Mandatory switch to Unix line endings for all 3 .R files before doing any more changes

RUN_PvSeroTAT.R

-#########################################################
-#########################################################
-###                                                   ###
-###     PvSeroTAT                                     ###
-###     R Shiny App Script                            ###
-###     WEHI and Institut Pasteur                     ###
-###                                                   ###
-#########################################################
-#########################################################
-
-#########################
-### CHECK ENVIRONMENT ###
-#########################
-
-# Check that current working directory is where all the shiny app files are located
-getwd()
-# If the working directory is incorrect, either
-# 1) Close R Studio and re-open this file (that should be in the correct directory)
-# 2) Set the working directory i.e. setwd(path) 
-
-
-######################
-### CHECK PACKAGES ###
-######################
-
-# List of required packaged to run app
-required_packages = c("readxl", "drc", "dplyr","tidyr","plyr","shiny","ggplot2",
-                      "shinythemes","stringr","ROCR","gplots","caTools","randomForest",
-                      "forcats","kernlab")
-# Check if any new packages need to be installed
-new_packages = required_packages[!(required_packages %in% installed.packages()[,"Package"])]
-# If any are missing, they will be installed
-if(length(new_packages)) install.packages(new_packages)
-
-# Note: this section only needs to be read in once so you can comment these lines after the first run
-
-
-###########
-### SVM ###
-###########
-
-# Please contact developers how to use this model and how to interpret results
-
-
-#####################
-### LOAD PACKAGES ###
-#####################
-
-library(readxl)
-library(drc)
-library(dplyr)
-library(tidyr)
-library(plyr)
-library(shiny)
-library(ggplot2)
-library(shinythemes)
-library(stringr)
-library(ROCR)
-library(gplots)
-library(caTools)
-library(randomForest)
-library(forcats)
-library(kernlab)
-
-
-#########################
-### RUN PVSEROTAT APP ###
-#########################
-
-# This line will run the PvSeroTat Shiny App by opening and running the script SHINY_APP.R
-# Either run this script manually or click on Run App (on the upper right ^)
-# Do not modify SHINY_APP.R unless asked to by the developer.
-# Once this line is run, the app window will be opened.
-
-runApp('SHINY_APP.R')
-
-# Enter all of the necessary information on the app and hit the submit button.
-# The progress of the analysis will be shown here on R in the console below.
-# If any errors arise, they will be shown here on R in the console below.
-
-# Once you opn the window and run one analysis, you can modify what is necessary on the app
-# and run the analysis as many times as you would like.
-# The output folders of the results will be indicated.
-
-
-
-
-
-
+#########################################################
+#########################################################
+###                                                   ###
+###     PvSeroTAT                                     ###
+###     R Shiny App Script                            ###
+###     WEHI and Institut Pasteur                     ###
+###                                                   ###
+#########################################################
+#########################################################
+
+#########################
+### CHECK ENVIRONMENT ###
+#########################
+
+# Check that current working directory is where all the shiny app files are located
+getwd()
+# If the working directory is incorrect, either
+# 1) Close R Studio and re-open this file (that should be in the correct directory)
+# 2) Set the working directory i.e. setwd(path) 
+
+
+######################
+### CHECK PACKAGES ###
+######################
+
+# List of required packaged to run app
+required_packages = c("readxl", "drc", "dplyr","tidyr","plyr","shiny","ggplot2",
+                      "shinythemes","stringr","ROCR","gplots","caTools","randomForest",
+                      "forcats","kernlab")
+# Check if any new packages need to be installed
+new_packages = required_packages[!(required_packages %in% installed.packages()[,"Package"])]
+# If any are missing, they will be installed
+if(length(new_packages)) install.packages(new_packages)
+
+# Note: this section only needs to be read in once so you can comment these lines after the first run
+
+
+###########
+### SVM ###
+###########
+
+# Please contact developers how to use this model and how to interpret results
+
+
+#####################
+### LOAD PACKAGES ###
+#####################
+
+library(readxl)
+library(drc)
+library(dplyr)
+library(tidyr)
+library(plyr)
+library(shiny)
+library(ggplot2)
+library(shinythemes)
+library(stringr)
+library(ROCR)
+library(gplots)
+library(caTools)
+library(randomForest)
+library(forcats)
+library(kernlab)
+
+
+#########################
+### RUN PVSEROTAT APP ###
+#########################
+
+# This line will run the PvSeroTat Shiny App by opening and running the script SHINY_APP.R
+# Either run this script manually or click on Run App (on the upper right ^)
+# Do not modify SHINY_APP.R unless asked to by the developer.
+# Once this line is run, the app window will be opened.
+
+runApp('SHINY_APP.R')
+
+# Enter all of the necessary information on the app and hit the submit button.
+# The progress of the analysis will be shown here on R in the console below.
+# If any errors arise, they will be shown here on R in the console below.
+
+# Once you opn the window and run one analysis, you can modify what is necessary on the app
+# and run the analysis as many times as you would like.
+# The output folders of the results will be indicated.
+
+
+
+
+
+