From 2318804ea0bd9e4fe7301188e0a83d9887c3ee7e Mon Sep 17 00:00:00 2001
From: hollorol <hollorol@gmail.com>
Date: Sun, 17 Feb 2019 13:40:21 +0100
Subject: [PATCH] string handling

---
 RBBGCMuso/R/assistantFunctions.R | 21 ++++++++++++++++++---
 RBBGCMuso/R/plotMuso.R           | 11 ++++++++---
 2 files changed, 26 insertions(+), 6 deletions(-)

diff --git a/RBBGCMuso/R/assistantFunctions.R b/RBBGCMuso/R/assistantFunctions.R
index 04a74a8..150df05 100644
--- a/RBBGCMuso/R/assistantFunctions.R
+++ b/RBBGCMuso/R/assistantFunctions.R
@@ -147,7 +147,7 @@ readValuesFromFile  <- function(epc, linums){
 #' @export
 
 readMeasuredMuso <- function(inFile,
-                             naString = getOption("datatable.na.strings","NA"), sep = ",",
+                             naString = NULL, sep = ",",
                              leapYearHandling = TRUE,
                              convert.var = NULL,
                              convert.scalar = 1,
@@ -157,9 +157,24 @@ readMeasuredMuso <- function(inFile,
                              filterVal = 1,
                              selVar = NULL
                              ){
+
+    if(!is.null(naString)){
+        if(is.numeric(naString)){
+            baseData <- fread(file = inFile, sep=sep)
+            baseData <- as.data.frame(baseData)            
+            baseData[baseData[,selVar] == naString,selVar] <- NA        
+        } else {
+            baseData <- fread(file = inFile, sep=sep, naString = naString)
+            baseData <- as.data.frame(baseData)                  
+        }
+        
+    
+    } else {
+        
+            baseData <- fread(file = inFile, sep=sep)
+            baseData <- as.data.frame(baseData)            
+    }
     
-    baseData <- fread(file = inFile, na.strings = as.character(naString), sep=sep)
-    baseData <- as.data.frame(baseData)
     if(!is.null(filterCol)){
         filterVar<- colnames(baseData)[filterCol]
         baseData[(baseData[,filterVar] == filterVal),selVar] <- NA
diff --git a/RBBGCMuso/R/plotMuso.R b/RBBGCMuso/R/plotMuso.R
index cee07c8..dbb392b 100644
--- a/RBBGCMuso/R/plotMuso.R
+++ b/RBBGCMuso/R/plotMuso.R
@@ -260,12 +260,17 @@ plotMusoWithData <- function(mdata, plotName=NULL,
                        modellSettings = settings,
                        startDate = startDate,
                        endDate = endDate, leapYear = FALSE),envir=environment())
-
-
+    
+    
     ## measuredData is created
     baseData <- calibMuso(settings = settings, silent = silent, prettyOut = TRUE)[modIndex,]
     baseData[,1] <- as.Date(baseData[,1],format = "%d.%m.%Y")
-    selVarName <- colnames(baseData)[selVar]    
+    selVarName <- colnames(baseData)[selVar]
+    if(colnames(baseData) != unique(colnames(baseData))){
+        notUnique <- setdiff((unlist(settings$dailyVarCodes)),unique(unlist(settings$dailyVarCodes)))
+        stop(paste0("Error: daily output variable list in the ini file must contain unique numbers. Check your ini files! Not unique codes: ",notUnique))
+    }
+    
     p <- baseData  %>%
         ggplot(aes_string("date",selVarName)) +
         geom_line(colour=colour[1]) +