Changes in version 4.6.1 (2024-10-09):
- Remove support for maOS with arm64 (i.e., kjohnson3
and kjohnson1 machines).
Changes in version 4.3.3 (2023-07-17):
- 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):
- 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.
Changes in version 4.1.4 (2023-03-08):
- Updated exprTk (thanks to pull request from Arash
Partow).
Changes in version 4.1.3 (2023-02-20):
- no need to specify CXX_STD = CXX14 (the default since
R-4.1.0).
Changes in version 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).
Changes in version 4.1 (2022-11-24):
- Faster, cleaner, and better tests of interventions.
Changes in version 4.0 (for BioC 3.16):
- 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.
Changes in version 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.
Changes in version 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.
Changes in version 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.
Changes in version 3.99.9 (2022-09-30):
- 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):
- Using "Unity builds" to decrease build (compilation) time;
see file inst/miscell/README_Unity_compilation.
Changes in version 3.99.7 (2022-09-13):
- Use c++14 and, in windows, do not use -O3: try to minimize
build time.
Changes in version 3.99.6 (2022-09-12):
- Udpated exprtk.
Changes in version 3.99.5 (2022-07-19):
- Funding logo added to README.md and vignette.
Changes in version 3.99.4 (2022-07-04):
- 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):
- Failing a test in test.Z-intervention.R in Mac OS
Changes in version 3.99.2 (2022-06-29):
- Vignette: author list and references.
Changes in version 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).
Changes in version 3.3.0 (2021-10-27):
- Bump version number for BioC
Changes in version 3.1.2 (2021-10-06):
- Better test of poset transformation
Changes in version 3.1.1 (2021-10-06):
- XOR, AND, OR dependencies: plots of DAGs honor all possible values.
- Few miscell minor changes.
Changes in version 3.0 (for BioC 3.13):
- MAJOR change: frequency dependent fitness available.
- Removed v.1 functionality.
- Multiple initMutants.
- Added MAGELLAN's sources and functionality from MAGELLAN.
Changes in version 2.99.93 (2021-04-30):
- Fixed bugs and improved testing of rfitness with
three-element scale vector.
Changes in version 2.99.92 (2021-04-27):
- rfitness: scale can take a three-element vector.
- Vignette: examples (not run) for deviations from SSWM.
Changes in version 2.99.9 (2021-04-22):
- Fixed date typo in one citation.
- We were inconsistent, allowing some examples of one gene.
- Readme: nem.
Changes in version 2.99.8 (2021-01-01):
- Removing unused code.
- Long tests: no longer using v.1.
Changes in version 2.99.7 (2020-12-30):
- Vignette: fixed two missing refs and add seed in two examples.
Changes in version 2.99.6 (2020-12-30):
- No longer v.1 functionality.
- Slightly faster vignette.
Changes in version 2.99.5 (2020-12-18):
- Random timeouts when building in tokay2 (Windows, BioC); fixing
seed in vignette.
Changes in version 2.99.4 (2020-12-17):
- Clean up of C++ code.
Changes in version 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.
Changes in version 2.99.2 (2020-12-11):
- Failed on test on Mac.
Changes in version 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.
Changes in version 2.21.995 (2020-12-09):
- Vignette: rewrote most FDF examples using names (not numbers)
for fitness specification.
Changes in version 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.
Changes in version 2.19.993 (2020-12-01):
- Added tests of mutator functionality with freq-dep-fitness.
Changes in version 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
Changes in version 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.
Changes in version 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]
Changes in version 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]
Changes in version 2.17.996 (2020-01-28):
- More freq-dep-fitness examples.
Changes in version 2.17.995 (2020-01-25):
- Reverted modifications to plot (see committ d182fbb)
Changes in version 2.17.994 (2020-01-25):
- plot: allow legend to be outside
Changes in version 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]
Changes in version 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.
Changes in version 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
Changes in version 2.15.996 (2019-06-12):
- Numerical issues in one test in i386 (Windows)
Changes in version 2.15.995 (2019-06-12):
- Added MAGELLAN's sources and functionality from MAGELLAN.
Changes in version 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.
Changes in version 2.15.99 (2019-05-14):
- Bumped version to match current Biocdevel.
Changes in version 2.13.99 (1970-01-01):
- frequency dependent fitness. This is a MAJOR addition.
- (the date is bogus, of course)
Changes in version 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.
Changes in version 2.13.1 (2019-02-07):
- bumped to one over the BioC-3.9 version
Changes in version 2.11.2 (2018-09-24):
- works with STRICT_R_HEADERS
Changes in version 2.11.1:
- robustify test.fixation.R, Local max, tolerance
Changes in version 2.10.0 (for BioC 3.7):
- 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.
Changes in version 2.9.10 (2018-04-19):
- test.Z-fixation: some tests only on Linux because rng is done in
C++.
Changes in version 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.
Changes in version 2.9.8 (2018-03-26):
- fixation allows exact genotypes, includes tolerance,
and checks for a successive number of specified periods
Changes in version 2.9.7 (2018-02-20):
- fixed crash in some conditions when run with
stringsAsFactors = FALSE as global option
Changes in version 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).
Changes in version 2.9.5 (2017-12-7):
- samplePop: new option "single-nowt"
Changes in version 2.9.4 (2017-11-30):
- Deal with the very rare NULL simulations in summary.
Changes in version 2.9.3 (2017-11-27):
- Make clang happy (do not use flandscape as DataFrame)
Changes in version 2.9.2 (2017-11-24):
- LOD: using only the strict Szendro et al. meaning.
- POM: computed in C++.
Changes in version 2.9.1 (2017-11-10):
- Using fitness landscape directly when given as input (no
conversion to epistasis)
Changes in version 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.
Changes in version 2.6.0 (for BioC 3.5):
- 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.
Changes in version 2.5.14 (2017-04-07):
- Fixed repeated entries in NEWS for BioC 3.5.
Changes in version 2.5.13 (2017-04-07):
- Updated NEWS for BioC 3.5.
Changes in version 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.
Changes in version 2.5.11 (2017-01-27):
- Transitive reduction: must call transitive.closure first.
Changes in version 2.5.10 (2017-01-27):
- Transitive reduction: calling nem in simOGraph
Changes in version 2.5.9 (2017-01-09):
- Added code coverage comments to vignette.
Changes in version 2.5.8 (2016-12-17):
- Handle trivial cases in genotFitness.
Changes in version 2.5.7 (2016-12-15):
- Clarified McFarland parameterization.
Changes in version 2.5.6 (2016-12-14):
- Fixed a few typos in help files.
Changes in version 2.5.5 (2016-12-14):
- Vignette: miscell changes (typos, etc)
Changes in version 2.5.4 (2016-12-12):
- Vignette: miscell changes (order of examples, typos, etc)
Changes in version 2.5.3 (2016-12-12):
- Vignette uses pander in tables.
- Typos fixed and other enhancements in vignette.
Changes in version 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.
Changes in version 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).
Changes in version 2.4.0 (for BioC 3.4):
- 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.
Changes in version 2.3.17 (2017-09-22):
- random2 for rfitness.
- Vignette: decrease size and running time.
Changes in version 2.3.16 (2017-09-19):
- Help was not accurate for some probSize args
Changes in version 2.3.15 (2017-09-14):
- Typo in name (progresion)
Changes in version 2.3.14 (2017-08-26):
- Documentation improvements.
Changes in version 2.3.13 (2017-08-19):
- bioRxiv citation.
- Using Rmd for vignette.
- Improvements in vignette.
Changes in version 2.3.12 (2017-08-10):
- Increase N in some tests.
Changes in version 2.3.11 (2017-08-10):
- evalAllGenotypes: order = FALSE by default.
- Clarified difference plotFitnessEffects and plotFitnessLandscape.
Changes in version 2.3.10 (2017-07-14):
- The windows check failure with mc.cores.
Changes in version 2.3.9 (2017-07-09):
- Accessible genotypes in rfitness and plotFitnessLandscape
Changes in version 2.3.8 (2017-07-08):
- PDBasline default is now 1.2.
Changes in version 2.3.7 (2016-07-05):
- Unused C++ code reorganiz.
- Added tests
- Vignette and documentation improvements.
- End simulations stochastically as a function of size.
Changes in version 2.3.6 (2016-06-25):
- Improved test coverage
Changes in version 2.3.5 (2016-06-25):
- to_Magellan.
Changes in version 2.3.4 (2016-06-24):
- Failing some tests in Win 32-bits
Changes in version 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.
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.