Changes in version 2.2.0 (for BioC 3.3): - Plots of genotypes. - Stacked area and stream plots (code from Marc Taylor). - Example of modules and no epistasis. - Removed requirement of Root in geneToModule. - More tests (and reorganized them) - Miscell. improvements and typos fixed in documentation and vignette. - Added mutationPropGrowth as argument. - Some minor bug fixes and additional checks for user errors. Changes in version 2.1.6 (2016-04-14): - Adapt to changes in today's release of testthat (1.0.0) Changes in version 2.1.5 (2016-04-09): - Added a test of driverCounts, that does not depend on OS/compiler. Changes in version 2.1.4 (2016-04-09): - Moved to manual tests that depend on OS/compiler (for reproduction of random number stream in C++). Changes in version 2.1.3 (2016-04-04): - Fixed sporadic bug in countDrivers Changes in version 2.1.2 (2016-03-27): - Arguments to BNB_Algo5 explicit. - Example of modules and no epistasis. - Removed requirement of Root in geneToModule. - More tests (and reorganized them) - Miscell. improvements in documentation and vignette. Changes in version 2.1.1 (2016-03-07): - Added mutationPropGrowth as argument. - Stacked area and stream plots (code from Marc Taylor). - Plots of genotypes. - Expanded vignette. Changes in version 1.99.9 (2015-10-08): - Fixed NEWS file. - Removed empty file. Changes in version 1.99.8 (2015-10-01): - Test "initMutant with oncoSimulSample, 2" occasionally failed. Changes in version 1.99.7 (2015-09-27): - initMutant available in oncoSimulPop and oncoSimulSample. Changes in version 1.99.6 (2015-09-26): - Improved test coverage and removed stringsAsfactors from tests. - Consistent handling of corner cases in Bozic. - Miscell minor documentation improvements. Changes in version 1.99.5 (2015-06-25): - Fixed bug in initMutant, added tests, and vignette section. Changes in version 1.99.4 (2015-06-22): - Plotting true phylogenies. - Tried randutils, from O'Neill. Won't work with gcc-4.6. - bool issue in Windows/gcc-4.6. - Most all to all.equal in tests. Changes in version 1.99.3 (2015-06-19): - More examples to vignette - Using Makevars - More functionality to plot.fitnessEffects - Will Windoze work now? Changes in version 1.99.2 (2015-06-19): - Fixed typos and other minor in vignett. Changes in version 1.99.1 (2015-06-18): - Try to compile in Windoze with the SSTR again. - Reduce size of RData objects with resaveRdaFiles. - Try to compile in Mac: mt RNG must include random in all files. Changes in version 1.99.01 (2015-06-17): - Many MAJOR changes: we are done moving to v.2 - New way of specifying restrictions (v.2) that allows arbitrary epistatic interactions and order effects, and very large (larger than 50000 genes) genomes. - When onlyCancer = TRUE, all iterations now in C++. - Many tests added. - Random DAG generation. - Some defaults for v.1 changed. Changes in version 1.99.00 (2015-04-23): - Accumulated changes of former 99.1.2 to 99.1.14: - changes in intermediate version 1.99.1.14 (2015-04-23): - Now are things OK (I messed up the repos) - changes in intermediate version 99.1.13 (2015-04-23) - Added a couple of drop = FALSE. Their absence lead to crashes in some strange, borderline cases. - Increased version to make unambiguous version used for anal. CBN. - changes in intermediate version 99.1.12 (2015-04-22) - Removed lots of unused conversion helpers and added more strict checks and tests of those checks. - changes in intermediate version 99.1.11 (2015-04-18) - Tests of conversion helpers now really working. - changes in intermediate version 99.1.10 (2015-04-16) - Added conversion helpers as separate file. - Added tests of conversion helpers. - Added generate-random-trees code (separate file). - More strict now on the poset format and conversions. - changes in intermediate version 99.1.9 (2015-04-09) - added null mutation for when we run out of mutable positions, and since not clear how to use BNB then. - changes in intermediate version 99.1.8 (2015-04-03) - added extraTime. - changes in intermediate version 99.1.7 (2015-04-03) - endTimeEvery removed. Now using minDDrPopSize if needed. - changes in intermediate version 99.1.6 (2015-03-20) - untilcancer and oncoSimulSample working together - changes in intermediate version 99.1.5 (2015-03-20) - Using the untilcancer branch - changes in intermediate version 99.1.4 (2014-12-24) - Added computation of min. of ratio birth/mutation and death/mutation. - changes in intermediate version 99.1.3 (2014-12-23) - Fixed segfault when hitting wall time and sampling only once. - changes in intermediate version 99.1.2 (2014-12-16) - Sampling only once Changes in version 0.99.2 (2014-07-14) - Consistently using indentation in .Rd files. Changes in version 0.99.1 (2014-07-14) - Minor changes for BioConductor submission: - extended description - minor changes to vignette - improved documentation of posets Changes in version 0.99.0 (2014-06-26) - First version submitted to BioConductor. Changes prior to the first BioC version. Left here for historical purposes simply. preBioC_1.0.4 2013-03-21 - Versions K, M, O, P working. - Versions O and P with u_1 and u_2 so as to provide comparable results to K and M. - Sometimes problems with ti==0. preBioC_1.0.5 2013-03-22 - Cleaned up the code and left only version P. - Added memory limits. preBioC_1.0.6 2013-03-22 - Added mutator genotype - Only species with fitness > 0 go through ti calculation. preBioC_1.0.7 2013-03-25 - Start run from a given mutation preBioC_1.0.8 2013-04-02 - Limits on outNS size to prevent segfaults. - Do not transpose outNS in R (do in C++). - Better code for sp_to_remove. preBioC_1.0.9 2013-04-02 - Some code in R moved to C++. - Minimize increases in RAM in R related to handling of temporaries. - Moved out of main R function the creation of rarely used objects. preBioC_1.0.10 2013-04-04 - Info on actual drivers returned from C++ preBioC_1.0.11 2013-04-04 - Added time limit to main C++ loop execution and changed exploration files accordingly. preBioC_1.0.12 2013-04-15 - Per sample driver and populations stats in C++. - Removed some rarely used output from C++. preBioC_1.0.13 2013-04-24 - Added continuous time Bozic fitness preBioC_1.0.14 2013-04-25 - Added Beerenwinkel et al., 2007 fitness. - Added a few checks for loss of precision. - Added thinning of output. preBioC_1.0.15 2013-04-26 - Unmet restrictions: allow variable penalty. - Safety initializations and a bug fix. preBioC_1.0.16 2013-05-01 - Unmet restrictions: better mechanism (which also fixes a bug). - Changed and cleared up the mess in the example trees. - This is the version used to launch the first set of massive simulations (bozic and exp) preBioC_1.0.17 2013-05-20 - Added McFarland et al. 2013 fitness. - Some code cleaning. - Fewer arguments in R function have default values (force user to be explicit). preBioC_1.0.18 2013-07-25 - Renamed the package - Tried to use Youn and Simon's method. Calling code added. - Tried to use Sakoparnig and Beerenwinkel's Bayesian CBN. Calling code added. - Fixed non-working code in metrics due to changes in functions in graph. - Added simple code for temporal order. - Added old code for clonal ordering (not finished). - Robustified other functions and start up (cbn, metrics, plotting, etc). - No dependencies on libgmp (multiprecission arith.) now; removed from Makevars. - Warning in R code if endTimeEvery is not negative in simulation models where it should probably be negative. preBioC_1.0.19 2014-xxx - Changes and addition to plotting functions. - Added comparison of adjacency matrices and other miscell functions from the processing code of the simulations.