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.