Changes in version 4.13.4 (2026-04-16) o Fixed miscell minor notes and warnings from r-universe. Changes in version 4.13.3 (2026-04-14) o Upgraded exprtk to version from 2025-01-01, commit cebb369. o And proper use of all.equal with check.attributes = FALSE! Changes in version 4.13.2 (2026-04-14) o Fixed the "More than one VignetteEngine specified" error in r-universe. o Added unexported complete_fitness_landscape function. o Added a few magellan epistasis tests. o Removed an equality comparison of floats. Changes in version 4.13.1 (2026-01-31) o Fixed NOTES in "R CMD check --as-cran" Changes in version 4.11.1 (2025-06-09) o Example using WT in interventions. Changes in version 4.9.1 (2025-03-04) o Fix three Notes in Rmd files. Changes in version 4.7.8 (2024-10-09) o Remove support for maOS with arm64 (i.e., kjohnson3 and kjohnson1 machines). Changes in version 4.7.7 (2024-09-18) o Try to work around (and ask for help) for tests that fail in the BioC kjohnson3 machine (maOS 13.6.5, arm64). Yes, more of this. Changes in version 4.7.6 (2024-09-16) o Try to work around (and ask for help) for tests that fail in the BioC kjohnson3 machine (maOS 13.6.5, arm64). Yes, more of this. Changes in version 4.7.5 (2024-09-12) o Try to work around (and ask for help) for tests that fail in the BioC kjohnson3 machine (maOS 13.6.5, arm64). Changes in version 4.7.4 (2024-07-30) o Try to work around (and ask for help) for a vignette example that fails in the BioC kjohnson3 machine (maOS 13.6.5, arm64). (Yes, a fourth place where it fails). Changes in version 4.7.3 (2024-07-26) o Try to work around (and ask for help) for a vignette example that fails in the BioC kjohnson3 machine (maOS 13.6.5, arm64). (Yes, a third place where it fails). Changes in version 4.7.2 (2024-07-25) o Try to work around (and ask for help) for a vignette example that fails in the BioC kjohnson3 machine (maOS 13.6.5, arm64). (Yes, a second place where it fails). Changes in version 4.7.1 (2024-07-23) o Try to work around (and ask for help) for a vignette example that fails in the BioC kjohnson3 machine (maOS 13.6.5, arm64). o Miscell minor: incorporate 361ccdc to 1bc3cbd (in main github repo) to the BioC version. o Fixed Note "Lost braces in \itemize; meant \describe ?" o Updated vignette address to IIBM new name. Changes in version 4.3.3 (2023-07-17) o One test failing on Linux aarch64: fixed (by commenting out, which is the right thing to do). Changes in version 4.3.2 (2023-06-03) o Allow passing a seed to MAGELLAN's random fitness landscapes in rfitness function. o Fixed bug in rfitness when using a 3-element vector for scaling, and one or more fitness values had the same value as WT. Changes in version 4.1.4 (2023-03-08) o Updated exprTk (thanks to pull request from Arash Partow). Changes in version 4.1.3 (2023-02-20) o no need to specify CXX_STD = CXX14 (the default since R-4.1.0). Changes in version 4.1.2 (2023-02-20) o NAMESPACE: do not import .rbind.data.table (no longer exported from data.table 1.14.8, and not needed with R >= 4.0.0). Changes in version 4.1 (2022-11-24) o Faster, cleaner, and better tests of interventions. Changes in version 4.0 o MAJOR change: users can simulate interventions and adaptive therapy, as well as define, track, and use in fitness-dependent specifications user-defined variables. o MAJOR change: users can specify birth and death rates as they want, including making both or just one frequency-dependent. o onlyCancer = FALSE by default in all calls to oncoSimul*. This is a possible BRAEKING CHANGE. o Plot fails with a meaningful error if simulations had unrecoverable exception or hit max wall time or max num tries. o Improvements in vignette speed. o Improvements in compilation speed. Changes in version 3.99.12 (2022-10-19) o Try to allow vignette to build successfully in the ARM64 Mac build: use a try(plot) in chunk fdfmutex2. o Use apa style citation and a few fixes to bib. o Minor additions to vignette. Changes in version 3.99.11 (2022-10-13) o Increase max.wall.time of two tests, as in very slow Windoze machines they can hit max wall time. Changes in version 3.99.10 (2022-10-13) o onlyCancer = FALSE by default in all calls to oncoSimul*. This is a possible BRAEKING CHANGE. o Plot fails with a meaningful error if simulations had unrecoverable exception or hit max wall time or max num tries. o Faster vignette. Changes in version 3.99.9 (2022-09-30) o Minor vignette split of code, to try to detect location of problem with ARM64 Mac build. Changes in version 3.99.8 (2022-09-15) o Using "Unity builds" to decrease build (compilation) time; see file inst/miscell/README_Unity_compilation. Changes in version 3.99.7 (2022-09-13) o Use c++14 and, in windows, do not use -O3: try to minimize build time. Changes in version 3.99.6 (2022-09-12) o Udpated exprtk. Changes in version 3.99.5 (2022-07-19) o Funding logo added to README.md and vignette. Changes in version 3.99.4 (2022-07-04) o Failing a test in test.Z-intervention.R in Mac OS; did not fix correctly previous time. Changes in version 3.99.3 (2022-06-30) o Failing a test in test.Z-intervention.R in Mac OS Changes in version 3.99.2 (2022-06-29) o Vignette: author list and references. Changes in version 3.99.1 (2022-06-25) o Users can specify birth and death rates as they want, including making both or just one frequency-dependent (thanks to Alberto González Klein). o Interventions (thanks to Javier Muñoz Haro). o User-defined variables and adaptive therapy (thanks to Javier López Cano). Changes in version 3.3.0 (2021-10-27) o Bump version number for BioC Changes in version 3.1.2 (2021-10-06) o Better test of poset transformation Changes in version 3.1.1 (2021-10-06) o XOR, AND, OR dependencies: plots of DAGs honor all possible values. o Few miscell minor changes. Changes in version 3.0 o MAJOR change: frequency dependent fitness available. o Removed v.1 functionality. o Multiple initMutants. o Added MAGELLAN's sources and functionality from MAGELLAN. Changes in version 2.99.93 (2021-04-30) o Fixed bugs and improved testing of rfitness with three-element scale vector. Changes in version 2.99.92 (2021-04-27) o rfitness: scale can take a three-element vector. o Vignette: examples (not run) for deviations from SSWM. Changes in version 2.99.9 (2021-04-22) o Fixed date typo in one citation. o We were inconsistent, allowing some examples of one gene. o Readme: nem. Changes in version 2.99.8 (2021-01-01) o Removing unused code. o Long tests: no longer using v.1. Changes in version 2.99.7 (2020-12-30) o Vignette: fixed two missing refs and add seed in two examples. Changes in version 2.99.6 (2020-12-30) o No longer v.1 functionality. o Slightly faster vignette. Changes in version 2.99.5 (2020-12-18) o Random timeouts when building in tokay2 (Windows, BioC); fixing seed in vignette. Changes in version 2.99.4 (2020-12-17) o Clean up of C++ code. Changes in version 2.99.3 (2020-12-13) o Remove unnecessary (and cluttering) output and irrelevant warnings when running tests. o Decrease execution time of longer running examples in man (Rd) files. o Decrease time of vignette. Changes in version 2.99.2 (2020-12-11) o Failed on test on Mac. Changes in version 2.99.1 (2020-12-10) o Bump version number for BioC, so it will become version 3.0.0 in next release. o Latest version of exprtk. Changes in version 2.21.995 (2020-12-09) o Vignette: rewrote most FDF examples using names (not numbers) for fitness specification. Changes in version 2.21.994 (2020-12-08) o Can start simulation from arbitrary configuration: multiple init mutants (and multispecies functionality). o Freq-dep-fitness does not need to have a WT in fitness tables. o Bumped version (to 2.21.xyz) for new BioC devel. Changes in version 2.19.993 (2020-12-01) o Added tests of mutator functionality with freq-dep-fitness. Changes in version 2.19.992 (2020-09-23) o currentTime can be used in freq-dep-fitness expressions o popSizes is passed to evalGenotypes (not genotypeFitness) o for freq-dep-fitness, type of freq. dep. argument can be guessed automatically Changes in version 2.19.991 (2020-06-03) o Updated ctb: added Magellan and exprTk and clarified contributions. o Updated version (to 2.19.xyz) for new BioC devel. Changes in version 2.17.998 (2020-05-20) o Fixed test.Z-magellan failure in Mac. o Occasional failures of @test.sample-prob.R#42 in Windows 386 o Fixed Wrestrict warnings in Windows from MAGELLAN's sources. o Cherry picked from master, as of 2020-05-20: o from: [13a4061] o to: [e1ef78a] o Already added: [519c8a7] to [f716534] Changes in version 2.17.997 (2020-04-27) o With R-devel, stringsAsFactors = FALSE by default. Fix tests o POM documentation. o With newest R-devel (01-28) getting "the condition has length > 1": fixed. o Cherry picked from master, as of 2020-03-17: o [6645512] : OK o [a273ac2] : OK o [307dc97] : already added [5436d80] o [bcb8543] : not needed (just version date/number) o [5f42713] : already added [3b488a0] o [eb2766b] : already added [3aba92d] Changes in version 2.17.996 (2020-01-28) o More freq-dep-fitness examples. Changes in version 2.17.995 (2020-01-25) o Reverted modifications to plot (see committ d182fbb) Changes in version 2.17.994 (2020-01-25) o plot: allow legend to be outside Changes in version 2.17.993 (2020-01-23) o Removed dependency on nem, to be deprecated. Adding nem's code (file nem_transitive_reduction.R). o Further additions of MAGELLAN's functionality and Additive model to rfitness. Merging from master. o These is from cherry-picking commits to master, as of 2020-01-22: o [eda2e75] o [4ab7e90] o [8e35201] o [832945b] o [aafb84e] o [fe0891e] o [286bf57] o [e221a8e] o [941df3d] o [59b9662] o [39c4d55] o [a245e44] o [114a930] o [49e8d40] o [df6d0cd] o [5a0be19] o [734bf76] Changes in version 2.17.992 (2019-12-19) o Oooops: forgot Makevars.win o fno-common: better way of dealing with verbose in magellan. [from commit 912503a and e7b549e in master ] o the equivalente of commit 9efd3ad is also included. Changes in version 2.17.991 (2019-12-18) o Compiles with fno-common (for gcc 10). o Fixed error "length(x) = 5 > 1' in coercion to 'logical(1)'" o rfitness: clarified log=TRUE and truncate_at_0 after log. o Magellan_stats: really return a vector. o Trying to prevent fscanf warning in FitnessLandscape/input.c o These is from cherry-picking commits to master, as of 2019-12-17: o [60533ab] o 2.17.3: (here is where fno-common should be) [though nothing needed to merge here] o [2dbc895] o link to Magellan_stats help o [73854e0] o fno-common o [92b7f4b] o renamed verbose [in one of MAGELLAN's C files] o [a6c95a3] o install-dir.sh o [ec15dbf] o Fixed error "length(x) = 5 > 1' in coercion to 'logical(1)'" o [8a06478] o Ochs and Desai: fixed typo o [94c9df7] o do not default to log when using Magellan_stats o [a8b5dae] o appveyor o [2e80c74] o rfitness: clarified log=TRUE and truncate_at_0 after log. o Magellan_stats: really return a vector. o [3e67e80] o Trying to prevent fscanf warning in FitnessLandscape/input.c o [b89a135] o appveyor file Changes in version 2.15.996 (2019-06-12) o Numerical issues in one test in i386 (Windows) Changes in version 2.15.995 (2019-06-12) o Added MAGELLAN's sources and functionality from MAGELLAN. Changes in version 2.15.994 (2019-05-25) o Windoze: giving up on current Rtools35, but working with Rtools40 (see Makevars.win) o Cleaned up a few compiler warnings. Changes in version 2.15.99 (2019-05-14) o Bumped version to match current Biocdevel. Changes in version 2.13.99 (1970-01-01) o frequency dependent fitness. This is a MAJOR addition. o (the date is bogus, of course) Changes in version 2.13.2 (2019-03-18) o changes in behavior of sample (see NEWS and https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17494) were leading to failures of some tests. Using RNGversion in some tests. Changes in version 2.13.1 (2019-02-07) o bumped to one over the BioC-3.9 version Changes in version 2.11.2 (2018-09-24) o works with STRICT_R_HEADERS Changes in version 2.11.1 o robustify test.fixation.R, Local max, tolerance Changes in version 2.10.0 o probDetect mechanism changed. This could be a BREAKING CHANGE. The expression divides by the baseline. For fixed initSize, this is simply a matter of changing the cPDetect. o fixation allows exact genotypes, includes tolerance, and checks for a successive number of specified periods o LOD: using only the strict Szendro et al. meaning. o POM: computed in C++. o Using fitness landscape directly when given as input (no conversion to epistasis) and several improvements in speed when using fitness landscapes as input. Changes in version 2.9.10 (2018-04-19) o test.Z-fixation: some tests only on Linux because rng is done in C++. Changes in version 2.9.9 (2018-04-10) o probDetect mechanism changed. This could be a BREAKING CHANGE. The expression divides by the baseline. For fixed initSize, this is simply a matter of changing the cPDetect. Changes in version 2.9.8 (2018-03-26) o fixation allows exact genotypes, includes tolerance, and checks for a successive number of specified periods Changes in version 2.9.7 (2018-02-20) o fixed crash in some conditions when run with stringsAsFactors = FALSE as global option Changes in version 2.9.6 (2017-12-27) o Updated citation. o An example (in miscell-files) about using and stopping with modules. o Prototype for sampling the single larges pop at last period (function largest_last_pop, commented out for now). Changes in version 2.9.5 o samplePop: new option "single-nowt" Changes in version 2.9.4 (2017-11-30) o Deal with the very rare NULL simulations in summary. Changes in version 2.9.3 (2017-11-27) o Make clang happy (do not use flandscape as DataFrame) Changes in version 2.9.2 (2017-11-24) o LOD: using only the strict Szendro et al. meaning. o POM: computed in C++. Changes in version 2.9.1 (2017-11-10) o Using fitness landscape directly when given as input (no conversion to epistasis) Changes in version 2.7.2 (2017-09-27) o genot_to_adj_mat in C++. o fast_peaks (for no backmutation cases). o Better explanation and testing of peaks and valleys. o Clarified simOGraph transitive reduction. o Better handling of ti corner cases. o Magellan reading fuctions adapted to output of newer (as of 2017-07) version of Magellan. o sorting gene names in allGenotypes_to_matrix. o sampledGenotypes: genotype names with sorted gene names. Changes in version 2.6.0 o Many additions to the vignette and documentation. o LOD and POM (lines of descent, path of maximum, sensu Szendro et al.). o Diversity of sampled genotypes. o Genotyping error can be added in samplePop. o fixation of a genotype/gene as stopping mechanism. o rfitness: shifting by subtraction and mu of normal distribution. o simOGraph: using proper transitive reduction. o simOGraph can also output rT data frames. o accessible genotypes now done in C++. o Handling of trivial cases in genotFitness. o Clarified McFarland parameterization. o Better (and better explained) estimates of simulation error for McFL. o AND of detectedSizeP and lastMaxDr. o sampledGenotypes in user code. o clonePhylog et al: deal with never any descendant. o samplePop can handle failed simulations graciously. o summary.oncosimulpop can handle failed simulations graciously. o Citation shows Bioinformatics paper. Changes in version 2.5.14 (2017-04-07) o Fixed repeated entries in NEWS for BioC 3.5. Changes in version 2.5.13 (2017-04-07) o Updated NEWS for BioC 3.5. Changes in version 2.5.12 (2017-02-18) o rfitness: allow simple forcing of wt to 1, shifting by subtraction, and specifying mu of normal distribution. o simOGraph: proper trm comparison. o Citation now shows Bioinformatics reference. Changes in version 2.5.11 (2017-01-27) o Transitive reduction: must call transitive.closure first. Changes in version 2.5.10 (2017-01-27) o Transitive reduction: calling nem in simOGraph Changes in version 2.5.9 (2017-01-09) o Added code coverage comments to vignette. Changes in version 2.5.8 (2016-12-17) o Handle trivial cases in genotFitness. Changes in version 2.5.7 (2016-12-15) o Clarified McFarland parameterization. Changes in version 2.5.6 (2016-12-14) o Fixed a few typos in help files. Changes in version 2.5.5 (2016-12-14) o Vignette: miscell changes (typos, etc) Changes in version 2.5.4 (2016-12-12) o Vignette: miscell changes (order of examples, typos, etc) Changes in version 2.5.3 (2016-12-12) o Vignette uses pander in tables. o Typos fixed and other enhancements in vignette. Changes in version 2.5.2 (2016-12-10) o Lots and lots of addition to vignette including benchmarks. o Diversity of sampled genotypes. o Genotyping error can be added in samplePop. o LOD and POM (lines of descent, path of maximum, sensu Szendro et al.). o simOGraph can also out rT data frames. o Better (and better explained) estimates of simulation error for McFL. Changes in version 2.5.1 (2016-11-12) o AND of detectedSizeP and lastMaxDr. o fixation as stopping mechanism. o sampledGenotypes in user code. o clonePhylog et al: deal with never any descendant. o samplePop can handle failed simulations graciously. o summary.oncosimulpop can handle failed simulations graciously. o accessible genotypes now done in C++. o OcurringDrivers should not be a factor. o samplePop always returns gene names. o to_Magellan is much faster with rfitness objects. o Several improvements in vignette (English and additional explanations). Changes in version 2.4.0 o Mutator phenotype and gene-specific mutation rates. o End simulations stochastically as a function of size. o Specify fitness by giving genotype-> fitness mapping. o Random fitness landscape generation. o Plots of fitness landscapes. o Vignette: using Rmd. o Several improvements in help and vignette. o Improved test coverage. o samplePop: sample at arbitrary sizes. o evalAllGenotypes: order = FALSE by default. Changes in version 2.3.17 (2017-09-22) o random2 for rfitness. o Vignette: decrease size and running time. Changes in version 2.3.16 (2017-09-19) o Help was not accurate for some probSize args Changes in version 2.3.15 (2017-09-14) o Typo in name (progresion) Changes in version 2.3.14 (2017-08-26) o Documentation improvements. Changes in version 2.3.13 (2017-08-19) o bioRxiv citation. o Using Rmd for vignette. o Improvements in vignette. Changes in version 2.3.12 (2017-08-10) o Increase N in some tests. Changes in version 2.3.11 (2017-08-10) o evalAllGenotypes: order = FALSE by default. o Clarified difference plotFitnessEffects and plotFitnessLandscape. Changes in version 2.3.10 (2017-07-14) o The windows check failure with mc.cores. Changes in version 2.3.9 (2017-07-09) o Accessible genotypes in rfitness and plotFitnessLandscape Changes in version 2.3.8 (2017-07-08) o PDBasline default is now 1.2. Changes in version 2.3.7 (2016-07-05) o Unused C++ code reorganiz. o Added tests o Vignette and documentation improvements. o End simulations stochastically as a function of size. Changes in version 2.3.6 (2016-06-25) o Improved test coverage Changes in version 2.3.5 (2016-06-25) o to_Magellan. Changes in version 2.3.4 (2016-06-24) o Failing some tests in Win 32-bits Changes in version 2.3.3 (2016-06-23) o Vignette improvements and typo fixes. o rfitness: generate fitness landscapes. o Plot of fitness landscapes. o Specify fitness by giving genotype-> fitness mapping. o Tests showing same gene in epist./DAG/order. o Clarified internal C++ unique/sorted in genotypes. o Checks initMutant correct and bug initMutant mutable pos. o samplePop: sample at arbitrary sizes. o plot.oncosimulpop using auto for color. o Mutator phenotype and gene-specific mutation rates. o Bug fixed: to_update set at 2 when mutating to pre-existing. o Lots and lots of new tests. Changes in version 2.2.0 o Plots of genotypes. o Stacked area and stream plots (code from Marc Taylor). o Example of modules and no epistasis. o Removed requirement of Root in geneToModule. o More tests (and reorganized them) o Miscell. improvements and typos fixed in documentation and vignette. o Added mutationPropGrowth as argument. o Some minor bug fixes and additional checks for user errors. Changes in version 2.1.6 (2016-04-14) o Adapt to changes in today's release of testthat (1.0.0) Changes in version 2.1.5 (2016-04-09) o Added a test of driverCounts, that does not depend on OS/compiler. Changes in version 2.1.4 (2016-04-09) o 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) o Fixed sporadic bug in countDrivers Changes in version 2.1.2 (2016-03-27) o Arguments to BNB_Algo5 explicit. o Example of modules and no epistasis. o Removed requirement of Root in geneToModule. o More tests (and reorganized them) o Miscell. improvements in documentation and vignette. Changes in version 2.1.1 (2016-03-07) o Added mutationPropGrowth as argument. o Stacked area and stream plots (code from Marc Taylor). o Plots of genotypes. o Expanded vignette. Changes in version 1.99.9 (2015-10-08) o Fixed NEWS file. o Removed empty file. Changes in version 1.99.8 (2015-10-01) o Test "initMutant with oncoSimulSample, 2" occasionally failed. Changes in version 1.99.7 (2015-09-27) o initMutant available in oncoSimulPop and oncoSimulSample. Changes in version 1.99.6 (2015-09-26) o Improved test coverage and removed stringsAsfactors from tests. o Consistent handling of corner cases in Bozic. o Miscell minor documentation improvements. Changes in version 1.99.5 (2015-06-25) o Fixed bug in initMutant, added tests, and vignette section. Changes in version 1.99.4 (2015-06-22) o Plotting true phylogenies. o Tried randutils, from O'Neill. Won't work with gcc-4.6. o bool issue in Windows/gcc-4.6. o Most all to all.equal in tests. Changes in version 1.99.3 (2015-06-19) o More examples to vignette o Using Makevars o More functionality to plot.fitnessEffects o Will Windoze work now? Changes in version 1.99.2 (2015-06-19) o Fixed typos and other minor in vignett. Changes in version 1.99.01 (2015-06-17) o Many MAJOR changes: we are done moving to v.2 o New way of specifying restrictions (v.2) that allows arbitrary epistatic interactions and order effects, and very large (larger than 50000 genes) genomes. o When onlyCancer = TRUE, all iterations now in C++. o Many tests added. o Random DAG generation. o Some defaults for v.1 changed. Changes in version 1.99.1 (2015-06-18) o Try to compile in Windoze with the SSTR again. o Reduce size of RData objects with resaveRdaFiles. o Try to compile in Mac: mt RNG must include random in all files. Changes in version 1.99.00 (2015-04-23) o Accumulated changes of former 99.1.2 to 99.1.14: o changes in intermediate version 1.99.1.14 (2015-04-23): o Now are things OK (I messed up the repos) o changes in intermediate version 99.1.13 (2015-04-23) o Added a couple of drop = FALSE. Their absence lead to crashes in some strange, borderline cases. o Increased version to make unambiguous version used for anal. CBN. o changes in intermediate version 99.1.12 (2015-04-22) o Removed lots of unused conversion helpers and added more strict checks and tests of those checks. o changes in intermediate version 99.1.11 (2015-04-18) o Tests of conversion helpers now really working. o changes in intermediate version 99.1.10 (2015-04-16) o Added conversion helpers as separate file. o Added tests of conversion helpers. o Added generate-random-trees code (separate file). o More strict now on the poset format and conversions. o changes in intermediate version 99.1.9 (2015-04-09) o added null mutation for when we run out of mutable positions, and since not clear how to use BNB then. o changes in intermediate version 99.1.8 (2015-04-03) o added extraTime. o changes in intermediate version 99.1.7 (2015-04-03) o endTimeEvery removed. Now using minDDrPopSize if needed. o changes in intermediate version 99.1.6 (2015-03-20) o untilcancer and oncoSimulSample working together o changes in intermediate version 99.1.5 (2015-03-20) o Using the untilcancer branch o changes in intermediate version 99.1.4 (2014-12-24) o Added computation of min. of ratio birth/mutation and death/mutation. o changes in intermediate version 99.1.3 (2014-12-23) o Fixed segfault when hitting wall time and sampling only once. o changes in intermediate version 99.1.2 (2014-12-16) o Sampling only once Changes in version 0.99.2 (2014-07-14) o Consistently using indentation in .Rd files. Changes in version 0.99.1 (2014-07-14) o Minor changes for BioConductor submission: o extended description o minor changes to vignette o improved documentation of posets Changes in version 0.99.0 (2014-06-26) o 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 o Versions K, M, O, P working. o Versions O and P with u_1 and u_2 so as to provide comparable results to K and M. o Sometimes problems with ti==0. preBioC_1.0.5 2013-03-22 o Cleaned up the code and left only version P. o Added memory limits. preBioC_1.0.6 2013-03-22 o Added mutator genotype o Only species with fitness > 0 go through ti calculation. preBioC_1.0.7 2013-03-25 o Start run from a given mutation preBioC_1.0.8 2013-04-02 o Limits on outNS size to prevent segfaults. o Do not transpose outNS in R (do in C++). o Better code for sp_to_remove. preBioC_1.0.9 2013-04-02 o Some code in R moved to C++. o Minimize increases in RAM in R related to handling of temporaries. o Moved out of main R function the creation of rarely used objects. preBioC_1.0.10 2013-04-04 o Info on actual drivers returned from C++ preBioC_1.0.11 2013-04-04 o Added time limit to main C++ loop execution and changed exploration files accordingly. preBioC_1.0.12 2013-04-15 o Per sample driver and populations stats in C++. o Removed some rarely used output from C++. preBioC_1.0.13 2013-04-24 o Added continuous time Bozic fitness preBioC_1.0.14 2013-04-25 o Added Beerenwinkel et al., 2007 fitness. o Added a few checks for loss of precision. o Added thinning of output. preBioC_1.0.15 2013-04-26 o Unmet restrictions: allow variable penalty. o Safety initializations and a bug fix. preBioC_1.0.16 2013-05-01 o Unmet restrictions: better mechanism (which also fixes a bug). o Changed and cleared up the mess in the example trees. o This is the version used to launch the first set of massive simulations (bozic and exp) preBioC_1.0.17 2013-05-20 o Added McFarland et al. 2013 fitness. o Some code cleaning. o Fewer arguments in R function have default values (force user to be explicit). preBioC_1.0.18 2013-07-25 o Renamed the package o Tried to use Youn and Simon's method. Calling code added. o Tried to use Sakoparnig and Beerenwinkel's Bayesian CBN. Calling code added. o Fixed non-working code in metrics due to changes in functions in graph. o Added simple code for temporal order. o Added old code for clonal ordering (not finished). o Robustified other functions and start up (cbn, metrics, plotting, etc). o No dependencies on libgmp (multiprecission arith.) now; removed from Makevars. o Warning in R code if endTimeEvery is not negative in simulation models where it should probably be negative. preBioC_1.0.19 2014-xxx o Changes and addition to plotting functions. o Added comparison of adjacency matrices and other miscell functions from the processing code of the simulations.