Clearing the environment and exception handling

.gitignore

@@ -5,3 +5,4 @@
 *.o
 *.a
 *~
+*.dll

RBBGCMuso/NAMESPACE

@@ -54,6 +54,7 @@ importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
 importFrom(limSolve,xsample)
 importFrom(magrittr,'%<>%')
+importFrom(rmarkdown,pandoc_version)
 importFrom(rmarkdown,render)
 importFrom(scales,percent)
 importFrom(tcltk,tk_choose.files)

RBBGCMuso/R/parametersweep.R

@@ -20,9 +20,9 @@ paramSweep <- function(inputDir="./",
                        outVar="daily_gpp",
                        htmlOutName = "paramsweep.html"){
     
-    if(is.null(rmarkdown::pandoc_version())){
-        stop("In order to use parameterSweep you have to have pandoc (1.12.3+) installed or run this function from Rstudio\n
-You can download pandoc from here: 'https://pandoc.org/', or Rstudio from here: 'https://www.rstudio.com/'")
+    if(is.null(pandoc_version())){
+        stop("In order to use parameterSweep you have to have\n pandoc (1.12.3+) installed or run this function from Rstudio\n
+You can download pandoc from here: 'https://pandoc.org/',\n or Rstudio from here: 'https://www.rstudio.com/'")
     }
     currDir <- getwd()
     opSystem <- Sys.info()[[1]]

RBBGCMuso/src/musoIO.cpp~

@@ -1,128 +0,0 @@
-#include <Rcpp.h>
-#include <numeric>
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <new>
-#include <algorithm>
-#include <numeric>
-#include <ctime>
-
-
-using namespace Rcpp;
-using namespace std;
-// [[Rcpp::plugins(cpp11)]]
-
-// [[Rcpp::export]]
-IntegerVector getWritePositions(double a){
-  //getWritePositions returns abstract rownumbers to rownumbers and other indexek
-  // getWritePositions(173.72) = c(173,7,3) // it supports up to 10 subvalues
-  IntegerVector outVec(3); // outVec is vector of rowIndex, colNumber, choosen Index
-  a = a * 100;
-  outVec[0] = (int)a / 100;
-  outVec[1] = ((int)a /10) % 10 + 1;
-  outVec[2] = (int)a % 10;
-  
-  return outVec;
-}
-
-IntegerMatrix getPositions(NumericVector v){
-
-  int numVari = v.size();
-  IntegerMatrix indexek(numVari,3);
-  IntegerVector positions(3);
-  for(int i = 0; i < numVari; ++i){
-    positions = getWritePositions(v[i]);
-    indexek(i,_) = positions;
-  }
-  return indexek;
-}
-
-
-void goNextLine(std::ifstream& fin){
-  char c='a';
-  while((c!='\n')&&(fin.get(c))){}
-}
-
-#define NEXT goNextLine(fin)
-int fileChanger(std::string inFile, std::string outFile, IntegerVector linum, NumericVector num, IntegerVector colnum, IntegerVector colindex){
-  std::ifstream fin(inFile);
-  if (!fin.is_open()) {
-    stop("Cannot open " + inFile + " for read");
-  }
-  std::ofstream fot(outFile);
-
-  if (!fot.is_open()) {
-    stop("Cannot open " + outFile + " for read");    
-  }
-  string tempString;
-
-  int counter = 1;
-  int counterV = 0;
-  while (!fin.eof()) {
-
-
-    if(counter == linum[counterV]){
-      if(colnum[counterV]==0){
-	fot << num[counterV] << "\n";
-	NEXT;
-      } else {
-	double * elements;
-	elements = new double [colnum[counterV]];
-	if(linum[counterV]!=linum[counterV+1]){
-	  for(int i=0;i<colnum[counterV];++i){
-
-	    fin >> elements[i];
-	    if(i==colindex[counterV]){
-	      elements[i]=num[counterV];
-	    }
-	    fot << elements[i] << '\t';
-	  }
-	} else {
-	  int k=0;
-	  for(int i=0;i<colnum[counterV];++i){
-
-	    fin >> elements[i];
-	    if(i==colindex[counterV + k]){
-	      elements[i]=num[counterV + k];
-	      if(linum[counterV +k]==linum[counterV + k + 1]){
-		++k;
-	      }
-	    }
-	    fot << elements[i] << '\t';
-
-	  }
-	  counterV = counterV + k;
-	}
-
-	fot << "\n";
-	delete [] elements;
-	NEXT;
-      }
-      ++counterV;
-    } else {
-      getline(fin,tempString);
-      fot << tempString << "\n";
-    }
-    ++counter;
-  }
-  fin.close();
-  fot.close();
-  return 0;
-}
-
-//' changeMusoC
-//' 
-//' This function is fastly randomize values based on min and max values
-//' @importFrom Rcpp evalCpp
-//' @useDynLib RBBGCMuso
-//' @param inFile is the big matrix
-//' @param outFile is the small matrix
-//' @export
-// [[Rcpp::export]]
-void changeMusoC(std::string inFile, std::string outFile, NumericMatrix inMat){
-  int  numChanges = inMat.nrow();
-  IntegerMatrix indexes(numChanges,3);
-  indexes = getPositions(inMat(_,0));
-  fileChanger(inFile,outFile,indexes(_,0),inMat(_,1),indexes(_,1),indexes(_,2));
-}

RBBGCMuso/src/musoRandomizer.cpp~

@@ -1,167 +0,0 @@
-#include <Rcpp.h>
-#include <numeric>
-#include <iostream>
-#include <algorithm>
-#include <numeric>
-#include <ctime>
-
-
-using namespace Rcpp;
-using namespace std;
-// [[Rcpp::plugins(cpp11)]]
-
-
-
-NumericMatrix randTypeZero(NumericMatrix m){
-  /*
-    A typical matrix like m:
-
-    | INDEX | DEPENDENCE | MIN  | MAX  |
-    |-------+------------+------+------|
-    |    21 |          0 | 0    | 364  |
-    |    57 |          0 | bkla | asdf |
-   
-   This randomization type is the easiest,
-   the function produces a matrix which first
-   column contains the indexes, and the second contains
-   random numbers, which was drawn from uniform distribution
-   with the corresponding min and max parameters, specified
-   by the matrix m.
-
-   */
-  int n=m.nrow()-1;
-  NumericMatrix M(n+1,2);
-  M(_,0)=m(_,0);
-  for(int i=0;i<=n;++i){
-    double min=m(i,2);
-    double max=m(i,3);
-    M(i,1)=runif(1,min,max)[0];
-  }
-  return M;
-}
-
-// [[Rcpp::export]]
-NumericMatrix randTypeOne(NumericMatrix m){
-  /*
-    The stucture of matrix m here is the same
-    as in randTypeZero.
-
-
-
-   */
-
-  
-  NumericVector dependence=m(_,2);
-  int n=m.nrow()-1;
-  NumericMatrix M(n+1,2);
-  M(_,0)=m(_,0);
-  M(0,1)=runif(1,m(0,2),m(0,3))[0];
-  for(int i=1;i<=n;++i){
-    int dep=m(i,1)-1;
-    double min=max(M(dep,1),m(i,2));
-    double max=m(i,3);
-    M(i,1)=runif(1,min,max)[0];
-  }
-  return M;
-}
-
-
-
-IntegerVector orderDec(NumericVector v){
-  Function f("order");
-  return f(v,_["decreasing"]=1);
-}
-
-NumericMatrix randTypeTwo(NumericMatrix m){
-  int n=m.nrow()-1;
-  int N=n-1;
-  NumericMatrix mv=m(Range(0,(n-1)),_);
-  NumericVector dependence=m(_,2);
-  NumericMatrix M(n+1,2);
-  M(_,0)=m(_,0);
-  IntegerVector indexes=orderDec(mv(_,2));
-  NumericVector sorban=mv(_,2);
-  sorban.sort(true);
-  NumericVector sor=cumsum(sorban);
-  sor.sort(true);
-  for(int i=0;i<=N;++i){
-    if(i!=N){
-      mv((indexes[i]-1),3)-= sor[i+1];
-    }
-  }
-  
-  double rollingNumber=0;
-  
-  for(int i=0;i<=N;++i){
-    double minimum=mv((indexes[i]-1),2);
-    double maximum=mv((indexes[i]-1),3)-rollingNumber;
-    M(i,1)=runif(1,minimum,maximum)[0];
-    rollingNumber+=M(i,1);
-    // cout << "minimum:\t" << minimum << endl;
-    // cout << "maximum:\t" << maximum << endl;
-    // cout << "indexes:\t" << indexes[i] << endl;
-    // cout << "rollingNumber:\t" << rollingNumber << endl;
-    // cout << "choosen:\t" << M(i,1) <<endl;
-    // cout << "sor:\t" << sor <<endl;
-    // cout << "\n\n\n" << mv;
-  }
-  M(n,1)=1-rollingNumber;
-  return M;
-}
-
-
-
-
-NumericMatrix copyMatSpec(NumericMatrix A, NumericMatrix B, int u, int v){
-  int k=0;
-  for(int i=u;i<=v;++i){
-    A(i,_)=B(k,_);
-    k+=1;
-  }
-  return A;
-}
-
-//' musoRandomizer
-//' 
-//' This function is fastly randomize values based on min and max values,
-//' and row indexes.
-//' @importFrom Rcpp evalCpp
-//' @useDynLib RBBGCMuso
-//' @param A is the big matrix
-//' @param B is the small matrix
-//' @export
-// [[Rcpp::export]]
-NumericMatrix musoRandomizer(NumericMatrix A, NumericMatrix B){
-  NumericMatrix M(A.nrow(),2);
-  int nGroup = B.nrow()-1;
-  int k=0; 
-  for(int i=0;i<=nGroup;++i)
-  {
-    int b=B(i,0)-1;
-    int till=b+k;
-    int t=B(i,1);
-    // cout << b << "\t" << t <<endl;
-    switch(t){
-    case 0:
-      M=copyMatSpec(M,randTypeZero(A(Range(k,till),_)),k,till);
-      // cout << M << endl;
-      break;
-    case 1:
-      M=copyMatSpec(M,randTypeOne(A(Range(k,till),_)),k,till);
-      // cout << M << endl;
-      break;
-    case 2:
-      M=copyMatSpec(M,randTypeTwo(A(Range(k,till),_)),k,till);
-      // cout << M << endl;
-      break;
-    }
-    k=till+1;
-    // cout << k << endl;
-  }
-  return M;
-}
-
-std::string concatenate(std::string A, std::string B){
-  std::string C = A + B;
-  return C;
-}