final fix getLoadings function. Tetsted by Nynke on 13-09-22.

R/getLoadings.R

@@ -18,12 +18,12 @@ getLoadings<-function(inputDF=read.csv("data/input_file_new_kla_div_20200729-0Ba
 
   df1<-inputDF
 
-#comment out these lines after testing
+  #comment out these lines after testing
   #df1<-df1[,c(1:42)]
   #colnames(df1)<-c(colnames(df1[,c(1:19)]),substr(colnames(df1[,c(20:42)]),1,nchar(colnames(df1[,c(20:42)]))-4))
   #colnames(df1)
   #df1$excreted<-rep(1e10,5)
-#comment out these lines after testing
+  #comment out these lines after testing
 
   pathogenGroups<-c("Virus","Bacteria","Protozoa","Helminth")
   index<-which(pathogenGroups==pathogenType)
@@ -33,7 +33,7 @@ getLoadings<-function(inputDF=read.csv("data/input_file_new_kla_div_20200729-0Ba
 
   #persistence model in pits
   persist<-read.csv("http://data.waterpathogens.org/dataset/eda3c64c-479e-4177-869c-93b3dc247a10/resource/f99291ab-d536-4536-a146-083a07ea49b9/download/k2p_persistence.csv",header=T)
-  persist<-read.csv("data/k2p_persistence_WR.csv",header=T)
+  #persist<-read.csv("data/k2p_persistence_WR.csv",header=T)
   persist<-persist[1:(length(persist)-1)]
   #persist<-persist[persist$matrix=="Fecal sludge",]
   persist<-subset(persist,matrix=="Fecal sludge")
@@ -320,4 +320,4 @@ getLoadings<-function(inputDF=read.csv("data/input_file_new_kla_div_20200729-0Ba
   )
   return(returned)
 
-}
+}
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