NEWS

---

OncoSimulR 4.7.7 (2024-09-18)

• 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.

OncoSimulR 4.7.6 (2024-09-16)

• 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.

OncoSimulR 4.7.5 (2024-09-12)

• Try to work around (and ask for help) for tests that fail in the BioC kjohnson3 machine (maOS 13.6.5, arm64).

OncoSimulR 4.7.4 (2024-07-30)

• 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).

OncoSimulR 4.7.3 (2024-07-26)

• 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).

OncoSimulR 4.7.2 (2024-07-25)

• 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).

OncoSimulR 4.7.1 (2024-07-23)

• Try to work around (and ask for help) for a vignette example that fails in the BioC kjohnson3 machine (maOS 13.6.5, arm64).
• Miscell minor: incorporate 361ccdc to 1bc3cbd (in main github repo) to the BioC version.
• Fixed Note "Lost braces in \itemize; meant \describe ?"
• Updated vignette address to IIBM new name.

OncoSimulR 4.3.3 (2023-07-17)

• One test failing on Linux aarch64: fixed (by commenting out, which is the right thing to do).

OncoSimulR 4.3.2 (2023-06-03)

• Allow passing a seed to MAGELLAN's random fitness landscapes in rfitness function.
• Fixed bug in rfitness when using a 3-element vector for scaling, and one or more fitness values had the same value as WT.

OncoSimulR 4.1.4 (2023-03-08)

• Updated exprTk (thanks to pull request from Arash Partow).

OncoSimulR 4.1.3 (2023-02-20)

• no need to specify CXX_STD = CXX14 (the default since R-4.1.0).

OncoSimulR 4.1.2 (2023-02-20)

• NAMESPACE: do not import .rbind.data.table (no longer exported from data.table 1.14.8, and not needed with R >= 4.0.0).

OncoSimulR 4.1 (2022-11-24)

• Faster, cleaner, and better tests of interventions.

OncoSimulR 4.0

• MAJOR change: users can simulate interventions and adaptive therapy, as well as define, track, and use in fitness-dependent specifications user-defined variables.
• MAJOR change: users can specify birth and death rates as they want, including making both or just one frequency-dependent.
• onlyCancer = FALSE by default in all calls to oncoSimul*. This is a possible BRAEKING CHANGE.
• Plot fails with a meaningful error if simulations had unrecoverable exception or hit max wall time or max num tries.
• Improvements in vignette speed.
• Improvements in compilation speed.

OncoSimulR 3.99.12 (2022-10-19)

• Try to allow vignette to build successfully in the ARM64 Mac build: use a try(plot) in chunk fdfmutex2.
• Use apa style citation and a few fixes to bib.
• Minor additions to vignette.

OncoSimulR 3.99.11 (2022-10-13)

• Increase max.wall.time of two tests, as in very slow Windoze machines they can hit max wall time.

OncoSimulR 3.99.10 (2022-10-13)

• onlyCancer = FALSE by default in all calls to oncoSimul*. This is a possible BRAEKING CHANGE.
• Plot fails with a meaningful error if simulations had unrecoverable exception or hit max wall time or max num tries.
• Faster vignette.

OncoSimulR 3.99.9 (2022-09-30)

• Minor vignette split of code, to try to detect location of problem with ARM64 Mac build.

OncoSimulR 3.99.8 (2022-09-15)

• Using "Unity builds" to decrease build (compilation) time; see file inst/miscell/README_Unity_compilation.

OncoSimulR 3.99.7 (2022-09-13)

• Use c++14 and, in windows, do not use -O3: try to minimize build time.

OncoSimulR 3.99.6 (2022-09-12)

• Udpated exprtk.

OncoSimulR 3.99.5 (2022-07-19)

• Funding logo added to README.md and vignette.

OncoSimulR 3.99.4 (2022-07-04)

• Failing a test in test.Z-intervention.R in Mac OS; did not fix correctly previous time.

OncoSimulR 3.99.3 (2022-06-30)

• Failing a test in test.Z-intervention.R in Mac OS

OncoSimulR 3.99.2 (2022-06-29)

• Vignette: author list and references.

OncoSimulR 3.99.1 (2022-06-25)

• Users can specify birth and death rates as they want, including making both or just one frequency-dependent (thanks to Alberto González Klein).
• Interventions (thanks to Javier Muñoz Haro).
• User-defined variables and adaptive therapy (thanks to Javier López Cano).

OncoSimulR 3.3.0 (2021-10-27)

• Bump version number for BioC

OncoSimulR 3.1.2 (2021-10-06)

• Better test of poset transformation

OncoSimulR 3.1.1 (2021-10-06)

• XOR, AND, OR dependencies: plots of DAGs honor all possible values.
• Few miscell minor changes.

OncoSimulR 3.0

• MAJOR change: frequency dependent fitness available.
• Removed v.1 functionality.
• Multiple initMutants.
• Added MAGELLAN's sources and functionality from MAGELLAN.

OncoSimulR 2.99.93 (2021-04-30)

• Fixed bugs and improved testing of rfitness with three-element scale vector.

OncoSimulR 2.99.92 (2021-04-27)

• rfitness: scale can take a three-element vector.
• Vignette: examples (not run) for deviations from SSWM.

OncoSimulR 2.99.9 (2021-04-22)

• Fixed date typo in one citation.
• We were inconsistent, allowing some examples of one gene.
• Readme: nem.

OncoSimulR 2.99.8 (2021-01-01)

• Removing unused code.
• Long tests: no longer using v.1.

OncoSimulR 2.99.7 (2020-12-30)

• Vignette: fixed two missing refs and add seed in two examples.

OncoSimulR 2.99.6 (2020-12-30)

• No longer v.1 functionality.
• Slightly faster vignette.

OncoSimulR 2.99.5 (2020-12-18)

• Random timeouts when building in tokay2 (Windows, BioC); fixing seed in vignette.

OncoSimulR 2.99.4 (2020-12-17)

• Clean up of C++ code.

OncoSimulR 2.99.3 (2020-12-13)

• Remove unnecessary (and cluttering) output and irrelevant warnings when running tests.
• Decrease execution time of longer running examples in man (Rd) files.
• Decrease time of vignette.

OncoSimulR 2.99.2 (2020-12-11)

• Failed on test on Mac.

OncoSimulR 2.99.1 (2020-12-10)

• Bump version number for BioC, so it will become version 3.0.0 in next release.
• Latest version of exprtk.

OncoSimulR 2.21.995 (2020-12-09)

• Vignette: rewrote most FDF examples using names (not numbers) for fitness specification.

OncoSimulR 2.21.994 (2020-12-08)

• Can start simulation from arbitrary configuration: multiple init mutants (and multispecies functionality).
• Freq-dep-fitness does not need to have a WT in fitness tables.
• Bumped version (to 2.21.xyz) for new BioC devel.

OncoSimulR 2.19.993 (2020-12-01)

• Added tests of mutator functionality with freq-dep-fitness.

OncoSimulR 2.19.992 (2020-09-23)

• currentTime can be used in freq-dep-fitness expressions
• popSizes is passed to evalGenotypes (not genotypeFitness)
• for freq-dep-fitness, type of freq. dep. argument can be guessed automatically

OncoSimulR 2.19.991 (2020-06-03)

• Updated ctb: added Magellan and exprTk and clarified contributions.
• Updated version (to 2.19.xyz) for new BioC devel.

OncoSimulR 2.17.998 (2020-05-20)

• Fixed test.Z-magellan failure in Mac.
• Occasional failures of @test.sample-prob.R#42 in Windows 386
• Fixed Wrestrict warnings in Windows from MAGELLAN's sources.
• Cherry picked from master, as of 2020-05-20:
• from: [13a4061]
• to: [e1ef78a]
• Already added: [519c8a7] to [f716534]

OncoSimulR 2.17.997 (2020-04-27)

• With R-devel, stringsAsFactors = FALSE by default. Fix tests
• POM documentation.
• With newest R-devel (01-28) getting "the condition has length > 1": fixed.
• Cherry picked from master, as of 2020-03-17:
• [6645512] : OK
• [a273ac2] : OK
• [307dc97] : already added [5436d80]
• [bcb8543] : not needed (just version date/number)
• [5f42713] : already added [3b488a0]
• [eb2766b] : already added [3aba92d]

OncoSimulR 2.17.996 (2020-01-28)

• More freq-dep-fitness examples.

OncoSimulR 2.17.995 (2020-01-25)

• Reverted modifications to plot (see committ d182fbb)

OncoSimulR 2.17.994 (2020-01-25)

• plot: allow legend to be outside

OncoSimulR 2.17.993 (2020-01-23)

• Removed dependency on nem, to be deprecated. Adding nem's code (file nem_transitive_reduction.R).
• Further additions of MAGELLAN's functionality and Additive model to rfitness. Merging from master.
• These is from cherry-picking commits to master, as of 2020-01-22:
• [eda2e75]
• [4ab7e90]
• [8e35201]
• [832945b]
• [aafb84e]
• [fe0891e]
• [286bf57]
• [e221a8e]
• [941df3d]
• [59b9662]
• [39c4d55]
• [a245e44]
• [114a930]
• [49e8d40]
• [df6d0cd]
• [5a0be19]
• [734bf76]

OncoSimulR 2.17.992 (2019-12-19)

• Oooops: forgot Makevars.win
• fno-common: better way of dealing with verbose in magellan. [from commit 912503a and e7b549e in master ]
• the equivalente of commit 9efd3ad is also included.

OncoSimulR 2.17.991 (2019-12-18)

• Compiles with fno-common (for gcc 10).
• Fixed error "length(x) = 5 > 1' in coercion to 'logical(1)'"
• rfitness: clarified log=TRUE and truncate_at_0 after log.
• Magellan_stats: really return a vector.
• Trying to prevent fscanf warning in FitnessLandscape/input.c
• These is from cherry-picking commits to master, as of 2019-12-17:
• [60533ab]
• 2.17.3: (here is where fno-common should be) [though nothing needed to merge here]
• [2dbc895]
• link to Magellan_stats help
• [73854e0]
• fno-common
• [92b7f4b]
• renamed verbose [in one of MAGELLAN's C files]
• [a6c95a3]
• install-dir.sh
• [ec15dbf]
• Fixed error "length(x) = 5 > 1' in coercion to 'logical(1)'"
• [8a06478]
• Ochs and Desai: fixed typo
• [94c9df7]
• do not default to log when using Magellan_stats
• [a8b5dae]
• appveyor
• [2e80c74]
• rfitness: clarified log=TRUE and truncate_at_0 after log.
• Magellan_stats: really return a vector.
• [3e67e80]
• Trying to prevent fscanf warning in FitnessLandscape/input.c
• [b89a135]
• appveyor file

OncoSimulR 2.15.996 (2019-06-12)

• Numerical issues in one test in i386 (Windows)

OncoSimulR 2.15.995 (2019-06-12)

• Added MAGELLAN's sources and functionality from MAGELLAN.

OncoSimulR 2.15.994 (2019-05-25)

• Windoze: giving up on current Rtools35, but working with Rtools40 (see Makevars.win)
• Cleaned up a few compiler warnings.

OncoSimulR 2.15.99 (2019-05-14)

• Bumped version to match current Biocdevel.

OncoSimulR 2.13.99 (1970-01-01)

• frequency dependent fitness. This is a MAJOR addition.
• (the date is bogus, of course)

OncoSimulR 2.13.2 (2019-03-18)

• 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.

OncoSimulR 2.13.1 (2019-02-07)

• bumped to one over the BioC-3.9 version

OncoSimulR 2.11.2 (2018-09-24)

• works with STRICT_R_HEADERS

OncoSimulR 2.11.1

• robustify test.fixation.R, Local max, tolerance

OncoSimulR 2.10.0

• 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.
• fixation allows exact genotypes, includes tolerance, and checks for a successive number of specified periods
• LOD: using only the strict Szendro et al. meaning.
• POM: computed in C++.
• Using fitness landscape directly when given as input (no conversion to epistasis) and several improvements in speed when using fitness landscapes as input.

OncoSimulR 2.9.10 (2018-04-19)

• test.Z-fixation: some tests only on Linux because rng is done in C++.

OncoSimulR 2.9.9 (2018-04-10)

• 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.

OncoSimulR 2.9.8 (2018-03-26)

• fixation allows exact genotypes, includes tolerance, and checks for a successive number of specified periods

OncoSimulR 2.9.7 (2018-02-20)

• fixed crash in some conditions when run with stringsAsFactors = FALSE as global option

OncoSimulR 2.9.6 (2017-12-27)

• Updated citation.
• An example (in miscell-files) about using and stopping with modules.
• Prototype for sampling the single larges pop at last period (function largest_last_pop, commented out for now).

OncoSimulR 2.9.5

• samplePop: new option "single-nowt"

OncoSimulR 2.9.4 (2017-11-30)

• Deal with the very rare NULL simulations in summary.

OncoSimulR 2.9.3 (2017-11-27)

• Make clang happy (do not use flandscape as DataFrame)

OncoSimulR 2.9.2 (2017-11-24)

• LOD: using only the strict Szendro et al. meaning.
• POM: computed in C++.

OncoSimulR 2.9.1 (2017-11-10)

• Using fitness landscape directly when given as input (no conversion to epistasis)

OncoSimulR 2.7.2 (2017-09-27)

• genot_to_adj_mat in C++.
• fast_peaks (for no backmutation cases).
• Better explanation and testing of peaks and valleys.
• Clarified simOGraph transitive reduction.
• Better handling of ti corner cases.
• Magellan reading fuctions adapted to output of newer (as of 2017-07) version of Magellan.
• sorting gene names in allGenotypes_to_matrix.
• sampledGenotypes: genotype names with sorted gene names.

OncoSimulR 2.6.0

• Many additions to the vignette and documentation.
• LOD and POM (lines of descent, path of maximum, sensu Szendro et al.).
• Diversity of sampled genotypes.
• Genotyping error can be added in samplePop.
• fixation of a genotype/gene as stopping mechanism.
• rfitness: shifting by subtraction and mu of normal distribution.
• simOGraph: using proper transitive reduction.
• simOGraph can also output rT data frames.
• accessible genotypes now done in C++.
• Handling of trivial cases in genotFitness.
• Clarified McFarland parameterization.
• Better (and better explained) estimates of simulation error for McFL.
• AND of detectedSizeP and lastMaxDr.
• sampledGenotypes in user code.
• clonePhylog et al: deal with never any descendant.
• samplePop can handle failed simulations graciously.
• summary.oncosimulpop can handle failed simulations graciously.
• Citation shows Bioinformatics paper.

OncoSimulR 2.5.14 (2017-04-07)

• Fixed repeated entries in NEWS for BioC 3.5.

OncoSimulR 2.5.13 (2017-04-07)

• Updated NEWS for BioC 3.5.

OncoSimulR 2.5.12 (2017-02-18)

• rfitness: allow simple forcing of wt to 1, shifting by subtraction, and specifying mu of normal distribution.
• simOGraph: proper trm comparison.
• Citation now shows Bioinformatics reference.

OncoSimulR 2.5.11 (2017-01-27)

• Transitive reduction: must call transitive.closure first.

OncoSimulR 2.5.10 (2017-01-27)

• Transitive reduction: calling nem in simOGraph

OncoSimulR 2.5.9 (2017-01-09)

• Added code coverage comments to vignette.

OncoSimulR 2.5.8 (2016-12-17)

• Handle trivial cases in genotFitness.

OncoSimulR 2.5.7 (2016-12-15)

• Clarified McFarland parameterization.

OncoSimulR 2.5.6 (2016-12-14)

• Fixed a few typos in help files.

OncoSimulR 2.5.5 (2016-12-14)

• Vignette: miscell changes (typos, etc)

OncoSimulR 2.5.4 (2016-12-12)

• Vignette: miscell changes (order of examples, typos, etc)

OncoSimulR 2.5.3 (2016-12-12)

• Vignette uses pander in tables.
• Typos fixed and other enhancements in vignette.

OncoSimulR 2.5.2 (2016-12-10)

• Lots and lots of addition to vignette including benchmarks.
• Diversity of sampled genotypes.
• Genotyping error can be added in samplePop.
• LOD and POM (lines of descent, path of maximum, sensu Szendro et al.).
• simOGraph can also out rT data frames.
• Better (and better explained) estimates of simulation error for McFL.

OncoSimulR 2.5.1 (2016-11-12)

• AND of detectedSizeP and lastMaxDr.
• fixation as stopping mechanism.
• sampledGenotypes in user code.
• clonePhylog et al: deal with never any descendant.
• samplePop can handle failed simulations graciously.
• summary.oncosimulpop can handle failed simulations graciously.
• accessible genotypes now done in C++.
• OcurringDrivers should not be a factor.
• samplePop always returns gene names.
• to_Magellan is much faster with rfitness objects.
• Several improvements in vignette (English and additional explanations).

OncoSimulR 2.4.0

• Mutator phenotype and gene-specific mutation rates.
• End simulations stochastically as a function of size.
• Specify fitness by giving genotype-> fitness mapping.
• Random fitness landscape generation.
• Plots of fitness landscapes.
• Vignette: using Rmd.
• Several improvements in help and vignette.
• Improved test coverage.
• samplePop: sample at arbitrary sizes.
• evalAllGenotypes: order = FALSE by default.

OncoSimulR 2.3.17 (2017-09-22)

• random2 for rfitness.
• Vignette: decrease size and running time.

OncoSimulR 2.3.16 (2017-09-19)

• Help was not accurate for some probSize args

OncoSimulR 2.3.15 (2017-09-14)

• Typo in name (progresion)

OncoSimulR 2.3.14 (2017-08-26)

• Documentation improvements.

OncoSimulR 2.3.13 (2017-08-19)

• bioRxiv citation.
• Using Rmd for vignette.
• Improvements in vignette.

OncoSimulR 2.3.12 (2017-08-10)

• Increase N in some tests.

OncoSimulR 2.3.11 (2017-08-10)

• evalAllGenotypes: order = FALSE by default.
• Clarified difference plotFitnessEffects and plotFitnessLandscape.

OncoSimulR 2.3.10 (2017-07-14)

• The windows check failure with mc.cores.

OncoSimulR 2.3.9 (2017-07-09)

• Accessible genotypes in rfitness and plotFitnessLandscape

OncoSimulR 2.3.8 (2017-07-08)

• PDBasline default is now 1.2.

OncoSimulR 2.3.7 (2016-07-05)

• Unused C++ code reorganiz.
• Added tests
• Vignette and documentation improvements.
• End simulations stochastically as a function of size.

OncoSimulR 2.3.6 (2016-06-25)

• Improved test coverage

OncoSimulR 2.3.5 (2016-06-25)

• to_Magellan.

OncoSimulR 2.3.4 (2016-06-24)

• Failing some tests in Win 32-bits

OncoSimulR 2.3.3 (2016-06-23)

• Vignette improvements and typo fixes.
• rfitness: generate fitness landscapes.
• Plot of fitness landscapes.
• Specify fitness by giving genotype-> fitness mapping.
• Tests showing same gene in epist./DAG/order.
• Clarified internal C++ unique/sorted in genotypes.
• Checks initMutant correct and bug initMutant mutable pos.
• samplePop: sample at arbitrary sizes.
• plot.oncosimulpop using auto for color.
• Mutator phenotype and gene-specific mutation rates.
• Bug fixed: to_update set at 2 when mutating to pre-existing.
• Lots and lots of new tests.

OncoSimulR 2.2.0

• 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.

OncoSimulR 2.1.6 (2016-04-14)

• Adapt to changes in today's release of testthat (1.0.0)

OncoSimulR 2.1.5 (2016-04-09)

• Added a test of driverCounts, that does not depend on OS/compiler.

OncoSimulR 2.1.4 (2016-04-09)

• Moved to manual tests that depend on OS/compiler (for reproduction of random number stream in C++).

OncoSimulR 2.1.3 (2016-04-04)

• Fixed sporadic bug in countDrivers

OncoSimulR 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.

OncoSimulR 2.1.1 (2016-03-07)

• Added mutationPropGrowth as argument.
• Stacked area and stream plots (code from Marc Taylor).
• Plots of genotypes.
• Expanded vignette.

OncoSimulR 1.99.9 (2015-10-08)

• Fixed NEWS file.
• Removed empty file.

OncoSimulR 1.99.8 (2015-10-01)

• Test "initMutant with oncoSimulSample, 2" occasionally failed.

OncoSimulR 1.99.7 (2015-09-27)

• initMutant available in oncoSimulPop and oncoSimulSample.

OncoSimulR 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.

OncoSimulR 1.99.5 (2015-06-25)

• Fixed bug in initMutant, added tests, and vignette section.

OncoSimulR 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.

OncoSimulR 1.99.3 (2015-06-19)

• More examples to vignette
• Using Makevars
• More functionality to plot.fitnessEffects
• Will Windoze work now?

OncoSimulR 1.99.2 (2015-06-19)

• Fixed typos and other minor in vignett.

OncoSimulR 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.

OncoSimulR 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.

OncoSimulR 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

OncoSimulR 0.99.2 (2014-07-14)

• Consistently using indentation in .Rd files.

OncoSimulR 0.99.1 (2014-07-14)

• Minor changes for BioConductor submission:
• extended description
• minor changes to vignette
• improved documentation of posets

OncoSimulR 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.