Squashed 'pystan/stan/' changes from e19382d..cc82d51

cc82d51 Merge pull request #131 from stan-dev/feature/logCDF_logCCDF
b3b3e35 Merge pull request #161 from stan-dev/feature/eigen-3.2
5877f74 Merge pull request #145 from stan-dev/feature/print_tweaks
8beb975 updated eigen lib to 3.2.0 from 3.1.3 and changed ref in makefile
22900fd added cdf_log and ccdf_log for rayleigh and fixed function signatures
ba9dfef Merge branch 'develop' of https://github.com/stan-dev/stan into develop
477697d Merge branch 'develop' into feature/logCDF_logCCDF
8f82d9d Merge pull request #157 from stan-dev/feature/boost-1.54.0
a300598 Merge pull request #154 from stan-dev/feature/update-bugs-examples
b662180 Merge pull request #156 from stan-dev/feature/issue-130
7fa8e33 Merge pull request #155 from stan-dev/feature/issue-112
3bb9bbf updated to boost 1.54, fixed includes for round and trunc, replaced log determinant cerr writes with stan error handling
b7c550d Merge branch 'develop' of https://github.com/stan-dev/stan into develop
3341517 changed EXPECT_EQ to EXPECT_FLOAT_EQ for floating-point tests in reader_test
60a263c Merge branch 'develop' into feature/issue-112
56f4831 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-112
9d5cb9a added includes to fix test-headers failure
23a3b1a Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-130
efd3bf1 fix is code complete and passing new tests
5101878 Merge pull request #144 from stan-dev/feature/issue-109
ade8a8d Merge branch 'develop' into feature/issue-109
2a4e25c Merge branch 'develop' of https://github.com/stan-dev/stan into develop
72462fa Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-112
408835b bugs example v2/endo vectorization
26d2fd9 bugs example v2/ice uses poisson+log
af6ee08 bugs example v2/alli vectorization
2a14e2a bugs example v1/salm uses poisson_log
e77f684 bugs example v2/air use binomial_log
a72815d bugs example v1/oxford uses poisson_log
d8e20a7 bugs example vol1/epil uses poisson_log
f4265c4 remove more commented-out lines
ff285df removing improper model from list of .PRECIOUS
862d183 fixing the make target for executables
b1e1f55 adding precious to improper.exe
10d1445 add minipage to fitem so that function args can have multiple lines
686f904 adding back the target for Windows models
a5db3ad updating make target
1fbd95e Merge pull request #146 from stan-dev/feature/issue-133
7efdd35 fixed merge with develop, just usings in generator
add0b15 cleaned up model generation code further by eliminating utility write methods and fixed bug in mcmc_writer by fishing the RNG through so that generated quantities could be replicated
6de4197 removed commented out junk code from generator
9cae270 simplified assign and moved to stan::math from stan::agrad, removed assign_to_var and specializations for agrad, more tests related to assign
1db18cf Merge pull request #141 from stan-dev/feature/test-headers2
037ed3c BUGS example models using binomial_logit
48856ef correct bugs example model vol1/magnesium
261e75e use bernoulli_logit and clean up a bugs example model
5bca17d bugs example vol3/fire using if else statement instead of if_else
e88d8b0 vectorize some BUGS example models
312a33b Merge pull request #135 from stan-dev/feature/issue-91
06f8b2a added log_prob_propto function in model/util.hpp and switched model template parameter to last position to allow inference
48830cb moved is_unitialized() and fill() out of agrad and into math, with overloads in agrad, plus tests
91a98dd moved grad_log_prob method to static util log_prob_grad, made most model methods and get_base1 const, removed get_base1 assign tests, added get_base1_lhs tests
1cfbeee Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-112
7e89e40 adding test stan file
ce1fd2c updating header test target
898208e Merge pull request #153 from stan-dev/feature/makefile_fix
7332ffa Merge branch 'develop' into feature/test-headers2
51bd015 moving test-headers out of unit tests, moving to all tests
3d485f0 Merge branch 'develop' into feature/issue-91
5b41321 removing improper model from list of .PRECIOUS
0c9abd2 fixing the make target for executables
3cf6755 removed prob_grad_ad and stanc_model and tests, fixed other tests to pass with new models
9df1731 adding precious to improper.exe
694166a added models with .txt suffix to avoid recompilation with unwanted main --- need better way to do this
0fd7003 refactored generated models to remove prob_grad_ad dependency, removed virtual funs, added templates for propto and jacobian_adjust_transform, updated tests, added utility class of static model functions
9155ec5 Merge remote-tracking branch 'origin/develop' into feature/update-bugs-examples
4ae1451 rearranged code generation order to remove redundancy
8efa58f fixed uniform cdf_log
486a2b9 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-112
0547ad6 Merge pull request #140 from stan-dev/feature/makefile_issue
e61a112 new generator with template param for including Jacobians (passing unit tests)
e3ff1db added check for y = upper bound in uniform ccdf_log
692559b fix the indentation (trivial issue)
154a37f added failing model as unit test for issue-133, added escapes to print with tests
144f0d3 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
7a0e4ef Merge pull request #142 from jrnold/bugfix/manual-fitem-minipage
7258462 Updated docs to conform to final bin/print format
cb0dc0a Updated footer to be consistent with new names
21c58ff changed header print order to column (last-index) major
07b0dea Precision -> sig figs, naming tweaks
e8c44e3 Change quantiles, Rhat -> R_hat
1d1a6b2 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
020c500 Merge pull request #103 from stan-dev/feature/add_rayleigh_distr
4b32d9e Merge pull request #120 from stan-dev/feature/bugs-shapes
b1c2188 Update manual to conform to new bin/print arguments and format
254a983 add minipage to fitem so that function args can have multiple lines
e0d7e90 git rm -rf src/test/file_includes
02f2e71 add a test-headers make target
d30ed0a adding includes to sort
203557f rename .hpp files that are not intended to (pre)compile as .h files
a501d71 remove unnecessary #include that created loop
d2f5142 add boost header
1f3d333 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
c7b67e4 Merge pull request #137 from stan-dev/feature/mcmc_writer_test_fix
b9911ed Merge pull request #114 from stan-dev/feature/stagnant-model-bugs-vol2
f08819e adding expected values to the funshapes tests
7bae346 adding test for model in issue #91
68bb1fa making operator<< for var safe for uninitialized values
4a06fb8 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
19d1ee1 Merge pull request #136 from stan-dev/feature/issue-83
a091d22 adding back the target for Windows models
62f6f47 updating make target
f4ab53d Merge branch 'develop' of https://github.com/stan-dev/stan into develop
859df0a Updated print documentation
5d61f56 Use precision for warmup/sampling time output
390c3c4 merge develop branch into feature/logCDF_logCCDF
9ef10cd Merge pull request #98 from stan-dev/feature/add_bessel_and_pochhammer
08ea112 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
4b98a09 Initialize HMC variables in mcmc_writer_test
93ec5db Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-83
d1d5441 fixes issue 83, disappearing spaces in printed string literals in models
47b32ee Merge pull request #129 from stan-dev/feature/issue100
e604633 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/issue-91
d1e1d4d initializing local variables fixes issue 91; still need automated test
519cdb6 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
97372b2 Merge pull request #134 from stan-dev/feature/rstan_issue8
f18fb99 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
d021cc2 adding tests for the rest of bugs_examples/vol3/funshapes
7875246 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
4b65a06 adding test for autocorrelation
bd1f3ff Merge pull request #124 from stan-dev/feature/issue123
88dccfa set next good fft size to 2 for 0 to avoid infinite loop
3d51d94 Merge pull request #125 from stan-dev/feature/fast_constructor
d37a3e4 Encapsulate memcpy in member function
ed8b191 Merge branch 'feature/fast_constructor' of github.com:stan-dev/stan into feature/fast_constructor
ce64b5e Merge branch 'develop' of https://github.com/stan-dev/stan into develop
e176464 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
e12e378 Merge pull request #108 from stan-dev/feature/add_command_test_to_unit_tests
3ba987a cleaned up function signatures and distribution files
dc3cbbd Merge pull request #126 from stan-dev/feature/fix_static_hmc
ebf4afb Merge branch 'develop' of https://github.com/stan-dev/stan into develop
66ccc18 Merge pull request #128 from stan-dev/feature/update_model_tests
8839c6a Merge branch 'develop' into feature/add_command_test_to_unit_tests
ac2cd8c added cdf, cdf_log, ccdf_log to manual and function signatures for gamma and chi_square distr
a2686a0 added cdf_log and ccdf_log to chi_square distr
139c4b9 vectorized normal cdf and removed broken tests
4c25781 clean up distribution files and test files
7968aa2 added cdf to chi_square distr
75ac227 added ccdf_log to gamma distr
f5b441a added cdf_log to gamma distr
157bde2 added cdf to gamma distr
66d27e0 added gamma_p to lib with tests
e9c804b adding a model test for stagnant2. not adding one for stagnant due to slow convergence.
86a9f2e Merge branch 'develop' of https://github.com/stan-dev/stan into develop
281463d updating clean targets. fixes #100
879a575 updating some bugs_models
af5bfad Merge pull request #127 from stan-dev/feature/update_model_tests
bf35117 Merge branch 'develop' into feature/logCDF_logCCDF
18ca439 Use boost::math::isnan instead of x != x trick for detecting NaNs
62c9709 Merge pull request #119 from stan-dev/feature/issue63-normal_mixture
8a7a9a4 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
40ddaee Gracefully handle NaNs in Hamiltonian
2a596ff swapped gamma_q into cdf tests for inv_chi_square, scaled_inv_chi_square, and inv_gamma distr
c5efad7 Merge branch 'develop' into feature/fast_constructor
3325012 added gamma_q to math lib, fwd/rev autodiff, and manual
21fb772 cleaned up distribution files
2b31a94 updating model tests to skip another parameter in the output
93ca527 clean up manual for distributions
75e4a34 Merge pull request #122 from stan-dev/feature/fix_stan_csv_reader
8b44d69 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
45f006e added ccdf_log functions to manual
c547ff0 added ccdf_log to function signatures for all distributions
05245af added ccdf_log to poisson distr
52aee5d added ccdf_log to neg_binomial distr
806743b added ccdf_log to binomial distr
1ba8a8e added ccdf_log to beta_binomial distr
9df72c6 added ccdf_log to bernoulli distr
f32f0ec added ccdf_log to weibull distr
ffd73d9 added ccdf_log to uniform distr
014ed7d added ccdf_log to student_t distr
47bd07a added ccdf_log to skew_normal distr
905381f added ccdf_log to scaled_inv_chi_square distr
e553c29 added ccdf_log for pareto distr
cdcfb3c adding default constructor for stan_csv_timing. Windows doesn't set the members to 0
c76c974 fixing typo. fixes #123
476481f fixing the stan_csv_reader for Mac for line endings terminating in \r
ddb6cbe Merge pull request #115 from stan-dev/feature/manual-patch
0c7959b added ccdf_log to normal distr
7382b4c added ccdf_log to logistic distr
6c309a4 added ccdf_log to lognormal distr
b10cdde added ccdf_log to inv_gamma distr
aed9d7f added ccdf_log to inv_chi_square distr
845cbfb added ccdf_log to gumbel distr
d8ea1c3 added ccdf_log to exponential distr
7e705ac added ccdf_log to exp_mod_normal distr
c382ed7 added ccdf_log to double_exp distr
eeaf7f5 added ccdf_log to cauchy distr
ff99c1f added ccdf_log to beta distr
ff7c168 added ccdf_log tests to distribution test_fixture
6cffd56 all funshapes working, with existing modified so there is no rejection
9e6eb7d fixed descriptions environment in functions.tex for to_vector
094ae69 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
f4cce70 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/manual-patch
a198447 manual update for bug in sample program + acknowledgment for same
2156915 added all cdf_logs to manual
07766a3 added function signatures with compile model tests for cdf_log of discrete distr
e006cf8 added cdf_log to neg_binomial distr
bc1537a added cdf_log to poisson distr
08d1c3b added cdf_log to binomial distr
04b7b3a added cdf_log to beta_binomial distr
ccf21d9 added missing using statement and missing rng test for rayleigh distr
942a98b added missing using statements
ba5ae4d Merge branch 'develop' of https://github.com/stan-dev/stan into develop
4d7e9da Merge pull request #116 from stan-dev/feature/add_to_vector
b66cb4c added function signatures with compiled model tests for all cdf_log functions for univariate continuous distributions
05675f9 added cdf_log to bernoulli distr
9558cdc added cdf and cdf_log to uniform distr
db61feb Merge branch 'develop' of https://github.com/stan-dev/stan into develop
232a56c added cdf_log to weibull distr
7118ea3 added operands_nad_partials to cdf for weibull
d4550a0 added cdf_log to skew_normal distr
e578130 added operands_and_partials to cdf for skew_normal distr
d0b9958 added cdf_log to student_t distr
db47da7 added cdf_log to scaled_inv_chi_square
2de7d94 added cdf_log to pareto distr
143d53d added operands_and_partials to cdf of normal distr
6d8e99f added cdf_log to lognormal distr
84966dd added operands_and_partials to cdf for lognormal
8ae1180 added cdf_log to logistic distr
b9ee5d1 added cdf_log to inv_gamma distr
6447140 added cdf_log to inv_chi_square distr
61b8fa0 added cdf_log to gumbel distribution
fb25a3f Merge pull request #117 from stan-dev/feature/issue62
ebb2089 added operands_and_partials to gumbel cdf
f8d7ab5 added cdf_log to exp_mod_normal
57abf27 vectorized cdf and use operands_and_partials for exp_mod_normal distr
8aa17f2 fixes issue #63.
a458491 adding a dependency on the test/models/command test for test-unit
4e870f0 added vectorized cdf_log to double exponential with test
7e62e2e added vectorized cdf to double exponential with test
b594b27 Change ordering of Wno-c++11-long-long to ensure it is respected.
e0cbe32 added -Wno-c++11-long-long flag for clang++ in mac
c4fe188 added cdf_log to beta distribution with test
42353a5 added cdf_log with test for cauchy distribution
74dade0 added cdf_log to exponential with test
83f8ef4 vectorized exponential_cdf and added missing test
689b515 added cdf_log to normal distribution with test
5446320 added cdf_log test to distribution test_fixture
d8c2cf2 added -Wno-c++11-long-long flag for clang++ in linux. Fixes issue #62
fdf37db added missing compiled model tests
025d3da added to_vector with tests
cbe0dcf Merge branch 'develop' of https://github.com/stan-dev/stan into feature/manual-patch
5dadece Merge branch 'develop' of https://github.com/stan-dev/stan into feature/stagnant-model-bugs-vol2
166d5f5 stagnant models from bugs volume 2
228ec3e Merge branch 'develop' of https://github.com/stan-dev/stan into develop
181a909 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/add_bessel_and_pochhammer
8b40652 adding default constructors to the stan_csv_reader's structures.
02b9e3b Merge pull request #113 from stan-dev/feature/fix_print_and_sci_note
8ead88f Merge branch 'develop' into feature/add_command_test_to_unit_tests
8af81ed Removed debug output line
e8cdfbf Merge branch 'develop' of https://github.com/stan-dev/stan into develop
de3a552 MUse boost::lexical cast for more robust reading of numbers in scientic notation
3a0869c Merge branch 'develop' of https://github.com/stan-dev/stan into develop
dea3c5b Merge pull request #97 from stan-dev/feature/fix_model_header_dependency_file
94315c6 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
9cff869 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
22f6843 adding command test to test-unit target
9443a18 Revert "Revert "Merge pull request #72 from stan-dev/feature/add_command_test_to_unit_tests""
b8a596d Merge branch 'develop' of https://github.com/stan-dev/stan into develop
7b3a2e0 Merge pull request #106 from stan-dev/feature/issue-104-rep-vector-int-arg
93ab0db Merge branch 'develop' of https://github.com/stan-dev/stan into develop
2350143 changes to functions for issue 104
6b4d24c fixes issue 104 -- rep_matrix, rep_vector, rep_row_vector with int replicants
93cae59 used OperandsAndPartials for gradients of cdf for rayleigh distr
7cea21b Merge branch 'develop' of https://github.com/stan-dev/stan into develop
7eac88b added tests for fvar<fvar<T>> and fvar<var> for falling factorial, rising factorial (and logs of them), bessel funciton of first/second kind, modified bessel function of first/second kind
371f62a changed function signature of bessel functions to ints,reals
20f8e9e Merge branch 'develop' of https://github.com/stan-dev/stan into develop
fe49267 decreased number of decimal places in rayleigh tests
3bd326e Merge pull request #89 from mbrubake/bfgs_improvements
6c99aff Replace copy_base with optimized assignment operator
cf61bf9 Merge pull request #95 from stan-dev/feature/output_tweaks
b01639b fixed headers in manual for rayleigh distribution
39b6942 removed extra manual file
93c6f38 added rayleigh distribution with tests and doc in manual
1871aa3 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
3a5418a Merge pull request #92 from stan-dev/feature/adding_inv_functions
9745023 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
126ea71 Fix command_test
e52ac6a Indicate the optimization algorithm being used to find the point estimate.
406fb56 Silence anonymous namespace warning message.
afa3998 Be sure to print last iteration info with BFGS.
f2c05d0 Introduce improved convergence criteria for BFGS optimizer.
2940e06 Use BFGS for point estimates by default.
f0dde86 Merge pull request #75 from randommm/feature/log1m
7a80682 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
aa8ccdd Optimized copy constructors
7a4ec7a added log falling factorial, log rising factorial, and modified bessel of first and second kind to manual
8c93cfb added modified bessel to function signatures with compile model test
3428517 added modified bessel function of first and second kind to var with tests
20cf9ed added modified bessel function of first and second kind to fvar
7ebd731 added modified bessel funtion of first and second kind to math lib
0512a86 Merge branch 'feature/output_tweaks' of github.com:stan-dev/stan into feature/output_tweaks
97e04bc added var,var signature with tests to falling_factorial and rising_factorial
251ed1e Properly handle appended samples
9d811d0 Tweak output to mirror old notation, update tests
7ae995d Merge branch 'develop' of github.com:stan-dev/stan into develop
55e81d3 Merge pull request #99 from stan-dev/feature/issue90-periods
aa9edec Merge branch 'develop' of https://github.com/stan-dev/stan into develop
c0acb3b Merge pull request #88 from stan-dev/feature/fix-grammar-assoc-expected-op
ee8e55d added log_falling_factorial and log_rising_factorial
dbd5085 added log_falling_factorial and log_rising_factorial to fvar with tests
04fcb74 Merge pull request #94 from stan-dev/feature/robust_stepsize_init
6162735 added log_falling_factorial and log_rising_factorial to math lib
d005a17 restricted bessel function to integer orders
d2b7beb variable declarations with periods now fail to parse with an appropriate error message
761d7a5 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
136ac2d Merge branch 'develop' of https://github.com/stan-dev/stan into develop
47a1099 changed tgamma/tgamma to exp(lmgamma - lmgamma) to reduce overflow in falling factorial and rising factorial
86d2e1e Merge branch 'develop' into feature/adding_inv_functions
e3a360e modified falling_factorial and rising_factorial tests
1857d62 added falling_factorial, rising_fatorial, and bessel functions to doc
4fdb863 add falling_factorial and rising_factorial to stan::math, var, and fvar with tests
5f9c52b Revert "added bessel functions to agrad"
7e2b80c added bessel functions to agrad
0be42d1 added bessel functions to function signatures and compiled model test
22c80aa added bessel_second_kind to var with tests
7132ff1 added bessel_first_kind to var with tests
a60c56a added bessel_second_kind to fvar with tests
4759fc1 added bessel_first_kind to fvar with tests
58a6eae added bessel_second_kind to stan::math with tests
8dd8b90 added bessel_first_kind to stan::math with tests
cce45e9 removed redundant operations in inv_sqrt, inv_square, pow
4679866 Merge pull request #84 from stan-dev/feature/rm_rstan
e7f950d Tweak output to mirror old notation, update tests
7666e08 Catch init_stepsize when initializating sampler, add tests
a730f53 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
fd2a8c1 refined boundary tests for inv, inv_sqrt, inv_square
40a39ac updating make instructions for generating src/stan/models/model_header.hpp.d
59edf43 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
c5328f2 fixed inv, inv_sqrt, inv_square functions and added boundary tests
e41e09a Decrease improper posterior threshold for stepsize to account for floating point precision noise
f1e234c Merge branch 'develop' of github.com:stan-dev/stan into develop
469a3ea added inv, inv_sqrt, inv_square to doc
2474528 Merge branch 'develop' into feature/adding_inv_functions
917bb72 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/fix-grammar-assoc-expected-op
04a5424 added include of <string> in ast.hpp
b43bd69 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
2c593e4 Merge pull request #86 from randommm/feature/sort
da21c9d Merge branch 'develop' of https://github.com/stan-dev/stan into develop
15e99b2 Improvement to ordered_logistic distribution: now it uses log1m_exp(.) instead of log1m(exp(.)).
bb6436b Added log_diff_exp: math, gradients, tests and doc
b9536ab Added log1m_exp: math, gradients, tests and doc
aec631b Merge pull request #74 from stan-dev/feature/robust_zero_init
6f38377 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
10bb010 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
bffc4a2 Merge pull request #81 from stan-dev/feature/new_mcmc_writer
bb212d0 made precedence of >> and > explicit in grammar rules
7f3d843 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/fix-grammar-assoc-expected-op
84c5b9a Merge pull request #71 from stan-dev/feature/remove_example
936b533 Merge pull request #68 from stan-dev/feature/tweak_make_clean-all
4520944 Merge pull request #58 from mbrubake/gp_improvements
cb9ff9f Fixed rank(v,s) unit test warning of implicit convertion from double to int.
7cc89db sort_asc and sort_desc: removed unecessary size vector checks and added some unit tests
19d9077 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
38c0422 Merge branch 'develop' into gp_improvements
7b26d39 Merge pull request #76 from stan-dev/feature/vari-delete-fix
e78ba38 remove folder rstan
adc1349 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
808bd22 Merge branch 'develop' into gp_improvements
8c0d210 added new function inv_square
9e2e765 added new function inv_sqrt
c53c230 added new funciton inv to stan
9ebffa7 Unified sampler output through mcmc_writer, updating output to include more information in samples.csv as well as introducing an explicit diagnostic dump option.  Tested and freshly merged with develop.
1516836 Unified sampler output through mcmc_writer, updating output to include more information in samples.csv as well as introducing an explicit diagnostic dump option.  Tested and freshly merged with develop.
ef4729e Merge branch 'develop' into feature/robust_zero_init
a22e19c Added initialization checks to user-specified initialization, updated tests.
4b91fd3 Merge branch 'develop' of github.com:stan-dev/stan into develop
b39fab9 Merge pull request #79 from stan-dev/feature/revert_pull_request_72
41582f9 Revert "Merge pull request #72 from stan-dev/feature/add_command_test_to_unit_tests"
0b4d3f2 Merge pull request #78 from stan-dev/feature/revert_pull_request_64
6991294 Revert "Merge pull request #64 from stan-dev/feature/mcmc_writer"
2d0cafe Merge pull request #72 from stan-dev/feature/add_command_test_to_unit_tests
e1edcea Merge branch 'develop' into gp_improvements
a0132a1 Merge pull request #64 from stan-dev/feature/mcmc_writer
5149cdd Merge branch 'develop' into gp_improvements
6b14294 add no-op virtual delete() method to chainable() so that ctor exceptions can be cleaned up without seg faulting
ba96f59 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
3286c25 Merge branch 'develop' of https://github.com/stan-dev/stan into feature/vari-delete-fix
e83baa2 Merge pull request #67 from stan-dev/feature/GTEST_USE_OWN_TR1_TUPLE
33de2dd Check for model failure with zero initialization, including tests
bfd2c84 Add math/matrix unit test for inverse_spd src/test/math/matrix/inverse_spd_test.cpp
3b67c93 Remove unused variable in LDLT to silence compiler warning.
c2eaf53 Remove unused error policy stuff.
5066bbe adding the test for command line args to test-unit
8f7c504 Removed example model inadvertantly added some time ago
5f398ea Slight tweak to bin/print to remove duplicate rows
8b09b53 Merged develop
4dda563 don't remove the test folder with make clean-all; only its contents
194702c pass -DGTEST_USE_OWN_TR1_TUPLE via CFLAGS_GTEST in makefile
280dab9 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
45b15d7 Merge remote-tracking branch 'upstream/develop' into gp_improvements
04cb639 Merge pull request #66 from stan-dev/feature/reduce_warnings
3c44061 Merge branch 'develop' into gp_improvements
ff06467 Merge branch 'develop' into feature/reduce_warnings
f7d959c supressing warnings regarding 'typename' used outside of template
c08496a Merge pull request #59 from randommm/feature/sort
0e90b35 yank done item regarding shuffling tests off of TO-DO.txt
f4ed6f2 Merge branch 'develop' into feature/reduce_warnings
4a2f696 removing unused variable
0832470 using EXPECT_TRUE and EXPECT_FALSE to supress warning
86438c9 supressing uninitialized warning
6f5fbf7 removing pragmas to supress warnings
84c1571 adding a FIXME to add checks on inputs
6241a9e supressing sign comparison warnings
bbc33a0 Add test/math/matrix/quad_form.
af233c2 Add a test/math/matrix/trace_quad_form
a80294d Split trace_gen_quad_form into its own header files.
728a72b Remove commented code.
a1b7790 Add quad_form, trace_quad_form and trace_gen_quad_form to the manual.
ad75168 Fix LaTeX error.
c321c7a reducing more comparison warnings
b9f1fa3 Merge branch 'develop' into feature/sort
34e2606 Merge branch 'develop' of https://github.com/stan-dev/stan into develop
d57c66b Merge pull request #57 from randommm/feature/matrix_organization
fa138f9 Merge branch 'develop' of github.com:stan-dev/stan into mcmc_writer
87f92b1 Format zero values appropriately
11cb761 Merge pull request #60 from stan-dev/feature/stop_narrowing
404edc2 eliminated sign compare warning from stan/command/print.cpp stan/mcmc/chains.hpp
00c4112 eliminated sign compare warning from stan/mcmc/hmc/hamiltonians/dense_e_point.hpp and stan/optimization/bfgs.hpp
0ffe7b2 eliminated sign compare warning from stan/agrad/rev/matrix/squared_dist.hpp
f758f96 eliminated sign compare warning from stan/agrad/fwd/matrix/dot_product.hpp
6e971b3 eliminated sign compare warning from stan/agrad/rev/matrix/ldlt.hpp
c2e46a5 Add function signature tests for quadratic forms.
3e04fe4 Add vector form of trace_quad_form.
e92d63d Add inverse_spd function signature tests.
426d455 Putting spaces between ) and {
ecc1e5f Merge branch 'develop' into feature/reduce_warnings
370e78f Merge pull request #56 from stan-dev/feature/shuffle
f90672c avoid integer division in tests
534c21d Added fwd-diff for sort and its unit tests
e4870b9 Added unit tests for rev-diff sort and some minor changes
f773f52 Add unit test for matrix_normal_prec distribution.
91ff828 Add unit test for trace_quad_form.
cd13fd2 Add unit test for quad_form and quad_form_sym.
1d58545 Expose matrix_normal_prec_log and quadratic forms to the model parser.
832185b Add a matrix_normal_prec distribution.
79318db Make use of quad_form and trace_inv_quad_form_ldlt in multi_normal_log.
f3b087a Make use of trace_inv_quad_form_ldlt in multi_gp_log.
969c73e Update matrix includes to include quad_forms.
dc75454 Allow the LDLT_factor class to be used when computing the trace of an (inverse) quadratic form.
06f6dc3 Implement functions which compute quadratic forms and the trace of quadratic forms.
6e4eb20 Add a matrix version of the value_of function.
45714bb Make dot_product vari use Eigen::Matrix::dot().
15f750f Removed unused includes in model_header.hpp (appled fixme) and added some lines to .gitignore (files generated by RStan make)
537223f In inverse_spd 0.5*(a + a') when computing LDLT to ensure that gradients are spread out and update tests.
020adf4 Added rev-diff sort versions
533a6e1 switching between spaces and tabs
a24b7d7 Added unit tests
6751a3f Added sort and rank to reference manual
4bd8ce6 Tested version
e8d5ea8 added: sort and rank functions
39ce036 shuffle the function_signature tests
c62582c Expose inverse_spd to the parser.
7f3c538 Documentation for inverse_spd
3a6d845 Add unit test for inverse_spd.
a976492 Add inverse_spd function which computes the inverse using the LDLT transform.
64baa97 Fixes issue #47. Removing some sign comparison warnings
e05a11e Updated test
b2878b9 Woops, I mean include transformed/generated parameters in header and sample output
96799ac Don't include transformed/generated parameter names in header
dadd041 Update command_test to account for new command line argument
070e69b Merge branch 'master' into reduce_warnings
c28c6b2 Merge branch 'master' into mcmc_writer
8ce7a79 Merge pull request #51 from betanalpha/mcmc_writer
ba7d25d Updated CSV reader test
966ec89 Revert additions of const to readers, which caused too many problems downstream, and fix bug in generate_param_names_array
d3f52c4 Added empty line to end of timing output, update tests
04993ae Add const qualifier to read-only methods
9439571 Tweaked MCMC writer diagnostic method name
fe20535 MCMC writer test
15f3349 New MCMC Writer tests
c5fc91d Updated reader tests
ceb67c3 Parse updated output format
ab508ae Parse updated output format, grab and print timing as well as ESS/time
7b93888 Added mcmc_writer class, which somehow disappeared from the branch
db7512e removing sign compare warning from src/mcmc/hmc/hamiltonians/diag_e_point.hpp
3be3f8e Fixed creation/use of diagnostic stream, use mcmc_writer for all sampling output
e9abd0f Take in unconstrained parameter names when generating diagnostic headers
188077f Change command name to reflect options besides nuts
01b23b8 Merge branch 'master' into mcmc_writer
b09194a Print diagnostic information
a614178 Intermediate reworking of command to use mcmc_writer
9be1d9d Added sample output method
29f0d6c Don't clear vectors before appending param names and values
9cdb317 Added write_sampler_state for general implementation display
a5719d9 Use pointer to stream instead of reference to stream to allow for null streams

git-subtree-dir: pystan/stan
git-subtree-split: cc82d51d492d26f754fd56efe22a99191c80217b
Update stan source, commit cc82d51d492d26f754fd56efe22a99191c80217b

Merge commit '67ef63f685c634db78a063813416067095322fe1' into develop
Update pystan to work with new version of stan

- optimizing now works
- new eigen and boost libraries
- additional documentation
- more tests