Project title

Sodium salicylate improves detection of amplitude-modulated sound in mice

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Description

This is the code to generate Figure panels for the manuscript "Sodium salicylate improves detection of amplitude-modulated sound in mice" by Van den Berg et al, 2024.

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Authors

• Maurits M. van den Berg*, m.m.vandenberg@erasmusmc.nl

• Aaron B. Wong*, a.wong@erasmusmc.nl (maintainer)

• Ghais Houtak, ghais.houtak@adelaide.edu.au

• Ross S. Williamson, ross.s.williamson@pitt.edu

• J. Gerard G. Borst, g.borst@erasmusmc.nl

* equal contributions

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Last updated

12 Mar 2024

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BUILD INSTRUCTIONS

1. Dependencies

• Obtain raw data files and extract the folder /Data/ in the root directory of this repository
• Matlab (version 2019a or later) for the vast majority of figures
• Igor Pro 9 for Figure S3
• R and RStudio (3.6.x) for statistics in Figures 4 and 5.
  • Install the following R packages ("here","lme4","nlme","plyr","multcomp") or run the following code in the R console:

  packages <- c("here","lme4","nlme","plyr","multcomp")
  install.packages(packages)
  

2. Directory structure

• \Data\ Stores raw and analyzed data.
• \Figures\ Stores illustrator files to assemble final figures.
• \src\paper\ Stores codes to generate figure panels and illustrations.
• \src\statistics\ Stores codes for statistics related to linear mixed models (Fig .
• \functions\ Stores miscellaneous functions needed to run the code

3. How to run the project

• Fig S3:
  • Open the Igor packaged experiment (.pxp) file src\paper\FigS3_Unit_Salicylate_effect_proportions.pxp in Igor Pro.
  • In the command window, type saveAllPics() and press enter.
• All other figures:
  • Extract the folder \Data\ from source data into the root directory
  • Run the script run_me_AllFigures.m in Matlab, with the root directory as the working directory.
• All figures subpanels will be stored under \Figures\Links\. This ensures all .ai files under \Figures\ can find them as linked files.
• Linear mixed-effect model statistics: Run the R markdown file src\statistics\StatisticsSalicylate_2022-09-15.rmd in R-studio.