updated readme

README.md

@@ -1 +1,82 @@
-# Mevis2023_S_pseud
+# Mevis2023_S_pseud
+
+
+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.