repurposing corr_data.R into a function to allow required params to be passed in

scripts/Header_TT.R

@@ -8,11 +8,35 @@
 
 require("getopt", quietly = TRUE) # cmd parse arguments
 
+if (!require ("DT")){
+  install.packages("DT")
+  library(DT)
+}
+
+if (!require ("plyr")){
+  install.packages("plyr")
+  library(plyr)
+}
+
 if (!require("tidyverse")) {
   install.packages("tidyverse", dependencies = TRUE)
   library(tidyverse)
 }
 
+#---------------------------
+# covered by tidyverse
+
+# if (!require("ggplot2")) {
+#   install.packages("ggplot2", dependencies = TRUE)
+#   library(ggplot2)
+# }
+
+# if (!require ("dplyr")){
+#    install.packages("dplyr")
+#    library(dplyr)
+#  }
+#-----------------------------
+
 if (!require("shiny")) {
   install.packages("shiny", dependencies = TRUE)
   library(shiny)
@@ -33,26 +57,6 @@ if (!require("ggridges")) {
   library(ggridges)
 }
 
-# if (!require("ggplot2")) {
-#   install.packages("ggplot2", dependencies = TRUE)
-#   library(ggplot2)
-# }
-
-# if (!require ("dplyr")){
-#   install.packages("dplyr")
-#   library(dplyr)
-# }
-
-if (!require ("DT")){
-  install.packages("DT")
-  library(DT)
-}
-
-if (!require ("plyr")){
-   install.packages("plyr")
-   library(plyr)
- }
-
 # Install
 #if(!require(devtools)) install.packages("devtools")
 #devtools::install_github("kassambara/ggcorrplot")
@@ -188,3 +192,17 @@ map(paste0(func_path, source_files), source)  # source all your R scripts!
 
 # set plot script dir
 plot_script_path = "~/git/LSHTM_analysis/scripts/plotting/"
+
+##################################################
+
+# Function name clashes with plyr and dplyr
+# # loading dplyr after plyr causes issues
+# if("dplyr" %in% (.packages())){
+#   detach("package:dplyr", unload=TRUE) 
+#   detach("package:plyr", unload=TRUE) 
+# } 
+# library(plyr)
+# library(dplyr)
+
+# another solution is to requireNamespace() instead of library()
+# so its function names don't collide with dplyr's.