library_size_estimates.hpp

/*    Copyright (C) 2014 University of Southern California and
 *                       Andrew D. Smith and Timothy Daley
 *
 *    Authors: Andrew D. Smith and Timothy Daley
 *
 *    This program is free software: you can redistribute it and/or modify
 *    it under the terms of the GNU General Public License as published by
 *    the Free Software Foundation, either version 3 of the License, or
 *    (at your option) any later version.
 *
 *    This program is distributed in the hope that it will be useful,
 *    but WITHOUT ANY WARRANTY; without even the implied warranty of
 *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *    GNU General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

#ifndef LIBRARY_SIZE_ESTIMATES_HPP
#define LIBRARY_SIZE_ESTIMATES_HPP

#include <vector>
#include <numeric>

double
chao87_lowerbound_unobserved(const std::vector<double> &counts_hist);

double 
cl92_estimate_unobserved(const std::vector<double> &counts_hist);

double 
cl92_truncated_estimate_unobserved(const std::vector<double> &counts_hist,
				   const size_t truncation_count);

double
harris_3moments_unobserved(const bool VERBOSE,
			   const std::vector<double> &counts_hist);

double
harris_newton_unobserved(const bool VERBOSE,
			 const std::vector<double> &counts_hist,
			 const double tolerance,
			 const size_t max_iter,
			 const size_t n_points);


double
quadrature_unobserved_lower_bound(const bool VERBOSE,
				  const std::vector<double> &counts_hist,
				  const double tolerance,
				  const size_t max_iter,
				  size_t &n_points);

double
quadrature_unobserved_upper_bound(const bool VERBOSE,
				  const std::vector<double> &counts_hist,
				  const double tolerance,
				  const size_t max_iter,
				  const double lower_limit,
				  size_t &n_points);

double
NegBin_quadrature_unobserved(const bool VERBOSE,
			     const std::vector<double> &counts_hist,
			     const double tolerance,
			     const size_t max_iter,
			     size_t &n_points);


#endif