diff --git a/RBBGCMuso/DESCRIPTION b/RBBGCMuso/DESCRIPTION
index ab96d06..c2d0d5b 100644
--- a/RBBGCMuso/DESCRIPTION
+++ b/RBBGCMuso/DESCRIPTION
@@ -35,7 +35,7 @@ Imports:
 LinkingTo: Rcpp
 SystemRequirements: C++11
 Maintainer: Roland Hollo's <hollorol@gmail.com>
-RoxygenNote: 7.0.0
+RoxygenNote: 7.1.0
 Suggests: knitr,
     rmarkdown,
 VignetteBuilder: knitr
diff --git a/RBBGCMuso/NAMESPACE b/RBBGCMuso/NAMESPACE
index ede2399..4eb00d3 100644
--- a/RBBGCMuso/NAMESPACE
+++ b/RBBGCMuso/NAMESPACE
@@ -16,6 +16,7 @@ export(getyearlycum)
 export(getyearlymax)
 export(mtclim)
 export(musoDate)
+export(musoGlue)
 export(musoMapping)
 export(musoMappingFind)
 export(musoMonte)
diff --git a/RBBGCMuso/R/calibration.R b/RBBGCMuso/R/calibration.R
index 70338b2..54ce8ba 100644
--- a/RBBGCMuso/R/calibration.R
+++ b/RBBGCMuso/R/calibration.R
@@ -198,6 +198,13 @@ calcLikelihoodsAndRMSE <- function(dataVar, mod, mes, likelihoods, alignIndexes,
     return(c(likelihoodRMSE[1,],likelihoodRMSE[2,]))
 }
 
+#' musoGlue
+#'
+#' This function calculates the -users specified- likelihood for random model input.
+#'
+#' @author Roland HOLLOS
+#' @param plotName u
+#' @export
 musoGlue <- function(preservedCalib, w){
     preservedCalib<- read.csv(preservedCalib)
     preservedCalib <- preservedCalib[-1,] #original
diff --git a/RBBGCMuso/man/alignData.Rd b/RBBGCMuso/man/alignData.Rd
index 3ba4f7f..0200b96 100644
--- a/RBBGCMuso/man/alignData.Rd
+++ b/RBBGCMuso/man/alignData.Rd
@@ -4,9 +4,16 @@
 \alias{alignData}
 \title{alignData}
 \usage{
-alignData(mdata, dataCol, modellSettings = NULL, startDate = NULL,
-  endDate = NULL, formatString = "\%Y-\%m-\%d", leapYear = TRUE,
-  continious = FALSE)
+alignData(
+  mdata,
+  dataCol,
+  modellSettings = NULL,
+  startDate = NULL,
+  endDate = NULL,
+  formatString = "\%Y-\%m-\%d",
+  leapYear = TRUE,
+  continious = FALSE
+)
 }
 \description{
 This function align the data to the model and the model to the data
diff --git a/RBBGCMuso/man/changemulline.Rd b/RBBGCMuso/man/changemulline.Rd
index 7acf438..e7ec966 100644
--- a/RBBGCMuso/man/changemulline.Rd
+++ b/RBBGCMuso/man/changemulline.Rd
@@ -4,8 +4,14 @@
 \alias{changemulline}
 \title{This is the function which is capable to change multiple specific lines to others using their row numbers.}
 \usage{
-changemulline(filePaths, calibrationPar, contents, fileOut, fileToChange,
-  modifyOriginal = FALSE)
+changemulline(
+  filePaths,
+  calibrationPar,
+  contents,
+  fileOut,
+  fileToChange,
+  modifyOriginal = FALSE
+)
 }
 \description{
 The function uses the previous changspecline function to operate.
diff --git a/RBBGCMuso/man/checkMeteoBGC.Rd b/RBBGCMuso/man/checkMeteoBGC.Rd
index 9d19096..02bdcfa 100644
--- a/RBBGCMuso/man/checkMeteoBGC.Rd
+++ b/RBBGCMuso/man/checkMeteoBGC.Rd
@@ -4,8 +4,12 @@
 \alias{checkMeteoBGC}
 \title{checkMeteoBGC}
 \usage{
-checkMeteoBGC(settings = NULL, skip = 4, numericReport = FALSE,
-  type = "normal")
+checkMeteoBGC(
+  settings = NULL,
+  skip = 4,
+  numericReport = FALSE,
+  type = "normal"
+)
 }
 \arguments{
 \item{settings}{The output of setupMuso}
diff --git a/RBBGCMuso/man/compareMuso.Rd b/RBBGCMuso/man/compareMuso.Rd
index 4890945..b4c6380 100644
--- a/RBBGCMuso/man/compareMuso.Rd
+++ b/RBBGCMuso/man/compareMuso.Rd
@@ -4,9 +4,15 @@
 \alias{compareMuso}
 \title{compareMuso}
 \usage{
-compareMuso(settings = NULL, parameters, variable = 1,
-  calibrationPar = NULL, fileToChange = "epc", skipSpinup = TRUE,
-  timeFrame = "day")
+compareMuso(
+  settings = NULL,
+  parameters,
+  variable = 1,
+  calibrationPar = NULL,
+  fileToChange = "epc",
+  skipSpinup = TRUE,
+  timeFrame = "day"
+)
 }
 \arguments{
 \item{settings}{RBBGCMuso uses variables that define the entire simulation environment. Those environment variables include the name of the INI files, the name of the meteorology files, the path to the model executable and its file name, the entire output list, the entire output variable matrix, the dependency rules for the EPC parameters etc. Using the runMuso function RBBGCMuso can automatically create those environment variables by inspecting the files in the working directory (this happens through the setupMuso function). It means that by default model setup is performed automatically in the background and the user has nothing to do. With this settings parameter we can force runMuso to skip automatic environment setup as we provide the environment settings to runMuso. In a typical situation the user can skip this option.}
diff --git a/RBBGCMuso/man/getConstMatrix.Rd b/RBBGCMuso/man/getConstMatrix.Rd
index 234fb65..8563459 100644
--- a/RBBGCMuso/man/getConstMatrix.Rd
+++ b/RBBGCMuso/man/getConstMatrix.Rd
@@ -4,8 +4,10 @@
 \alias{getConstMatrix}
 \title{getConstMatrix}
 \usage{
-getConstMatrix(filetype = "epc",
-  version = as.character(getOption("RMuso_version")))
+getConstMatrix(
+  filetype = "epc",
+  version = as.character(getOption("RMuso_version"))
+)
 }
 \arguments{
 \item{filetype}{It can be "epc" or "soil".}
diff --git a/RBBGCMuso/man/getMeteoData1BGC.Rd b/RBBGCMuso/man/getMeteoData1BGC.Rd
index 677b2cc..6f4265e 100644
--- a/RBBGCMuso/man/getMeteoData1BGC.Rd
+++ b/RBBGCMuso/man/getMeteoData1BGC.Rd
@@ -4,10 +4,19 @@
 \alias{getMeteoData1BGC}
 \title{getMeteoData1BGC}
 \usage{
-getMeteoData1BGC(startYear = 2017, endYear = 2017, lon = 18.8,
-  lat = 47.3, timeOut = 7200, monthList = sprintf("\%02d", 1:12),
-  dayList = sprintf("\%02d", 1:31), hourList = sprintf("\%02d:00",
-  0:23), destDir = NULL, apiFile = NULL, fileDir = NULL)
+getMeteoData1BGC(
+  startYear = 2017,
+  endYear = 2017,
+  lon = 18.8,
+  lat = 47.3,
+  timeOut = 7200,
+  monthList = sprintf("\%02d", 1:12),
+  dayList = sprintf("\%02d", 1:31),
+  hourList = sprintf("\%02d:00", 0:23),
+  destDir = NULL,
+  apiFile = NULL,
+  fileDir = NULL
+)
 }
 \arguments{
 \item{startYear}{Start year of the downloading data. It shall be greater than 1978.}
diff --git a/RBBGCMuso/man/musoDate.Rd b/RBBGCMuso/man/musoDate.Rd
index d8096e7..d2d47f6 100644
--- a/RBBGCMuso/man/musoDate.Rd
+++ b/RBBGCMuso/man/musoDate.Rd
@@ -4,8 +4,14 @@
 \alias{musoDate}
 \title{musoDate}
 \usage{
-musoDate(startYear, endYears = NULL, numYears, combined = TRUE,
-  leapYearHandling = FALSE, prettyOut = FALSE)
+musoDate(
+  startYear,
+  endYears = NULL,
+  numYears,
+  combined = TRUE,
+  leapYearHandling = FALSE,
+  prettyOut = FALSE
+)
 }
 \description{
 This function generates MuSo compatibla dates for the data
diff --git a/RBBGCMuso/man/musoGlue.Rd b/RBBGCMuso/man/musoGlue.Rd
new file mode 100644
index 0000000..b4960e7
--- /dev/null
+++ b/RBBGCMuso/man/musoGlue.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/calibration.R
+\name{musoGlue}
+\alias{musoGlue}
+\title{musoGlue}
+\usage{
+musoGlue(preservedCalib, w)
+}
+\arguments{
+\item{plotName}{u}
+}
+\description{
+This function calculates the -users specified- likelihood for random model input.
+}
+\author{
+Roland HOLLOS
+}
diff --git a/RBBGCMuso/man/musoMonte.Rd b/RBBGCMuso/man/musoMonte.Rd
index cffa6ee..04732a4 100644
--- a/RBBGCMuso/man/musoMonte.Rd
+++ b/RBBGCMuso/man/musoMonte.Rd
@@ -4,12 +4,27 @@
 \alias{musoMonte}
 \title{musoMonte}
 \usage{
-musoMonte(settings = NULL, parameters = NULL, inputDir = "./",
-  outLoc = "./calib", iterations = 10, preTag = "mont-",
-  outputType = "moreCsv", fun = mean, varIndex = 1, outVars = NULL,
-  silent = TRUE, skipSpinup = TRUE, debugging = FALSE,
-  keepEpc = FALSE, constrains = NULL, skipZero = TRUE,
-  postProcString = NULL, ...)
+musoMonte(
+  settings = NULL,
+  parameters = NULL,
+  inputDir = "./",
+  outLoc = "./calib",
+  iterations = 10,
+  preTag = "mont-",
+  outputType = "moreCsv",
+  fun = mean,
+  varIndex = 1,
+  outVars = NULL,
+  silent = TRUE,
+  skipSpinup = TRUE,
+  debugging = FALSE,
+  keepEpc = FALSE,
+  constrains = NULL,
+  skipZero = TRUE,
+  postProcString = NULL,
+  modifyOut = TRUE,
+  ...
+)
 }
 \arguments{
 \item{settings}{A list of environmental variables for the Monte Carlo experiment. These settings are generated by the setupMuso function. By default the settings parameter is generated automatically.}
diff --git a/RBBGCMuso/man/musoQuickEffect.Rd b/RBBGCMuso/man/musoQuickEffect.Rd
index 1676a4e..57879e4 100644
--- a/RBBGCMuso/man/musoQuickEffect.Rd
+++ b/RBBGCMuso/man/musoQuickEffect.Rd
@@ -4,9 +4,19 @@
 \alias{musoQuickEffect}
 \title{musoQuickEffect}
 \usage{
-musoQuickEffect(settings = NULL, calibrationPar = NULL, startVal,
-  endVal, nSteps = 1, fileToChange = "epc", outVar,
-  parName = "parVal")
+musoQuickEffect(
+  settings = setupMuso(),
+  calibrationPar = NULL,
+  startVal,
+  endVal,
+  nSteps = 1,
+  fileToChange = "epc",
+  modifyOriginal = TRUE,
+  outVar,
+  parName = "parVal",
+  yearNum = 1,
+  year = (settings$startYear + yearNum - 1)
+)
 }
 \arguments{
 \item{settings}{RBBGCMuso uses variables that define the entire simulation environment. Those environment variables include the name of the INI files, the name of the meteorology files, the path to the model executable and its file name, the entire output list, the entire output variable matrix, the dependency rules for the EPC parameters etc. Using the runMuso function RBBGCMuso can automatically create those environment variables by inspecting the files in the working directory (this happens through the setupMuso function). It means that by default model setup is performed automatically in the background and the user has nothing to do. With this settings parameter we can force runMuso to skip automatic environment setup as we provide the environment settings to runMuso. In a typical situation the user can skip this option.}
diff --git a/RBBGCMuso/man/musoRand.Rd b/RBBGCMuso/man/musoRand.Rd
index 5fff6d5..d512ce1 100644
--- a/RBBGCMuso/man/musoRand.Rd
+++ b/RBBGCMuso/man/musoRand.Rd
@@ -4,9 +4,7 @@
 \alias{musoRand}
 \title{musoRand}
 \usage{
-musoRand(parameters, iterations = 3000, fileType = "epc",
-  version = as.character(getOption("RMuso_version")),
-  constrains = getConstMatrix(fileType = fileType, version = version))
+musoRand(parameters, iterations = 3000, fileType = "epc", constrains = NULL)
 }
 \arguments{
 \item{parameters}{This is a dataframe (heterogeneous data-matrix), where the first column is the name of the parameter, the second is a numeric vector of the rownumbers of the given variable in the input EPC file, and the last two columns describe the minimum and the maximum of the parameter (i.e. the parameter ranges), defining the interval for the randomization.}
diff --git a/RBBGCMuso/man/musoSensi.Rd b/RBBGCMuso/man/musoSensi.Rd
index b291be2..13afa5e 100644
--- a/RBBGCMuso/man/musoSensi.Rd
+++ b/RBBGCMuso/man/musoSensi.Rd
@@ -4,13 +4,27 @@
 \alias{musoSensi}
 \title{musoSensi}
 \usage{
-musoSensi(monteCarloFile = NULL, parameters = NULL, settings = NULL,
-  inputDir = "./", outLoc = "./calib", outVars = NULL,
-  iterations = 30, preTag = "mont-", outputType = "moreCsv",
-  fun = mean, varIndex = 1, outputFile = "sensitivity.csv",
-  plotName = "sensitivity.png", plotTitle = "Sensitivity",
-  skipSpinup = TRUE, skipZero = TRUE, postProcString = NULL,
-  dpi = 300)
+musoSensi(
+  monteCarloFile = NULL,
+  parameters = NULL,
+  settings = NULL,
+  inputDir = "./",
+  outLoc = "./calib",
+  outVars = NULL,
+  iterations = 30,
+  preTag = "mont-",
+  outputType = "moreCsv",
+  fun = mean,
+  varIndex = 1,
+  outputFile = "sensitivity.csv",
+  plotName = "sensitivity.png",
+  plotTitle = "Sensitivity",
+  skipSpinup = TRUE,
+  skipZero = TRUE,
+  postProcString = NULL,
+  modifyOut = TRUE,
+  dpi = 300
+)
 }
 \arguments{
 \item{parameters}{This is a dataframe (heterogen data-matrix), which first column is the name of the parameters, the second is a numeric vector of the rownumbers of the given variable in the epc-fie, the last two column consist the endpont of the parameter-ranges, where the parameters will be randomized.}
diff --git a/RBBGCMuso/man/optiMuso.Rd b/RBBGCMuso/man/optiMuso.Rd
index 191b22e..d338cbc 100644
--- a/RBBGCMuso/man/optiMuso.Rd
+++ b/RBBGCMuso/man/optiMuso.Rd
@@ -4,14 +4,26 @@
 \alias{optiMuso}
 \title{optiMuso}
 \usage{
-optiMuso(measuredData, parameters = NULL, startDate = NULL,
-  endDate = NULL, formatString = "\%Y-\%m-\%d",
-  leapYearHandling = TRUE, dataVar, outLoc = "./calib",
-  preTag = "cal-", settings = NULL, outVars = NULL,
-  iterations = 30, skipSpinup = TRUE, constrains = NULL,
-  plotName = "calib.jpg", likelihood = function(x, y) {    
-  exp(-sqrt(mean((x - y)^2))) }, continious, modelVar = 3009,
-  naVal = NULL, postProcString = NULL)
+optiMuso(
+  measuredData,
+  parameters = NULL,
+  startDate = NULL,
+  endDate = NULL,
+  formatString = "\%Y-\%m-\%d",
+  dataVar,
+  outLoc = "./calib",
+  preTag = "cal-",
+  settings = setupMuso(),
+  outVars = NULL,
+  iterations = 30,
+  skipSpinup = TRUE,
+  plotName = "calib.jpg",
+  modifyOriginal = TRUE,
+  likelihood,
+  naVal = NULL,
+  postProcString = NULL,
+  w = NULL
+)
 }
 \arguments{
 \item{parameters}{b}
@@ -30,8 +42,6 @@ optiMuso(measuredData, parameters = NULL, startDate = NULL,
 
 \item{skipSpinup}{a}
 
-\item{constrains}{d}
-
 \item{plotName}{u}
 
 \item{likelihood}{d}
@@ -50,6 +60,8 @@ optiMuso(measuredData, parameters = NULL, startDate = NULL,
 
 \item{calPar}{a}
 
+\item{constrains}{d}
+
 \item{leapYear}{b}
 }
 \description{
diff --git a/RBBGCMuso/man/paramSweep.Rd b/RBBGCMuso/man/paramSweep.Rd
index 39d435a..8933dce 100644
--- a/RBBGCMuso/man/paramSweep.Rd
+++ b/RBBGCMuso/man/paramSweep.Rd
@@ -4,9 +4,14 @@
 \alias{paramSweep}
 \title{paramSweep}
 \usage{
-paramSweep(inputDir = "./", parameters = NULL, outputDir = NULL,
-  iterations = 10, outVar = "daily_gpp",
-  htmlOutName = "paramsweep.html")
+paramSweep(
+  inputDir = "./",
+  parameters = NULL,
+  outputDir = NULL,
+  iterations = 10,
+  outVar = "daily_gpp",
+  htmlOutName = "paramsweep.html"
+)
 }
 \arguments{
 \item{inputDir}{The directory which contains the MuSo model's ini files}
diff --git a/RBBGCMuso/man/randEpc.Rd b/RBBGCMuso/man/randEpc.Rd
index 6087be7..4a83540 100644
--- a/RBBGCMuso/man/randEpc.Rd
+++ b/RBBGCMuso/man/randEpc.Rd
@@ -4,8 +4,13 @@
 \alias{randEpc}
 \title{randEpc}
 \usage{
-randEpc(parameterFile = "parameters.csv", location = "./epcDir",
-  sourceEpc = "maize.epc", iterations = 1000, constrains = NULL)
+randEpc(
+  parameterFile = "parameters.csv",
+  location = "./epcDir",
+  sourceEpc = "maize.epc",
+  iterations = 1000,
+  constrains = NULL
+)
 }
 \arguments{
 \item{parameterFile}{parameters.csv file location}
diff --git a/RBBGCMuso/man/readObservedData.Rd b/RBBGCMuso/man/readObservedData.Rd
index 622b4a3..e079014 100644
--- a/RBBGCMuso/man/readObservedData.Rd
+++ b/RBBGCMuso/man/readObservedData.Rd
@@ -4,11 +4,19 @@
 \alias{readObservedData}
 \title{readMeasuredMuso}
 \usage{
-readObservedData(inFile, naString = NULL, sep = ",",
-  leapYearHandling = TRUE, convert.var = NULL, convert.scalar = 1,
+readObservedData(
+  inFile,
+  naString = NULL,
+  sep = ",",
+  leapYearHandling = TRUE,
+  convert.var = NULL,
+  convert.scalar = 1,
   convert.fun = (function(x) {     x * convert.scalar }),
-  convert.file = NULL, filterCol = NULL, filterVal = 1,
-  selVar = NULL)
+  convert.file = NULL,
+  filterCol = NULL,
+  filterVal = 1,
+  selVar = NULL
+)
 }
 \description{
 MuSo data reader
diff --git a/RBBGCMuso/man/saveAllMusoPlots.Rd b/RBBGCMuso/man/saveAllMusoPlots.Rd
index 79b184b..ec4c9d8 100644
--- a/RBBGCMuso/man/saveAllMusoPlots.Rd
+++ b/RBBGCMuso/man/saveAllMusoPlots.Rd
@@ -4,9 +4,15 @@
 \alias{saveAllMusoPlots}
 \title{saveAllMusoPlots}
 \usage{
-saveAllMusoPlots(settings = NULL, plotName = ".png", silent = TRUE,
-  type = "line", outFile = "annual.csv", colour = NULL,
-  skipSpinup = FALSE)
+saveAllMusoPlots(
+  settings = NULL,
+  plotName = ".png",
+  silent = TRUE,
+  type = "line",
+  outFile = "annual.csv",
+  colour = NULL,
+  skipSpinup = FALSE
+)
 }
 \arguments{
 \item{settings}{RBBGCMuso uses variables that define the entire simulation environment. Those environment variables include the name of the INI files, the name of the meteorology files, the path to the model executable and its file name, the entire output list, the entire output variable matrix, the dependency rules for the EPC parameters etc. Using the runMuso function RBBGCMuso can automatically create those environment variables by inspecting the files in the working directory (this happens through the setupMuso function). It means that by default model setup is performed automatically in the background and the user has nothing to do. With this settings parameter we can force runMuso to skip automatic environment setup as we provide the environment settings to runMuso. In a typical situation the user can skip this option.}
diff --git a/RBBGCMuso/man/stampAndDir.Rd b/RBBGCMuso/man/stampAndDir.Rd
index c1d2843..c30516e 100644
--- a/RBBGCMuso/man/stampAndDir.Rd
+++ b/RBBGCMuso/man/stampAndDir.Rd
@@ -4,8 +4,15 @@
 \alias{stampAndDir}
 \title{stampAndCopy}
 \usage{
-stampAndDir(outputLoc, names, stampDir, wrongDir, type = "output",
-  errorsign, logfiles)
+stampAndDir(
+  outputLoc,
+  names,
+  stampDir,
+  wrongDir,
+  type = "output",
+  errorsign,
+  logfiles
+)
 }
 \arguments{
 \item{outputLoc}{This is the location of the output files.}
diff --git a/RBBGCMuso/man/updateMusoMapping.Rd b/RBBGCMuso/man/updateMusoMapping.Rd
index 8f343b4..bbf40b9 100644
--- a/RBBGCMuso/man/updateMusoMapping.Rd
+++ b/RBBGCMuso/man/updateMusoMapping.Rd
@@ -4,8 +4,7 @@
 \alias{updateMusoMapping}
 \title{updateMusoMapping}
 \usage{
-updateMusoMapping(excelName, dest = "./",
-  version = getOption("RMuso_version"))
+updateMusoMapping(excelName, dest = "./", version = getOption("RMuso_version"))
 }
 \arguments{
 \item{excelName}{Name of the excelfile which contains the parameters}