From 3c7f47dd19027edf00cb39ed9d3bc98b001cf023 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Roland=20Holl=C3=B3s?= <hollorol@gmail.com>
Date: Sat, 23 May 2020 13:31:15 +0200
Subject: [PATCH] nastrings

---
 RBBGCMuso/R/assistantFunctions.R | 2 +-
 RBBGCMuso/R/quickeffect.R        | 2 +-
 RBBGCMuso/R/setupMuso.R          | 7 +++++--
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/RBBGCMuso/R/assistantFunctions.R b/RBBGCMuso/R/assistantFunctions.R
index 6c8c904..5cc50af 100644
--- a/RBBGCMuso/R/assistantFunctions.R
+++ b/RBBGCMuso/R/assistantFunctions.R
@@ -164,7 +164,7 @@ readObservedData <- function(inFile,
             baseData <- as.data.frame(baseData)            
             baseData[baseData[,selVar] == naString,selVar] <- NA        
         } else {
-            baseData <- fread(file = inFile, sep=sep, naString = naString)
+            baseData <- fread(file = inFile, sep=sep, na.strings = naString)
             baseData <- as.data.frame(baseData)                  
         }
         
diff --git a/RBBGCMuso/R/quickeffect.R b/RBBGCMuso/R/quickeffect.R
index c76a4f7..1b8b150 100644
--- a/RBBGCMuso/R/quickeffect.R
+++ b/RBBGCMuso/R/quickeffect.R
@@ -15,7 +15,7 @@
 #' @importFrom tidyr separate
 #' @export
 
-musoQuickEffect <- function(settings = NULL,calibrationPar = NULL,  startVal, endVal, nSteps = 1, fileToChange="epc",modifyOriginal=TRUE, outVar, parName = "parVal"){
+musoQuickEffect <- function(settings = NULL, calibrationPar = NULL,  startVal, endVal, nSteps = 1, fileToChange="epc",modifyOriginal=TRUE, outVar, parName = "parVal"){
 
     if(is.character(outVar)){
                       varNames <- as.data.frame(musoMappingFind(outVar))
diff --git a/RBBGCMuso/R/setupMuso.R b/RBBGCMuso/R/setupMuso.R
index bfa9378..8873478 100644
--- a/RBBGCMuso/R/setupMuso.R
+++ b/RBBGCMuso/R/setupMuso.R
@@ -108,8 +108,11 @@ setupMuso <- function(executable=NULL,
         normals<-grep("n.ini$",list.files(inputLoc),value=TRUE)
 
         if(length(spinups)==1){
-            iniInput[1]<-file.path(inputLoc,spinups)
-        } else {stop("There are multiple or no spinup ini files, please choose")}
+            iniInput[1] <- file.path(inputLoc,spinups)
+        } else {
+            iniInput[1] <- "no spinup" 
+            # stop("There are multiple or no spinup ini files, please choose")
+        }
         
 
         if(length(normals)==1){