This package reproduces analysis found in "Longitudinal antimicrobial susceptibility trends of canine Staphylococcus pseudintermedius" Step 1. Open R Project File 'Mevis2023_S_pseud.Rproj', then getwd() to check that the path of this project file is the active directory. Step 2. In R, open the "scripts/Staph pseud analysis.R" file and source/run it with echo.
De-identified data is in the data folder.
Data Citation: Cornell University Animal Health Diagnostic Laboratory (Cassandra Guarino, Director of Bacteriology). (2022). "Canine Staph 2007-2020". [Excel file "Staph_fulldata.csv"]. Note that the publicly available data is de-identified. Some processing steps using sample identifiers are not present in this reproducible package.
R.Version() $platform [1] "x86_64-w64-mingw32"
$arch [1] "x86_64"
$os [1] "mingw32"
$crt [1] "ucrt"
$system [1] "x86_64, mingw32"
$status [1] ""
$major [1] "4"
$minor [1] "2.3"
$year [1] "2023"
$month [1] "03"
$day [1] "15"
$svn rev
[1] "83980"
$language [1] "R"
$version.string [1] "R version 4.2.3 (2023-03-15 ucrt)"
$nickname [1] "Shortstop Beagle"
R.Studio Version RStudio 2023.03.0+386 "Cherry Blossom" Release (3c53477afb13ab959aeb5b34df1f10c237b256c3, 2023-03-09) for Windows Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2023.03.0+386 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36 Run on Windows 11, 64-bit
General information Article Citation:
Title of the paper: Longitudinal antimicrobial susceptibility trends of canine Staphylococcus pseudintermedius
Author(s) and ORCID(s): Caroline Calabro Ritwik Sadhu - 0000-0003-0262-4012 Yuchen Xu - 0000-0003-1128-3774 Melissa Aprea Cassandra Guarino - 0000-0002-7295-7448 Casey L. Cazer - 0000-0002-2290-1868 Corresponding author: Casey L. Cazer Contact details: email: clc248@cornell.edu
Code Citation: Caroline Calabro, Ritwik Sadhu, Yuchen Xu, and Casey L. Cazer. (2023). "Longitudinal antimicrobial susceptibility trends of canine Staphylococcus pseudintermedius" (version 1) [R files].
Code Author ORCID: Casey L. Cazer: 0000-0002-2290-1868 Code last updated: July 13, 2023.