2018-05-01 George G. Vega Yon <g.vegayon@gmail.com> * R/pies.r: All dependencies have been moved to polygons. * R/predict.r: idem. 2018-04-17 George G. Vega Yon <g.vegayon@gmail.com> * src/phylo.cpp: Removed prediction functions (wrongly implemented). * R/predict-bis.r: Documenting posterior probabilities. * R/predict.r: Updating predict methods to use the correct version of the posterior probabilities. * tests/testthat/test-predict.r: Adding new tests. 2018-04-11 George G. Vega Yon <g.vegayon@gmail.com> * src/predict.cpp: New function implementing posterior probabilities. Now we are using pre-order to compute such probs (see paper). * R/predict-bis.r: Idem. Including a brute-force version intended to be used for testing. * src/*: Fixing iter++ to ++iter when necesary (an bad practice that now warns when compiling). 2018-02-28 George G. Vega Yon <g.vegayon@gmail.com> * tests/*: Adding test checking that likelihood in model with eta = 1/2 is proportional to the likelihood without etas. 2018-02-27 George G. Vega Yon <g.vegayon@gmail.com> * src/phylo.cpp: Updating etas in the model. Now it is the probability of not reporting a discovery given the observed state (before it was the true state). * src/sim_phylo.cpp: idem. * tests/*: idem. 2018-02-22 George G. Vega Yon <g.vegayon@gmail.com> * src/phylo.cpp: Fixing 'error' back. * R/predict.r: Adding eta to the call. * R/plot_loglike.r: idem. * R/estimation.r: idem, and adding function to try to compute inv. * tests/testthat/*.r: Adding eta to the tests. 2018-02-21 George G. Vega Yon <g.vegayon@gmail.com> * src/phylo.cpp: Adding the eta parameter for controlling for annotation bias. * src/sim_phylo.cpp: Idem. * R/estimation.r: Idem. * R/simulation.r: Idem. * R/plot_loglike.r: Idem. * R/loglike.r: Idem. 2018-01-25 George G. Vega Yon <g.vegayon@gmail.com> * R/simulation.r: Values of `informative` and `maxtries` were not passed to simulate_fun_on_tree. 2018-01-18 George G. Vega Yon <g.vegayon@gmail.com> * R/estimation.r: Fixing checking of non-informative data. * R/predict.r: Indexing of edges was wrong. * src/phylo.cpp: predict_fun was taking the wrong id for root node. Also, when the node was the rootnode, d0i should yield probabilities equal to pi. * R/data-management.r: Removing functions that are no longer required. * src/tree.cpp: Idem. * tests/testthat/test-data-management.r: New set of tests. 2018-01-11 George G. Vega Yon <g.vegayon@gmail.com> * R/ape.r: Fixing case in which as.phylo.matrix processes a tree with only leafs and a root. * R/data-management.r: Fixing bug in plot.aphylo. 2018-01-10 George G. Vega Yon <g.vegayon@gmail.com> * R/estimation.r: Doc + estimation checks whether aphylo is informative. * R/prune.r: Completely removed. No longer needed. * R/simulation.r: Working on Doc + sim functions check if the resulting tree is informative or not + new function rdrop_annotations. * tests/testthat/*: Several new tests on the previous point. 2018-01-09 George G. Vega Yon <g.vegayon@gmail.com> * R/ape.r: Working on documentation. * R/data-management.r: idem * R/simulation.r: idem. * R/predict.r: Adapting pred functions to new structure of aphylo. 2018-01-04 George G. Vega Yon <g.vegayon@gmail.com> * src/misc.cpp: New function reduce_pseq proposes a peeling seq that skips ininformative nodes. * R/data-management.r: Remove a bunch of routines that wont be used anymore related to PO trees. 2018-01-03 George G. Vega Yon <g.vegayon@gmail.com> * src/sim_phylo.cpp: Simulating trees using ape's phylo convention. about 20x faster than rtree. Returns a phylo object. * R/simulation.r: Idem. * src/tree.cpp: Function to list offspring of a tree. * R/data-management.r: idem. * src/phylo.cpp: Likelihood was not been computed at the root node! but this is for the new method. The old one was OK. * 2017-12-20 George G. Vega Yon <g.vegayon@gmail.com> * playground/*: Working on functions to prune trees using po traversal or pre-order traversal. Algorithms working and good exercise to have a better understanding of the pruning algorithm. 2017-10-18 George G. Vega Yon <g.vegayon@gmail.com> * R/data-management.r: Fixing bug in plot.aphylo. * playground/presentations: Working on EAC presentation. 2017-10-04 George G. Vega Yon <g.vegayon@gmail.com> * R/data-management.r: Working in a standard method to point to nodes ids. * R/predict.r: Idem. * R/prune.r: New example prunning leafs. 2017-10-03 George G. Vega Yon <g.vegayon@gmail.com> * R/data-management.r: New constructor method for class po_tree. Now it also includes branch lengths. * R/simulation.r: Move documentation of sim_tree. * src/sim_tree.cpp: Efficiency. * src/tree.cpp: Change sorting in final edgelist. 2017-09-28 George G. Vega Yon <g.vegayon@gmail.com> * R/data-management.r: Removing names for the po_tree labels. * R/prune.r: New (a bit complex) function to prune trees. 2017-09-07 George G. Vega Yon <g.vegayon@gmail.com> * R/data-management.r: leafs now has its own manual, plus new internal checks checking labels. * src/phylo.cpp: -noffspring- removed since now we use Rf_length. This included changes in all the functions that used that argument. * R/simulation.r: po_tree now has the labels as attributes, including the offspring. * src/sim_phylo.cpp: sim_tree now returns an integer matrix (edgelist). Only offspring and labels are included as attributes. 2017-09-07 George G. Vega Yon <g.vegayon@gmail.com> * R/panther.r: Now the user can choose which one to use. * playground/ape_now_supports_singletons*: A small benchmark between rncl and ape. 2017-09-05 George G. Vega Yon <g.vegayon@gmail.com> * R/panther.r: Now using nrcl to read newick 2017-08-31 George G. Vega Yon <g.vegayon@gmail.com> * R/pies.r: New function to rescale y-coords so that aspect ratio is kept. 2017-08-29 George G. Vega Yon <g.vegayon@gmail.com> * R/panther.r: Capturing info from newick extended version. * R/pies.r: Adding more features to the pieplot. * R/predict.r: New plot method for prediction. * configure.ac: Compaling using OpenMP. * condigure: idem. * src/Makevars.in: idem. 2017-08-04 George G. Vega Yon <g.vegayon@gmail.com> * R/panther.r: New function to read panther trees' annotation. 2017-08-01 George G. Vega Yon <g.vegayon@gmail.com> * R/data-management.r: Working on aphylo-class. Plot method using ggtree. * R/estimation.r: Removing ABC method and cleaning code. * tests/*: Adding more tests. 2017-07-31 George G. Vega Yon <g.vegayon@gmail.com> * Overall, working on the -aphylo- class object. Now it is better integrated with ape-phylo objects. Also, including class checks for the class creation method. 2017-07-12 George G. Vega Yon <g.vegayon@gmail.com> * playground/simulations: Moved to a different project aphylo_paper. * src/phylo.cpp: Changed Pi to be -double- no longer an -arma::mat-. * R/mle.r, R/plog_loglike.r: Idem. * tests/testthat/test-loglikelihood.r: Idem. 2017-07-11 George G. Vega Yon <g.vegayon@gmail.com> * src/quality.cpp, R/predict.r: Included new function to compute expected value of random imputation given parameter alpha. 2017-05-31 George G. Vega Yon <g.vegayon@gmail.com> * R/simulations.r: Fixed a small bug related to names of a vector. 2017-05-02 George G. Vega Yon <g.vegayon@gmail.com> * R/mle.r: Added new functions to predict and evaluate prediction. Plus, some code improvement. * R/plot_loglike.r: Making code more clear. * src/phylo.cpp: Prediction functions. * src/misc.cpp: Function to compute geodesics. * vignettes/*: Working on doc, including data imputation. 2017-04-19 George G. Vega Yon <g.vegayon@gmail.com> * R/mle.r: Using fnscale and parscale in optim and abc_optim. Now the functions maximize so its all out of the box. 2017-04-18 George G. Vega Yon <g.vegayon@gmail.com> * *: Moved the MCMC to a new project: USCbiostats/amcmc 2017-04-13 George G. Vega Yon <g.vegayon@gmail.com> * R/data-management.r: Functions as.phylo and recode_vertices rewritten and renamed to as.apephylo and as_ape_tree. Also now all use an edgelist instead of offspring and parent vectors. * src/phylo.cpp: Changing name from Z to annotations (makes more sense). * R/mle.r: Idem. * src/sim_phylo.cpp: Name conventions, again, now edgelists are always in the form of (parent, offspring). * src/tree.cpp: Function to relabel edgelist so that these form a partial ordered tree. Plus more doc. 2017-04-12 George G. Vega Yon <g.vegayon@gmail.com> * src/tree: New functions for recoding trees as PO. * R/*: Changing language... now phylo_tree is aphylo (Annotated phylogenetic tree). * R/data-management.r: get_offspring changed to new_aphylo, and now includes more checks on the edge and annotations. 2017-03-29 George G. Vega Yon <g.vegayon@gmail.com> * R/mcmc.r: Moved phylo_mcmc to R/mle.r * R/mle.r: MLE now uses stats::optim rather than own NR. * tests/testthat/*: new tests 2017-03-22 George G. Vega Yon <g.vegayon@gmail.com> * R/mcmc.r: Multiple parallel chains and passing extra arguments to fun. * R/mle.r: Working on printing method. * R/simulation.r: Adding templates for doc. * tests/*: Adding more tests. * src/phylo.cpp: Cleaning code and collapsing prob loops. 2017-03-08 George G. Vega Yon <g.vegayon@gmail.com> * R/mle.r: New print method + covar matrix in phylo_mle. 2017-03-07 George G. Vega Yon <g.vegayon@gmail.com> * R/data-management.r: Working with -as.phylo- method. * src/sim_phylo.cpp: Moving the sim_tree function there. * src/sim_tree.cpp: . . * playground/simulating_and_estimating_data.r: Check the performance of the mle estimator. * R/simulation.r: Implements the function for sim annotated phylo trees. * tests/testthat/test-data-management.r: New set of tests 2017-02-28 George G. Vega Yon <g.vegayon@gmail.com> * src/sim_tree.cpp: A function to simulate Directed Acyclic Graphs is faster than ape::rtree and more convenient since it creates the labelling that we require. 2017-02-23 George G. Vega Yon <g.vegayon@gmail.com> * R/mcmc.r: -scale- now a vector. New example using MVN dist. * src/mcmc.cpp: idem. * src/sim_phylo.cpp: Multiple functions can be generated at the time. * vignettes/*: Just doing some cleaning. 2017-02-22 George G. Vega Yon <g.vegayon@gmail.com> * R/data-management.r: -as.phylo- method for -phylo_offspring-, and removed igraph links (replaced by -ape-). * playground/FormatTreeR_24Oct2012.pdf: Formally describes the phylo objects. * src/sim_phylo.cpp: Function to simulate phylo trees. 2017-02-16 George G. Vega Yon <g.vegayon@gmail.com> * R/mcmc.r: Fixing small bug in output. * R/mle.r: Adding an example with MCMC and improving doc. * playground/*.r: Some tests of the performance of MCMC including speed comparisons against the mcmc::metrop function. 2017-02-15 George G. Vega Yon <g.vegayon@gmail.com> * src/mcmc_misc.cpp -> src/mcmc.cpp: New version of the mcmc algorithm implemented using Rcpp. * R/mcmc.r: New option -useCpp- allows using a C++ version of the algorithm. Speed improvement of ~ 50%. * R/mle.r: Working on documentation for the phylo_mcmc function. * playground/mcmc_benchmark...: Measuring speed gains of new MCMC implementation. 2017-02-14 George G. Vega Yon <g.vegayon@gmail.com> * R/mcmc.r: mcmc now is MCMC and returns an object of class mcmc from the coda R package. Also, new argument -thin- allows 'thinning' the samples to reduce autocorrelation between draws. Also, working on aperiodicity of MCMC. 2017-02-09 George G. Vega Yon <g.vegayon@gmail.com> * src/mcmc_misc.cpp: Started to write Gibbs Sampler. 2017-02-03 George G. Vega Yon <g.vegayon@gmail.com> * R/mcmc.r: Adding example and fixing travis (doc missing). Also including check of -ub- and -lb- parameters. * tests/testthat/test-mcmc.r: New test for MCMC. 2017-02-02 George G. Vega Yon <g.vegayon@gmail.com> * R/mle.r: Improving doc. Now optim pars are passed via `control`. mcmc using own method. * src/mcmc_misc.cpp, R/mcmc.r: New function for implemting MCMC with hastings ratio. 2017-02-01 George G. Vega Yon <g.vegayon@gmail.com> * R/mle.r: Adding more examples (filling zeros), plus more tunning options for the NR method. 2017-01-18 George G. Vega Yon <g.vegayon@gmail.com> * R/mle.r, R/plot_loglike.r: Changing coding style. * R/mle.r: Working on NR (now gives more reasonable ans and identical to ABCoptim). * src/phylo.cpp: leaf_prob can be computed faster now, and gain_loss_prob changed to prob_mat. * src/phylo.h: Adding header. * tests/testthat/*.r: leaf_prob now uses mu instead of M. 2017-01-18 George G. Vega Yon <g.vegayon@gmail.com> * R/mle.r: Improving doc + output (class) structure. * R/phylogenetic.r: Adding more imports + doc data. * test/testthat/*: Adding tests (making sure the ll works). * readme.rmd: Adding code coverage, travis and appveyor. * src/peeling_cpp.cpp: Improving documentation. 2017-01-11 George G. Vega Yon <g.vegayon@gmail.com> * R/mle.r: Maximum Likelihood estimation function and methods. * R/phylogenetic.r: Adding package requirements for MLE. 2017-01-11 George G. Vega Yon <g.vegayon@gmail.com> * R/data-management.r: get_offspring now returns neat experiment * R/plot_loglike.r: Fixed bug * playground/example.r: Accomodating script to changes in get_offspring * playground/root_node_prob.rmd: Notes on root node. 2017-01-10 George G. Vega Yon <g.vegayon@gmail.com> * R/data-management.r: Changing offsprings to offspring * R/methods.r: Idem. * R/phylogenetic.r: Adding new imports. * playground/example.r: Fixing N-R optim. * vignettes/phylogenetic_trees.rmd: Working on doc. * src/peeling_rcpp.cpp: Adding beta dist prior for psi, and, fixing bug on leaf probabilities. * R/plot_loglike.r: New function to visualize LogLike. 2017-01-03 George G. Vega Yon <g.vegayon@gmail.com> * R/data-management.r: Now experimental data is filled. and adding new set of functions. * vignettes/phylogemetic_trees.rmd: Working on doc. 2017-01-03 George G. Vega Yon <g.vegayon@gmail.com> * data/*: Adding data more neatly. * R/*.r: Adding new methods for printing and preparing data. * vignettes/*: Using html_vignette output. 2016-12-20 George G. Vega Yon <g.vegayon@gmail.com> * Initial commit.