fixing warnings and errors

RBBGCMuso/DESCRIPTION

@@ -39,9 +39,12 @@ Imports:
     tcltk,
     Boruta,
     rpart,
+    plotly,
     rpart.plot
 Maintainer: Roland Hollo's <hollorol@gmail.com>
 Suggests: knitr,
     rmarkdown,
 VignetteBuilder: knitr
 ByteCompile: true
+RoxygenNote: 7.2.3
+Encoding: UTF-8

RBBGCMuso/NAMESPACE

@@ -11,6 +11,7 @@ export(copyMusoExampleTo)
 export(corrigMuso)
 export(createSoilFile)
 export(flatMuso)
+export(genEpc)
 export(getAnnualOutputList)
 export(getConstMatrix)
 export(getDailyOutputList)
@@ -19,7 +20,9 @@ export(getFilesFromIni)
 export(getyearlycum)
 export(getyearlymax)
 export(multiSiteCalib)
+export(musoCompareFiles)
 export(musoDate)
+export(musoGetValues)
 export(musoGlue)
 export(musoMapping)
 export(musoMappingFind)
@@ -40,6 +43,9 @@ export(saveAllMusoPlots)
 export(setupMuso)
 export(spinupMuso)
 export(supportedMuso)
+export(tuneMuso)
+export(tuneMusoServer)
+export(tuneMusoUI)
 export(updateMusoMapping)
 import(ggplot2)
 import(utils)
@@ -84,12 +90,38 @@ importFrom(lubridate,leap_year)
 importFrom(magrittr,'%<>%')
 importFrom(magrittr,'%>%')
 importFrom(openxlsx,read.xlsx)
+importFrom(plotly,add_trace)
+importFrom(plotly,plot_ly)
+importFrom(plotly,plotlyOutput)
+importFrom(plotly,renderPlotly)
 importFrom(rmarkdown,pandoc_version)
 importFrom(rmarkdown,render)
 importFrom(rpart,rpart)
 importFrom(rpart,rpart.control)
 importFrom(rpart.plot,rpart.plot)
 importFrom(scales,percent)
+importFrom(shiny,HTML)
+importFrom(shiny,actionButton)
+importFrom(shiny,checkboxInput)
+importFrom(shiny,fluidPage)
+importFrom(shiny,getShinyOption)
+importFrom(shiny,isolate)
+importFrom(shiny,mainPanel)
+importFrom(shiny,numericInput)
+importFrom(shiny,observeEvent)
+importFrom(shiny,radioButtons)
+importFrom(shiny,reactiveValues)
+importFrom(shiny,selectInput)
+importFrom(shiny,shinyApp)
+importFrom(shiny,shinyOptions)
+importFrom(shiny,sidebarLayout)
+importFrom(shiny,sidebarPanel)
+importFrom(shiny,tabPanel)
+importFrom(shiny,tabsetPanel)
+importFrom(shiny,tagList)
+importFrom(shiny,tags)
+importFrom(shiny,textAreaInput)
+importFrom(shiny,titlePanel)
 importFrom(stats,approx)
 importFrom(tcltk,tk_choose.files)
 importFrom(tibble,rownames_to_column)

RBBGCMuso/R/calibration.R

@@ -270,10 +270,14 @@ musoGlue <- function(presCalFile, w, delta = 0.17, settings=setupMuso(), paramet
 
     par(pari)
     dev.off()
-    maxParValues <- preservedCalibtop5[which.max(preservedCalibtop5$combined),]
+    maxParValues <- unlist(preservedCalibtop5[which.max(preservedCalibtop5$combined),])[1:length(paramIndex)]
     maxParIndexes <- paramIndex
-    write.csv(cbind.data.frame(calibrationPar=maxParValues,parameters=maxParIndexes),"maxLikelihood.csv")
+    maxLikelihoodParameters <- data.frame(parameter_index=maxParIndexes,parameter_value=maxParValues)
+    write.csv(cbind.data.frame(parameters=maxParIndexes, calibrationPar=maxParValues),
+              "maxlikelihood_parameters.csv")
+    cat("\n\n- A file containing the parameters with the maximum likelihood (maxlikelihood_parameters.csv) has been created.\n")
     write.csv(optRanges,"optRanges.csv")
+    cat("- GLUE interval values have been written into optRanges.csv\n")
     # browser()
     # There are some serious problems with this implementation. The uncertainity bouns are not for the parameters, but for the output values. The median is pointwise median for all simulation.
     # And the 95 and 5 percentile also.

RBBGCMuso/R/changeMuso.R

@@ -5,7 +5,7 @@
 #' @author Roland Hollos
 #' @export
 
-changemulline <- function(filePaths, calibrationPar, contents, src, outFiles=filePaths){
+changemulline <- function(filePaths, calibrationPar, contents, src=NULL, outFiles=filePaths){
     # browser()
     if(is.null(src)){
         src <- filePaths
@@ -31,3 +31,38 @@ changeByIndex <- function (rowIndex, parameter, fileStringVector){
     fileStringVector[i] <- changeNth(fileStringVector[i], h, parameter)        
     fileStringVector
 }
+
+
+#' musoGetValues 
+#' 
+#' Get values from a musofile by supplying muso indices
+#'
+#' @param filename The name of the musofile we want the value from (e.g. epc file)
+#' @param indices muso indices
+#' @usage musoGetValues(filename, indices)
+#' @export 
+
+musoGetValues <- function(filename, indices){
+    sapply(indices, function(index){
+               colIndex <- round((index*100) %% 10) + 1
+               rowIndex <- as.integer(index)
+               as.numeric(unlist(strsplit(readLines(filename)[rowIndex],split="\\s+"))[colIndex])
+
+})
+}
+
+#' musoCompareFiles 
+#' 
+#' A simple wrapper function based on musoGetValues where you can get multiple values from multiple files 
+#' using the supplied indices. It is useful for comparing files.
+#'
+#' @param  filenames The name of the files where you can get the data from
+#' @param indices muso indices
+#' @usage musoCompareFiles(filenames, indices) 
+#' @export 
+
+musoCompareFiles <- function(filenames, indices){
+    sapply(filenames, function(fn){
+        musoGetValues(fn,indices)
+    })
+}

RBBGCMuso/R/genEpc.R

@@ -29,7 +29,22 @@ randEpc <- function(parameterFile = "parameters.csv", location = "./epcDir",
     for(i in seq(iterations)){
         epcOut <- gsub("\\.",paste0("-",i,"."),basename(sourceEpc))
         changemulline(filePaths = basename(sourceEpc), calibrationPar = randVals[[1]],
-                      contents = randVals[[2]][i,],fileOut = epcOut, fileToChange = "epc")        
+                      contents = randVals[[2]][i,],outFiles = epcOut)        
     }
    setwd(currDir)
 }
+
+#' genEpc
+#'
+#' randEpc is a random epc creator based on musoMonte
+#' @author Roland HOLLOS
+#' @param sourceEpc the original epc file-the template
+#' @param parameters dataframe where in the first column there are the indices and the second column the values
+#' @param location output location directory
+#' @export
+
+genEpc <- function (sourceEpc, targetEpc, parameters) {
+   changemulline(filePaths=sourceEpc,outFiles=targetEpc,
+                 calibrationPar=parameters[,1],contents=parameters[,2]) 
+}
+

RBBGCMuso/R/multiSite.R

@@ -590,7 +590,7 @@ agroLikelihood <- function(modVector,measured){
 #' compareCalibratedWithOriginal
 #'
 #' This functions compareses the likelihood and the RMSE values of the simulations and the measurements
-#' @param key
+#' @param key keyword
 compareCalibratedWithOriginal <- function(key, modOld, modNew, mes,
                              likelihoods, alignIndexes, musoCodeToIndex, nameGroupTable,
                              groupFun){

RBBGCMuso/R/musoTime.R

@@ -2,12 +2,12 @@
 #'
 #' This function generates MuSo compatibla dates for the data
 #' @author Roland HOLLOS
-#' @param startYear
+#' @param startYear Start year of the simulations
-#' @param numYears
+#' @param numYears Number of the years of the simulation
-#' @param timestep
+#' @param timestep timestep of date creation
-#' @param combined
+#' @param combined using separate y m d columns or not?
-#' @param corrigated
+#' @param corrigated If leapyear ...
-#' @param format
+#' @param format "the date format"
 #' @importFrom lubridate leap_year
 #' @export
 

RBBGCMuso/R/normalMuso.R

@@ -90,9 +90,9 @@ normalMuso<- function(settings=NULL,parameters=NULL,timee="d",debugging=FALSE,lo
     
     if(!is.null(parameters)){
         switch(fileToChange,
-               "epc" = tryCatch(changemulline(filename = epc[1],calibrationPar,parameters), #(:DONE: trycatch :INSIDE: changeMuso.R)
+               "epc" = tryCatch(changemulline(epc[1],calibrationPar,parameters), #(:DONE: trycatch :INSIDE: changeMuso.R)
                                 error = function (e) {stop("Cannot change the epc file")}),
-               "ini" = tryCatch(changemulline(filename = iniInput[1],calibrationPar,parameters), #(:DONE: trycatch :INSIDE: changeMuso.R)
+               "ini" = tryCatch(changemulline(iniInput[1],calibrationPar,parameters), #(:DONE: trycatch :INSIDE: changeMuso.R)
                                 error = function (e) {stop("Cannot change the ini file")}),
                "both" = (stop("This option is not implemented yet, please choose epc or ini"))
                )

RBBGCMuso/R/plotMuso.R

@@ -68,9 +68,9 @@ plotMuso <- function(settings = NULL, variable = "all",
                                         stop("Cannot read binary output, please check if the output type is set 2 in the ini files!")})
         colnames(Reva) <- unlist(settings$outputVars[[1]])
         rownames(Reva) <- NULL
-        musoData <- cbind(musoDate(startYear = startYear,numYears = numberOfYears,combined = TRUE,corrigated=FALSE),
+        musoData <- cbind(musoDate(startYear = startYear,numYears = numberOfYears,combined = TRUE),
               rep(1:365,numberOfYears),
-              musoDate(startYear = startYear,numYears = numberOfYears,combined = FALSE,corrigated=FALSE),as.data.frame(Reva))
+              musoDate(startYear = startYear,numYears = numberOfYears,combined = FALSE),as.data.frame(Reva))
         colnames(musoData)[1:5]<-c("date","yearDay","year","day","month")
         musoData <-musoData %>%
             mutate(date=as.Date(as.character(date),"%d.%m.%Y"))
@@ -275,28 +275,29 @@ plotMusoWithData <- function(mdata, plotName=NULL,
                        modellSettings = settings,
                        startDate = startDate,
                        endDate = endDate, leapYear = leapYearHandling, continious = continious),envir=environment())
-    mesData <- numeric(settings$numYears*365)
+    # mesData <- numeric(settings$numYears*365)
-    k <- 1
+    # k <- 1
-    for(i in seq(mesData)){
+    # for(i in seq(mesData)){
-        if(i %in% modIndex){
+    #     if(i %in% modIndex){
-            mesData[i] <- measuredData[k]
+    #         mesData[i] <- measuredData[k]
-            k <- k + 1
+    #         k <- k + 1
-        } else {
+    #     } else {
-            mesData[i] <- NA
+    #         mesData[i] <- NA
-        }
+    #     }
-    }
+    # }
-    rm(k)
+    # rm(k)
     # modIndex and measuredData are created.
     ## measuredData is created
     ## baseData <- calibMuso(settings = settings, silent = silent, prettyOut = TRUE)[modIndex,]
-    baseData <- calibMuso(settings = settings, silent = silent, prettyOut = TRUE)
+    baseData <- calibMuso(settings = settings, silent = silent, prettyOut = TRUE)[modIndex,]
     baseData[,1] <- as.Date(baseData[,1],format = "%d.%m.%Y")
     selVarName <- colnames(baseData)[selVar]
     if(!all.equal(colnames(baseData),unique(colnames(baseData)))){
         notUnique <- setdiff((unlist(settings$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))
     }
-    mesData<-cbind.data.frame(baseData[,1],mesData)
+    # mesData<-cbind.data.frame(baseData[,1],mesData)
+    mesData<-cbind.data.frame(baseData[,1],measuredData)
     colnames(mesData) <- c("date", "measured")
     p <- baseData  %>%
         ggplot(aes_string("date",selVarName)) +

RBBGCMuso/R/rungetMuso.R

@@ -254,7 +254,7 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
         Reva <- corrigMuso(settings,Reva)
         rownames(Reva) <- musoDate(settings$startYear, settings$numYears)
     } else { 
-        rownames(Reva) <- musoDate(settings$startYear, settings$numYears, corrigated=FALSE)
+        rownames(Reva) <- musoDate(settings$startYear, settings$numYears) # TODO: Need fix
     }
 
     if(export!=FALSE){

RBBGCMuso/R/spinupMuso.R

@@ -52,9 +52,9 @@ spinupMuso <- function(settings=NULL, parameters=NULL, debugging=FALSE, logfilen
     
      if(!is.null(parameters)){
         switch(fileToChange,
-               "epc" = tryCatch(changemulline(filename = epc[1],calibrationPar,parameters), #(:INSIDE: changeMuso.R)
+               "epc" = tryCatch(changemulline(filePaths = epc[1],calibrationPar,parameters), #(:INSIDE: changeMuso.R)
                               error = function (e) {stop("Cannot change the epc file")}),
-               "ini" = tryCatch(changemulline(filename = iniInput[1],calibrationPar,parameters), #(:INSIDE: changeMuso.R)
+               "ini" = tryCatch(changemulline(filePaths = iniInput[1],calibrationPar,parameters), #(:INSIDE: changeMuso.R)
                               error = function (e) {stop("Cannot change the ini file")}),
                "both" = (stop("This option is not implemented yet, please choose epc or ini"))
                )

RBBGCMuso/R/tuner.R

@@ -0,0 +1,173 @@
+#' tuneMusoUI 
+#' 
+#' This is a simple parameter tuner function which works great in a flat directory systemj
+#'
+#' @param parameterFile optional, the parameter csv file
+#' @importFrom plotly plotlyOutput
+#' @importFrom shiny tags actionButton numericInput HTML checkboxInput titlePanel radioButtons textAreaInput fluidPage sidebarLayout sidebarPanel mainPanel getShinyOption tabsetPanel tabPanel tagList selectInput
+#' @usage ...
+#' @export 
+
+tuneMusoUI <- function(parameterFile = NULL, ...){
+    setwd(getShinyOption("musoRoot"))
+    dir.create("bck",showWarnings = FALSE)
+    file.copy("n.ini","bck/n.ini", overwrite=FALSE)
+    if(is.null(parameterFile)){
+        parameterFile <- "parameters.csv"
+    }
+    parameters <- read.csv(parameterFile, stringsAsFactors=FALSE)
+    settings <- setupMuso(...)
+    defaultValues <- musoGetValues(settings$epcInput[2],parameters[,2])            
+    fluidPage(
+        # tags$head(tags$style(HTML("#iniContainer {width: 80vw;}"))),
+        tags$head(tags$style(HTML("#contolp {height: 80vh;overflow-y:scroll;}"))),
+        titlePanel("Biome-BGCMuSo parameter tuner"),
+        sidebarLayout(
+            sidebarPanel(tabsetPanel(type="tabs",
+                tabPanel("params",
+                   checkboxInput("autoupdate","Automatic update"),
+                   tags$div(id="controlp",selectInput("ovar",
+                       label="Select output Variable",
+                       choices=settings$dailyOutputTable$name,
+                       width="40%"
+                       ),
+                    do.call(tagList,lapply(1:nrow(parameters),function(x){
+                                               numericInput(paste0("param_",x),
+                                                            parameters[x,1],
+                                                            defaultValues[x],
+                                                            step=defaultValues[x]/10,
+                                                            width="40%"
+                                               )
+}))),
+              tags$div(actionButton(inputId="runModel","Run MuSo"),
+                       radioButtons(inputId="destination",
+                                    label="reference or modified",
+                                    choiceValues=c("auto","prev","next"),
+                                    choiceNames=c("automatic","reference","modified")))),
+                tabPanel("ini",tags$div(id="iniContainer",
+                                        textAreaInput("inifile","Normal Ini file",
+                                                      value=paste(readLines(settings$iniInput[2]),
+                                                                  collapse="\n"))),
+                         actionButton(inputId="getOriginalIni", "Load original"),
+                         actionButton(inputId="overwriteIni", "overwrite")
+
+                )
+                )),
+            mainPanel(plotlyOutput(outputId="Result"))
+        ) 
+    )
+}
+
+#' tuneMusoServer 
+#' 
+#' Server program for tumeMuso
+#'
+#' @param input shiny input
+#' @param output shiny output
+#' @param session dinamic session management for shiny
+#' @importFrom shiny reactiveValues isolate observeEvent
+#' @importFrom plotly renderPlotly plot_ly add_trace
+#' @usage ...
+#' @export 
+
+tuneMusoServer <- function(input, output, session){
+
+    settings <- setupMuso()
+    dates <- as.Date(musoDate(settings$startYear, numYears=settings$numYears),"%d.%m.%Y") 
+
+    parameters <- read.csv("parameters.csv", stringsAsFactors=FALSE)
+
+    outputList <- vector(mode = "list", length = 2)
+    outputList <- reactiveValues()
+    outputList[['prev']] <- character(0)
+    outputList[['next']] <- character(0)
+
+
+    observeEvent(input$runModel,{
+
+                     paramVal <- sapply(1:nrow(parameters),function(x){
+                                            input[[paste0("param_", x)]]
+              })
+
+
+                     if(isolate(input$destination) == "auto"){
+                         outputList[['prev']] <- isolate(outputList[['next']]) 
+                         outputList[['next']] <- calibMuso(settings = settings,
+                                                           calibrationPar = parameters[,2],
+                                                           parameters = paramVal)       
+                     } else {
+                         outputList[[isolate(input$destination)]] <- calibMuso(settings = settings,
+                                                           calibrationPar = parameters[,2],
+                                                           parameters = paramVal)       
+
+                     }
+
+
+
+                     
+    })
+
+    observe({
+        if(input$autoupdate){
+                     paramVal <- sapply(1:nrow(parameters),function(x){
+                                            input[[paste0("param_", x)]]
+              })
+
+
+                     if(isolate(input$destination) == "auto"){
+                         outputList[['prev']] <- isolate(outputList[['next']]) 
+                         outputList[['next']] <- calibMuso(settings = settings,
+                                                           calibrationPar = parameters[,2],
+                                                           parameters = paramVal)       
+                     } else {
+                         outputList[[isolate(input$destination)]] <- calibMuso(settings = settings,
+                                                           calibrationPar = parameters[,2],
+                                                           parameters = paramVal)       
+
+                     }
+            
+        }
+    })
+
+
+    observe({
+        if(length(outputList[['next']])!=0){
+            output$Result <- renderPlotly(
+                                          {
+                                              p <- plot_ly()
+                                              if(length(outputList[['prev']])!=0){
+                                                  p <- add_trace(p, x=dates, y=outputList[['prev']][,input$ovar], type='scatter',
+                                                                    mode='lines')
+                                              }
+                                              add_trace(p, x=dates, y=outputList[['next']][,input$ovar], color="red", type='scatter',
+                                                                    mode='lines')
+                                          }
+            )
+
+
+        }
+    })
+
+    observeEvent(input$getOriginalIni,{
+                     updateTextAreaInput(session, "inifile", value=paste(readLines("bck/n.ini"),
+                                                                                              collapse="\n") )
+    })
+
+}
+
+
+#' tuneMuso
+#'
+#' launchApp launch the shiny app
+#' @param ... Other parameters for shinyApp function
+#' @importFrom shiny shinyApp shinyOptions
+#' @export
+tuneMuso <- function(directory = NULL,...){ 
+    shinyOptions(workdir = getwd())
+    if(is.null(directory)){
+        shinyOptions(musoRoot = ".")
+    } else {
+        shinyOptions(musoRoot = normalizePath(directory))
+    }
+    shinyApp(ui = tuneMusoUI(), server = tuneMusoServer, options = list(...))
+}

RBBGCMuso/man/calibrateMuso.Rd

@@ -24,7 +24,7 @@ calibrateMuso(
   naVal = NULL,
   postProcString = NULL,
   thread_prefix = "thread",
-  numCores = (parallel::detectCores() - 1),
+  numCores = max(c(parallel::detectCores() - 1, 1)),
   pb = txtProgressBar(min = 0, max = iterations, style = 3),
   maxLikelihoodEpc = TRUE,
   pbUpdate = setTxtProgressBar,

RBBGCMuso/man/changemulline.Rd

@@ -4,7 +4,13 @@
 \alias{changemulline}
 \title{changemulline}
 \usage{
-changemulline(filePaths, calibrationPar, contents, src, outFiles = filePaths)
+changemulline(
+  filePaths,
+  calibrationPar,
+  contents,
+  src = NULL,
+  outFiles = filePaths
+)
 }
 \description{
 The function uses the previous changspecline function to operate.

RBBGCMuso/man/compareCalibratedWithOriginal.Rd

@@ -16,6 +16,9 @@ compareCalibratedWithOriginal(
   groupFun
 )
 }
+\arguments{
+\item{key}{keyword}
+}
 \description{
 This functions compareses the likelihood and the RMSE values of the simulations and the measurements
 }

RBBGCMuso/man/createSoilFile.Rd

@@ -3,6 +3,16 @@
 \name{createSoilFile}
 \alias{createSoilFile}
 \title{createSoilFile}
+\usage{
+createSoilFile(
+  lat,
+  lon,
+  outputFile = "recent.soi",
+  method = "constant",
+  apiURL,
+  template = system.file("examples/hhs/hhs.soi", package = "RBBGCMuso")
+)
+}
 \description{
 This function collects soil data from a given restapi, de default is soilGrid
 }

RBBGCMuso/man/genEpc.Rd

@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/genEpc.R
+\name{genEpc}
+\alias{genEpc}
+\title{genEpc}
+\usage{
+genEpc(sourceEpc, targetEpc, parameters)
+}
+\arguments{
+\item{sourceEpc}{the original epc file-the template}
+
+\item{parameters}{dataframe where in the first column there are the indices and the second column the values}
+
+\item{location}{output location directory}
+}
+\description{
+randEpc is a random epc creator based on musoMonte
+}
+\author{
+Roland HOLLOS
+}

RBBGCMuso/man/getSoilDataFull.Rd

@@ -3,6 +3,9 @@
 \name{getSoilDataFull}
 \alias{getSoilDataFull}
 \title{getSoilDataFull}
+\usage{
+getSoilDataFull(lat, lon, apiURL)
+}
 \description{
 This function collects soil data from a given restapi, de default is soilGrid
 }

RBBGCMuso/man/musoCompareFiles.Rd

@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/changeMuso.R
+\name{musoCompareFiles}
+\alias{musoCompareFiles}
+\title{musoCompareFiles}
+\usage{
+musoCompareFiles(filenames, indices)
+}
+\arguments{
+\item{filenames}{The name of the files where you can get the data from}
+
+\item{indices}{muso indices}
+}
+\description{
+A simple wrapper function based on musoGetValues where you can get multiple values from multiple files 
+using the supplied indices. It is useful for comparing files.
+}

RBBGCMuso/man/musoDate.Rd

@@ -13,6 +13,19 @@ musoDate(
   prettyOut = FALSE
 )
 }
+\arguments{
+\item{startYear}{Start year of the simulations}
+
+\item{numYears}{Number of the years of the simulation}
+
+\item{combined}{using separate y m d columns or not?}
+
+\item{timestep}{timestep of date creation}
+
+\item{corrigated}{If leapyear ...}
+
+\item{format}{"the date format"}
+}
 \description{
 This function generates MuSo compatibla dates for the data
 }

RBBGCMuso/man/musoGetValues.Rd

@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/changeMuso.R
+\name{musoGetValues}
+\alias{musoGetValues}
+\title{musoGetValues}
+\usage{
+musoGetValues(filename, indices)
+}
+\arguments{
+\item{filename}{The name of the musofile we want the value from (e.g. epc file)}
+
+\item{indices}{muso indices}
+}
+\description{
+Get values from a musofile by supplying muso indices
+}

RBBGCMuso/man/readObservedData.Rd

@@ -11,7 +11,9 @@ readObservedData(
   leapYearHandling = TRUE,
   convert.var = NULL,
   convert.scalar = 1,
-  convert.fun = (function(x) {     x * convert.scalar }),
+  convert.fun = (function(x) {
+     x * convert.scalar
+ }),
   convert.file = NULL,
   filterCol = NULL,
   filterVal = 1,

RBBGCMuso/man/setupMuso.Rd

@@ -42,7 +42,7 @@ nitInput=NULL, iniInput=NULL, epcInput=NULL)
 
 \item{plougInput}{Via the plougInput parameter, the user can specify the location of the file that contains the ploughing information. By default the package reads this information from the INI files.}
 
-\item{fertInput}{Via the fertInput parameter, ythe user can specify the location of the file that contains the fertilizing information. By default the package reads this information from the INI files.}
+\item{fertInput}{Via the fertInput parameter, the user can specify the location of the file that contains the fertilizing information. By default the package reads this information from the INI files.}
 
 \item{irrInput}{Via the irrInput parameter, the user can specify the location of the file that contains the irrigation information. By default the package reads this information from the INI files.}
 

RBBGCMuso/man/tuneMuso.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tuner.R
+\name{tuneMuso}
+\alias{tuneMuso}
+\title{tuneMuso}
+\usage{
+tuneMuso(directory = NULL, ...)
+}
+\arguments{
+\item{...}{Other parameters for shinyApp function}
+}
+\description{
+launchApp launch the shiny app
+}

RBBGCMuso/man/tuneMusoServer.Rd

@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tuner.R
+\name{tuneMusoServer}
+\alias{tuneMusoServer}
+\title{tuneMusoServer}
+\usage{
+...
+}
+\arguments{
+\item{input}{shiny input}
+
+\item{output}{shiny output}
+
+\item{session}{dinamic session management for shiny}
+}
+\description{
+Server program for tumeMuso
+}

RBBGCMuso/man/tuneMusoUI.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tuner.R
+\name{tuneMusoUI}
+\alias{tuneMusoUI}
+\title{tuneMusoUI}
+\usage{
+...
+}
+\arguments{
+\item{parameterFile}{optional, the parameter csv file}
+}
+\description{
+This is a simple parameter tuner function which works great in a flat directory systemj
+}

RBBGCMuso/man/updateMusoMapping.Rd

@@ -7,7 +7,7 @@
 updateMusoMapping(excelName, dest = "./", version = getOption("RMuso_version"))
 }
 \arguments{
-\item{excelName}{Name of the excelfile which contains the parameters}
+\item{excelName}{Name of the Excel file which contains the parameters}
 }
 \value{
 The output code-variable matrix, and also the function changes the global variable