Added copenhagen case study rmd for adapting

EPIET · Sep 1, 2023 · 3f522aa · 3f522aa
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diff --git a/...015_Brief introduction to R_Proj_AM.Rproj → Copenhagen_introsim/Copenhagen_2022.Rproj b/...015_Brief introduction to R_Proj_AM.Rproj → Copenhagen_introsim/Copenhagen_2022.Rproj
diff --git a/Copenhagen_introsim/Copenhagen_R_guide.R b/Copenhagen_introsim/Copenhagen_R_guide.R
diff --git a/Copenhagen_introsim/Copenhagen_R_guide.Rmd b/Copenhagen_introsim/Copenhagen_R_guide.Rmd
diff --git a/Copenhagen_introsim/Copenhagen_R_guide_files/figure-html/hist_age-1.png b/Copenhagen_introsim/Copenhagen_R_guide_files/figure-html/hist_age-1.png
diff --git a/Copenhagen_introsim/Copenhagen_R_guide_files/figure-html/onset_histogram-1.png b/Copenhagen_introsim/Copenhagen_R_guide_files/figure-html/onset_histogram-1.png
diff --git a/Copenhagen_introsim/data/Copenhagen_clean.xlsx b/Copenhagen_introsim/data/Copenhagen_clean.xlsx
diff --git a/Copenhagen_introsim/data/Copenhagen_raw.csv b/Copenhagen_introsim/data/Copenhagen_raw.csv
diff --git a/Copenhagen_introsim/guide/Copenhagen_R_guide.html b/Copenhagen_introsim/guide/Copenhagen_R_guide.html
diff --git a/Copenhagen_introsim/rscripts/Copenhagen_R_template.R b/Copenhagen_introsim/rscripts/Copenhagen_R_template.R
diff --git a/Copenhagen_introsim/rscripts/Copenhagen_pkgs2install.R b/Copenhagen_introsim/rscripts/Copenhagen_pkgs2install.R
@@ -0,0 +1,42 @@
+########################################################
+# COPENHAGEN CASE STUDY - PACKAGES TO INSTALL
+########################################################
+
+# INSTRUCTIONS:
+
+# Open a fresh RStudio session
+# Make sure no scripts, files or data are open.
+# Go to Session --> Restart R and select it to start a fresh R session
+# Highlight this script and press the run button
+# Do not attempt to do anything in R until it is finished; 
+# The script will take a few minutes
+# Happy R coding!
+
+
+# Install pacman ----------------------------------------------------------
+
+# Check if the 'pacman' package is installed, if not install it:
+if (!requireNamespace("pacman", quietly = TRUE)) install.packages("pacman")
+
+
+
+# Install remaining packages ----------------------------------------------
+
+# Load the required libraries into the current R session:
+pacman::p_load(rio, 
+               here, 
+               tidyverse, 
+               skimr, 
+               janitor,
+               lubridate,
+               gtsummary, 
+               flextable,
+               officer,
+               EpiStats,
+               epikit, 
+               apyramid, 
+               scales, 
+               update = TRUE)
+
+###########################################################################
+
diff --git a/IntroductoryCourse.Rproj b/IntroductoryCourse.Rproj
@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
diff --git a/...015_Brief introduction to R_Script_AM.Rmd → ...015_Brief introduction to R_Script_AM.Rmd b/...015_Brief introduction to R_Script_AM.Rmd → ...015_Brief introduction to R_Script_AM.Rmd
diff --git a/exampleIC2019stata12.dta → R_demo_tutorial/exampleIC2019stata12.dta b/exampleIC2019stata12.dta → R_demo_tutorial/exampleIC2019stata12.dta
diff --git a/fig1_rproject.png → R_demo_tutorial/fig1_rproject.png b/fig1_rproject.png → R_demo_tutorial/fig1_rproject.png
diff --git a/fig2_rscript.png → R_demo_tutorial/fig2_rscript.png b/fig2_rscript.png → R_demo_tutorial/fig2_rscript.png