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################################################################################
# Copyright (c) 2015 Genome Research Ltd.
#
# Author: Nicola Roberts <nr3@sanger.ac.uk>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License version 3 as published by the Free Software
# Foundation.
#
# 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 <http://www.gnu.org/licenses/>.
#
# This R package is adapted from MATLAB and C code written by Yee Whye Teh, downloaded from
# http://www.stats.ox.ac.uk/~teh/research/npbayes/npbayes-r21.tgz
#
# Copyright statement on original code:
# ===============================================================
# (C) Copyright 2004, Yee Whye Teh (ywteh -at- eecs -dot- berkeley -dot- edu)
# http://www.cs.berkeley.edu/~ywteh
#
# Permission is granted for anyone to copy, use, or modify these
# programs and accompanying documents for purposes of research or
# education, provided this copyright notice is retained, and note is
# made of any changes that have been made.
#
# These programs and documents are distributed without any warranty,
# express or implied. As the programs were written for research
# purposes only, they have not been tested to the degree that would be
# advisable in any important application. All use of these programs is
# entirely at the user's own risk.
# ===============================================================
#
################################################################################
File: R/aaa-classes-input.R
Copyright: 2015 Nicola D Roberts
File: R/aaa-classes-output.R
Copyright: 2015 Nicola D Roberts
File: R/aaa-generics-input.R
Copyright: 2015 Nicola D Roberts
File: R/aaa-generics-output.R
Copyright: 2015 Nicola D Roberts
File: R/cull_posterior_samples.R
Copyright: 2015 Nicola D Roberts
File: R/dp_activate.R
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/dp_activate.m by Yee Whye Teh
File: R/dp_freeze.R
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/dp_freeze.m by Yee Whye Teh
File: R/hdp.R
Copyright: 2015 Nicola D Roberts
File: R/hdp_addconparam.R
Copyright: 2015 Nicola D Roberts
File: R/hdp_adddp.R
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/hdp_adddp.m by Yee Whye Teh
File: R/hdp_extract_comp_multi.R
Copyright: 2015 Nicola D Roberts
File: R/hdp_extract_comp_single.R
Copyright: 2015 Nicola D Roberts
File: R/hdp_getstate.R
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/hdp_getstate.m by Yee Whye Teh
File: R/hdp_init.R
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/hdp_init.m by Yee Whye Teh
File: R/hdp_multi_chain.R
Copyright: 2015 Nicola D Roberts
File: R/hdp_posterior.R
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/hdp_posterior.m by Yee Whye Teh
File: R/hdp_prior_init.R
Copyright: 2016 Nicola D Roberts
File: R/hdp_quick_init.R
Copyright: 2015 Nicola D Roberts
File: R/hdp_setdata.R
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/hdp_setdata.m by Yee Whye Teh
File: R/iterate.R
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/hdp_iterate.m by Yee Whye Teh
File: R/plot_chain.R
Copyright: 2015 Nicola D Roberts
File: R/plot_components.R
Copyright: 2015 Nicola D Roberts
File: R/stirling.R
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/utilities/stirling.m by Yee Whye Teh
File: R/utilities.R
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/private/check*.m by Yee Whye Teh
Comment: Adapted from npbayesr21/distributions/multinomial/Multinomial*.m by Yee Whye Teh
Comment: Adapted from npbayesr21/hdpmix/private/qq_addclass.m by Yee Whye Teh
Comment: Adapted from npbayesr21/utilities/randnumtable.m by Yee Whye Teh
Comment: Adapted from npbayesr21/utilities/randstick.m by Yee Whye Teh
File: R/utilities_nr3.R
Copyright: 2015 Nicola D Roberts
File: R/zzz.R
Copyright: 2015 Nicola D Roberts
File: src/R-base.c
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/base.c by Yee Whye Teh
File: src/R-conparam.c
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/conparam.c by Yee Whye Teh
File: src/R-dp.c
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/dp.c by Yee Whye Teh
File: src/R-hdp.c
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/hdp.c by Yee Whye Teh
File: src/R-hdpMultinomial_iterate.c
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/hdpmix/hdpMultinomial_iterate.c by Yee Whye Teh
File: src/R-multinomial.c
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/distributions/multinomial/multinomial.c by Yee Whye Teh
File: src/R-multinomial.c
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/distributions/multinomial/multinomial.c by Yee Whye Teh
File: src/R-utils.c
Copyright: 2004 Yee Whye Teh
2015 Nicola D Roberts
Comment: Adapted from npbayesr21/utilities/mxutils.c by Yee Whye Teh
File: src/randutils.c
Copyright: 2004 Yee Whye Teh
Comment: Original in npbayesr21/utilities/randutils.c by Yee Whye Teh