added shannonrange calc.

[mothur.git] / shannonrange.h

diff --git a/shannonrange.h b/shannonrange.h
index 2123e05928c0be0bef9db1f18dbcffae0d3940fe..c5acd69096ba04cd3e9c5edece2047f2ff9f90ba 100644 (file)
--- a/shannonrange.h
+++ b/shannonrange.h
@@ -6,6 +6,13 @@
 //  Copyright (c) 2014 Schloss Lab. All rights reserved.
 //
 
+/*
+ 1] Haegeman, B., Hamelin, J., Moriarty, J., Neal, P., Dushoff, J., & Weitz, J. S. (2013). Robust estimation of microbial diversity in theory and in practice. The ISME journal, 7(6), 1092–1101.
+ [2] Hill, M. O. (1973). Diversity and evenness: A unifying notation and its consequences. Ecology, 54(2), 427–432.
+ [3] Orlitsky, A., Santhanam, N. P., & Zhang, J. (2003). Always Good Turing: Asymptoti- cally optimal probability estimation. Science, 302(5644), 427–431.
+ [4] Roesch, L. F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K., Kent, A. D., et al. (2007). Pyrosequencing enumerates and contrasts soil microbial diversity. The ISME Journal, 1(4), 283–290.
+ */
+
 #ifndef Mothur_shannonrange_h
 #define Mothur_shannonrange_h
 
@@ -16,10 +23,12 @@
 class RangeShannon : public Calculator  {
        
 public:
-       RangeShannon() : Calculator("rangeshannon", 3, false) {};
+       RangeShannon(int a) : alpha(a), Calculator("rangeshannon", 3, false) {};
        EstOutput getValues(SAbundVector*);
        EstOutput getValues(vector<SharedRAbundVector*>) {return data;};
-       string getCitation() { return "http://www.mothur.org/wiki/rangeshannon"; }
+       string getCitation() { return "Haegeman, B., Hamelin, J., Moriarty, J., Neal, P., Dushoff, J., & Weitz, J. S. (2013). Robust estimation of microbial diversity in theory and in practice. The ISME journal, 7(6), 1092–1101., http://www.mothur.org/wiki/rangeshannon"; }
+private:
+    int alpha;
 };
 
 /***********************************************************************/