Consistent naming convention #4
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closed by #45 |
dunleavy005
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Nov 21, 2018
* forward algorithm only should run once * removed 'init_scaler_count' variables * changing fn name * change from 'resize' to 'assign' * added naive sequence sampling! * re-ordering 'naive' to be 1st taxa * changed partis cached data variable * unified MSA for [Simple|Phylo]HMM + SimpleHMM now does star-tree likelihood * added naive seq sampling tests * RevBayes tree reader * linearham tree writer * unnecessary getter fn * fixed handling of RevBayes trees * removed 'Posterior' column from revbayes example TSV * switching header order * forward probs re-compute with new tree * 'const'ing some member fns * refactored the tree writing code * added 'caache_forward' to tests * added 'cache_forward' and RB tree stuff to tests * EPS modification * updated submodules * handling missing branch lengths * wercker fix #1 * wercker fix #2 * wercker fix #3 * wercker fix #4 * wercker fix #5 * wercker fix #6 * wercker fix #7 * adding header to utils.cpp * wercker fix #8 * wercker fix #9 * wercker fix #10 * wercker bot wercksgit add wercker.yml ! * fixed burnin mechanism * now a one-pass procedure * updated phylolikelihood in R * moved utility functions to utils.*pp * add TCLAP submodule * removed burnin handling * added functionality for cmd-line sampler + revbayes batch inference * fixed comments * variable name change * fixed tree destructor in PhyloHMM * added linearham executable * comment fix * updated submodules * cleaning up root dir * added doxygen comments for VDJGermline and utils * adding assert header * added HMM doxygen comments * moved linalg.*pp to utils.*pp * small comment changes * added SimpleHMM doxygen comments * fixed some doxygen comments * comment change * removed word 'range' from comment * added PhyloHMM doxygen comments * updated Doxyfile * unnecessary README * gh-pages deploy * added weighted bootstrap w/ ASR script * wercker fix #1 * wercker fix #2 * wercker fix #3 * wercker fix #4 * wercker fix #5 * wercker fix #6 * wercker fix #7 * wercker fix #8 * wercker fix #9 * wercker fix #10 * wercker fix #11 * wercker fix #12 * added graphviz to wercker * try fix * break on purpose * unbreak wercker * modified SConstruct comments * added RevBayes template * README updates. * added RevBayes templater script * added partis submodule * partial scons-nestly pipeline * fixed wercker.yml * now fixed wercker.yml * now fixed wercker.yml again * now fixed wercker.yml again again * THIS BETTER WORK * THIS BETTER WORK UGHH * PRAY TO GOD * try wercker again * fix wercker build FOR REALZZZZ * minor tweaks * small tweak * added RevBayes submodule * added RevBaves inference step * wercker webhook check * wercker webhook check #2 * wercker check * wercker update too slow - stop for now * added 'num_rates' to revbayes step * let RevBayes exit if reading data fails * spelling change * added intermediate linearham scons target * added final linearham scons target * wercker fix start * adding libz-dev * adding libncurses-dev * adding libyaml-cpp-dev * adding numpy * adding colored-traceback * adding psutil * adding scipy * adding dendropy * adding dendropy again * adding pysam * checking HOME * worth a try * whoops * whooops * now try * now tryy * now tryyy * check the wercker env * manually export HOME * partis fixed so HOME isnt required * add matplotlib * try building linearham without yaml-cpp * fixed NPadding transition checking * removed submodule yaml-cpp * no more yaml-cpp source build * added liao (2013) example dataset * adding Dockerfile template * only build revbayes * only build partis * Docker can run 'scons --build-deps' * updating submodules * whoops! ASR script did not account for N naive bases * added option to treat FASTA as full CF * updated Dockerfile * install R packages in Dockerfile * removed submodule phylomd * whoops re-added phylomd * removing revbayes build from SConstruct * fully complete Dockerfile! * updated wercker script * fix wercker yaml * i dont always get things wrong, but when i do, its bc of YAML * now? * better! * added germline gene class concepts * added S-W information concepts * added hidden state space concepts * whoops forgot to clang-format ^ * added line to state space section * added hidden state trans prob matrix concepts * added germline padding and emission probability matrix concepts * added scaling concepts * added xmsa concepts * whoops * updated README * Some doxyedits. * updated linearham docs per Erick's comments * more docs update * formula fix * Erick fixes * Final edits on my end. * One more note about the figure. * more edits re: Erick comments * updated submodules * updated partis * updated partis * add a few comments on docs * updated submodules * updated linearham docs
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Right now sometimes matrices have
matrixin the title, sometimes not. Same for vectors.Make this consistent.
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