From cfd6a1f7be1b523ebf5022385574fe2c3a9ac2f1 Mon Sep 17 00:00:00 2001
From: hollorol <hollorol@gmail.com>
Date: Tue, 19 Feb 2019 15:44:26 +0100
Subject: [PATCH] use of testthat and post processing

---
 RBBGCMuso/R/calibMuso.R                  |  13 ++++++++++---
 RBBGCMuso/R/postProc.R                   |  10 ++++++++++
 RBBGCMuso/inst/examples/hhs/muso         | Bin
 RBBGCMuso/inst/tests/test_postProcMuso.R |  21 +++++++++++++++++++++
 RBBGCMuso/man/optiMuso.Rd                |  12 ++++++------
 5 files changed, 47 insertions(+), 9 deletions(-)
 create mode 100644 RBBGCMuso/R/postProc.R
 mode change 100644 => 100755 RBBGCMuso/inst/examples/hhs/muso
 create mode 100644 RBBGCMuso/inst/tests/test_postProcMuso.R

diff --git a/RBBGCMuso/R/calibMuso.R b/RBBGCMuso/R/calibMuso.R
index 8deb21c..10938fd 100644
--- a/RBBGCMuso/R/calibMuso.R
+++ b/RBBGCMuso/R/calibMuso.R
@@ -31,7 +31,8 @@ calibMuso <- function(settings=NULL, calibrationPar=NULL,
                       silent=FALSE, aggressive=FALSE,
                       keepBinary=FALSE,
                       binaryPlace="./", fileToChange="epc",
-                      skipSpinup = TRUE, modifyOriginal =FALSE, prettyOut = FALSE){
+                      skipSpinup = TRUE, modifyOriginal =FALSE, prettyOut = FALSE,
+                      postProcString = NULL){ #
 ########################################################################
 ###########################Set local variables and places###############
 ########################################################################
@@ -321,6 +322,9 @@ calibMuso <- function(settings=NULL, calibrationPar=NULL,
         stop("Modell Failure")
     }
 
+    
+
+    
     if(timee=="d"){
         if(!prettyOut){
             colnames(Reva) <- unlist(settings$outputVars[[1]])
@@ -338,7 +342,9 @@ calibMuso <- function(settings=NULL, calibrationPar=NULL,
             colnames(Reva) <- unlist(settings$outputVars[[2]])
     }
 
-
+    if(!is.null(postProcString)){
+        Reva <- postProcMuso(Reva,postProcString)
+    }
 
     ## if(leapYear){
     ##     Reva <- corrigMuso(settings,Reva)
@@ -372,5 +378,6 @@ calibMuso <- function(settings=NULL, calibrationPar=NULL,
         
     } else{
         setwd(whereAmI)
-        return(Reva)}
+        return(Reva)
+    }
 }
diff --git a/RBBGCMuso/R/postProc.R b/RBBGCMuso/R/postProc.R
new file mode 100644
index 0000000..502cece
--- /dev/null
+++ b/RBBGCMuso/R/postProc.R
@@ -0,0 +1,10 @@
+postProcMuso  <- function(modelData, procString){
+    cNames <- colnames(modelData)
+    tocalc <- gsub("(@)(\\d)","modelData[,\\2]",procString)
+    newVarName <- gsub("\\s","",unlist(strsplit(procString,"<-"))[1])
+    assign(newVarName,eval(parse(text = unlist(strsplit(tocalc,"<-"))[2])))
+    modelData <- cbind.data.frame(modelData,eval(parse(text = newVarName)))
+    colnames(modelData) <- c(cNames,newVarName)
+    modelData
+}
+
diff --git a/RBBGCMuso/inst/examples/hhs/muso b/RBBGCMuso/inst/examples/hhs/muso
old mode 100644
new mode 100755
diff --git a/RBBGCMuso/inst/tests/test_postProcMuso.R b/RBBGCMuso/inst/tests/test_postProcMuso.R
new file mode 100644
index 0000000..1234d0f
--- /dev/null
+++ b/RBBGCMuso/inst/tests/test_postProcMuso.R
@@ -0,0 +1,21 @@
+context("Post processing")
+library(testthat)
+library(RBBGCMuso)
+setwd(system.file("examples/hhs","",package = "RBBGCMuso"))
+
+test_that("Post processing string",{
+    testMatrix1 <- data.frame(first = rep(1,5), second = rep(2,5), third = rep(3,5))
+    testMatrix1c <- testMatrix1 
+    testMatrix1c[,"newCol"] <- testMatrix1c[,2] + 3 * testMatrix1c[,3] 
+    expect_equal(postProcMuso(testMatrix1,"newCol <- @2 + 3*@3"),testMatrix1c)
+})
+
+test_that("calibMuso with postprocessing",{
+    model <- calibMuso(skipSpinup = FALSE, silent = TRUE)
+    modelc<- model
+    newCol <- modelc[,1]
+    modelc<- cbind.data.frame(modelc,newCol)
+    modelc[,"newCol"]<- model[,5]+3*model[,7]
+    expect_equal(calibMuso(skipSpinup = FALSE,silent = TRUE, postProcString = "newCol <- @5 + 3* @7"), modelc)
+})
+
diff --git a/RBBGCMuso/man/optiMuso.Rd b/RBBGCMuso/man/optiMuso.Rd
index 819e91e..85ab4b3 100644
--- a/RBBGCMuso/man/optiMuso.Rd
+++ b/RBBGCMuso/man/optiMuso.Rd
@@ -5,11 +5,11 @@
 \title{optiMuso}
 \usage{
 optiMuso(measuredData, parameters = NULL, startDate, endDate,
-  formatString = "\%Y-\%m-\%d", leapYear = TRUE, dataVar,
+  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))) }, calPar = 3009)
+  y) {     exp(-sqrt(mean((x - y)^2))) }, continious, modelVar = 3009)
 }
 \arguments{
 \item{parameters}{b}
@@ -20,8 +20,6 @@ optiMuso(measuredData, parameters = NULL, startDate, endDate,
 
 \item{formatString}{a}
 
-\item{leapYear}{b}
-
 \item{outLoc}{c}
 
 \item{settings}{e}
@@ -36,8 +34,6 @@ optiMuso(measuredData, parameters = NULL, startDate, endDate,
 
 \item{likelihood}{d}
 
-\item{calPar}{a}
-
 \item{measuredDataFile}{a}
 
 \item{sep}{c}
@@ -49,6 +45,10 @@ optiMuso(measuredData, parameters = NULL, startDate, endDate,
 \item{selVar}{c}
 
 \item{pretag}{a}
+
+\item{calPar}{a}
+
+\item{leapYear}{b}
 }
 \description{
 This function calculates the -users specified- likelihood for random model input.