMM into consistent, easily readable strings. With optional argument sep = TRUE, it instead returns a data frame, with separate columns for area name and fishery type (e.g. "Troll", "Sport", "Net").
• filter-catch-by-regulation.R has example code to work with test fishing data.
• months-spanned.R takes start and end dates (either atomics or vectors) and returns a data frame with the months the period or periods spanned and the days and proportions of those months spanned. With optional argument return.empties = TRUE, it also returns all other months in the associated years with 0s for the days and proportions columns
• period-2daily.R takes a dataframe with a row per period (e.g., per regulatory period), and expands this to a dataframe with one entry per day. Optional "dividee" argument allows easy distribution of aggregated values to daily averages (e.g., total fish caught in a period can be divided into average fish caught per day).
• timestep-finder.R calculates the chinook timestep from a vector of dates. Without knowing run-year, timesteps 1 and 4 entirely overlap; this function returns dates in that period as timestep 4.
• metadata_saver.R has tools to streamline saving a dataframe or tibble with metadata.

File manipulation

• db-pull-example.R has example code to pull information from a local database. When working with FRAM files, note that the FRAMrsquared package (https://github.com/FRAMverse/framrsquared) has a lot of functions that massively streamline working with the FRAM databases. When appropriate, we strongly recommend the FRAMrsquared functions instead.

Quarto and Rmarkdown

R/markdown and quarto/ contains

• custom-yaml-header.Rmd which contains a template YAML header for an Rmarkdown or Quarto document to handle some good defaults (include table of contents, allow code folding, turn off warnings and messages so that reading in packages doesn't lead to messiness). Any of these arguments can be changed; this is just meant to be an efficient starting point. Note that this is designed for use with style.css, which adds the WDFW logo to the header.
• style.css is a style file that can be used to the wdfw logo to Quarto files. Put a copy of style.css into the folder of the quarto file, and include css: style.css in the YAML header of the quarto file (already in custom-yaml-header.Rmd). Pulls logo from the wdfw website, so will only work when computer is connected to the internet.

Misc

• example-ode-solver.R has example code for numerically solving and plotting a system of ordinary differential equations (a form of continuous time dynamic models). Many theoretical ecology models are constructed of ordinary differential equations.
• multi-list-dopar.R has an example of parallelization with multiple objects output per loop.
• framrsquared-style-checker.R has functions to check an R script for (a) use of <- for assignment, and (b) use of snake_case for variable assignment. These are not foolproof, but server as helpers for more consistent coding.
• cell-range-translate.R has a function to translate excel cell range specifications to corresponding rows and columns to streamline working with R dataframes that come from excel spreadsheets. If only a subset of the data frame was read in, use the optional start argument to specify where the excel reading started. This function is included in the TAMMsupport package, and any further developments will be implemented there.

Excel template files, in excel/