Major bug fixes in setupMuso and calibMuso

RBBGCMuso/.gitignore

@@ -1 +1,4 @@
 inst/doc
+swp$
+'~'$
+'#'$

RBBGCMuso/R/.Rhistory

@@ -4,3 +4,37 @@ ls()
 rm(list=ls)
 rm(list=ls())
 ls()
+stop("asdf")
+ls()
+?registerDoParallel
+getDoParallel()
+?clusterExport
+vignette(parallel)
+vignette("parallel")
+stopCluster(cl)
+?registerDoParallel
+list.files()
+list.files()
+?intersect
+library(hash)
+hash(list.files())
+hash(1
+)
+?hash
+hash( a=1, b=2, c=3 )
+list.files()
+setwd("~/Documents/tmp")
+list.files()
+list.files()
+list.files()
+list.files()
+list.files()
+paste("a","b",collapse = "/")
+paste("a","b",sep = "/")
+list.files()
+24000*100000
+24000*100000/1000000
+exit())
+exit()
+quit()
+y

RBBGCMuso/R/setupMuso.R

@@ -226,17 +226,17 @@ setupMuso <- function(executable=NULL,
                     outputNames=outputName,
                     inputLoc=inputLoc,
                     iniInput=iniInput,
-                    metInput=metInput,
+                    metInput=inputs$metInput,
-                    epcInput=epcInput,
+                    epcInput=inputs$epcInput,
-                    thinInput=thinInput,
+                    thinInput=inputs$thinInput,
-                    CO2Input=CO2Input,
+                    CO2Input=inputs$CO2Input,
-                    mowInput=mowInput,
+                    mowInput=inputs$mowInput,
-                    grazInput=grazInput,
+                    grazInput=inputs$grazInput,
-                    harvInput=harvInput,
+                    harvInput=inputs$harvInput,
-                    plougInput=plougInput,
+                    plougInput=inputs$plougInput,
-                    fertInput=fertInput,
+                    fertInput=inputs$fertInput,
-                    irrInput=irrInput,
+                    irrInput=inputs$irrInput,
-                    nitInput=nitInput,
+                    nitInput=inputs$nitInput,
                     inputFiles=inputFiles,
                     numData=numData,
                     startyear=startyear,