inst/NEWS
2d6b9859
 Changes in version 2.16.1 (2020-04-10):
 	- Fixed warning from POM and LOD help (undocumented ...)
 	- Dealing with "the condition has length > 1" and
 	  "length(x) = 5 > 1' in coercion to 'logical(1)' errors.
 
fefc3cfd
 Changes in version 2.15.2 (2019-08-14):
 	- Trying to prevent fscanf warning in FitnessLandscape/input.c
 
fd073de1
 Changes in version 2.15.1 (2019-06-06):
 	- Added MAGELLAN's sources and functionality from MAGELLAN.
 	
 Changes in version 2.15.0 (2019-06-06):
 	- Bumped version to match current Biocdevel.
 	
4ac900b7
 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.
 
edc25f80
 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
 	
65fa139d
 Changes in version 2.11.1:
 	- robustify test.fixation.R, Local max, tolerance
 	
302b1612
 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++.
 	
e719a81d
 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
 	
885ead9e
 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.
 
23b7c973
 Changes in version 2.9.3 (2017-11-27):
 	- Make clang happy (do not use flandscape as DataFrame)
 	
ab439943
 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)
 
f9a38e24
 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.
 
556ae3e1
 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.
565c4431
 	- fixation of a genotype/gene as stopping mechanism.
556ae3e1
 	- rfitness: shifting by subtraction and mu of normal distribution.
 	- simOGraph: using proper transitive reduction.
565c4431
 	- simOGraph can also output rT data frames.
 	- accessible genotypes now done in C++.
556ae3e1
 	- 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.
565c4431
 	- Citation shows Bioinformatics paper.
 
 Changes in version 2.5.14 (2017-04-07):
 	- Fixed repeated entries in NEWS for BioC 3.5.
556ae3e1
 
 Changes in version 2.5.13 (2017-04-07):
 	- Updated NEWS for BioC 3.5.
 
b137a4a3
 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
 	
f7b64a1d
 Changes in version 2.5.9 (2017-01-09):
a9ecbe56
 	- Added code coverage comments to vignette.
 
c06244a8
 Changes in version 2.5.8 (2016-12-17):
a9ecbe56
 	- Handle trivial cases in genotFitness.
c06244a8
 
c3eeacb4
 Changes in version 2.5.7 (2016-12-15):
 	- Clarified McFarland parameterization.
 
bdb105ad
 Changes in version 2.5.6 (2016-12-14):
 	- Fixed a few typos in help files.
 
f9f9ab96
 Changes in version 2.5.5 (2016-12-14):
 	- Vignette: miscell changes (typos, etc)
 	
74449e3b
 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):
bbd76086
 	- Vignette uses pander in tables.
 	- Typos fixed and other enhancements in vignette.
 	
fc38a875
 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.
 
c95df82d
 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).
 
31ab9f94
 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.
c95df82d
 	
34c1b54f
 Changes in version 2.3.17 (2017-09-22):
 	- random2 for rfitness.
 	- Vignette: decrease size and running time.
 	
eea5a8e9
 Changes in version 2.3.16 (2017-09-19):
 	- Help was not accurate for some probSize args
 	
5a471d04
 Changes in version 2.3.15 (2017-09-14):
 	- Typo in name (progresion)
 	
08de3ba7
 Changes in version 2.3.14 (2017-08-26):
 	- Documentation improvements.
 	
6610ac26
 Changes in version 2.3.13 (2017-08-19):
 	- bioRxiv citation.
 	- Using Rmd for vignette.
 	- Improvements in vignette.
 
9f2114c1
 Changes in version 2.3.12 (2017-08-10):
 	- Increase N in some tests.
 
13b90b40
 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):
d43030e1
 	- The windows check failure with mc.cores.
 	
 Changes in version 2.3.9 (2017-07-09):
7c1a570f
 	- Accessible genotypes in rfitness and plotFitnessLandscape
 
3bbfa52f
 Changes in version 2.3.8 (2017-07-08):
 	- PDBasline default is now 1.2.
 	
4d70b942
 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.
 
df131087
 Changes in version 2.3.6 (2016-06-25):
4d70b942
 	- Improved test coverage
df131087
 	
65cb86f3
 Changes in version 2.3.5 (2016-06-25):
 	- to_Magellan.
 
c9e1cd01
 Changes in version 2.3.4 (2016-06-24):
 	- Failing some tests in Win 32-bits
 	
50a94207
 Changes in version 2.3.3 (2016-06-23):
 	- Vignette improvements and typo fixes.
65cb86f3
 	- 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.
50a94207
 	- samplePop: sample at arbitrary sizes.
 	- plot.oncosimulpop using auto for color.
 	- Mutator phenotype and gene-specific mutation rates.
65cb86f3
 	- Bug fixed: to_update set at 2 when mutating to pre-existing.
50a94207
 	- Lots and lots of new tests.
 
8d75a8a6
 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.
 
f80d4777
 Changes in version 2.1.6 (2016-04-14):
 	- Adapt to changes in today's release of testthat (1.0.0)
 
fc927bc1
 Changes in version 2.1.5 (2016-04-09):
 	- Added a test of driverCounts, that does not depend on
           OS/compiler.
 
996c94ee
 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++).
 
8d75a8a6
 Changes in version 2.1.3 (2016-04-04):
 	- Fixed sporadic bug in countDrivers
 
1b1e5e0c
 Changes in version 2.1.2 (2016-03-27):
 	- Arguments to BNB_Algo5 explicit.
 	- Example of modules and no epistasis.
8d75a8a6
 	- Removed requirement of Root in geneToModule.
1b1e5e0c
 	- More tests (and reorganized them)
 	- Miscell. improvements in documentation and vignette.
 
debcf5f5
 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.
 
ae77079b
 Changes in version 1.99.9 (2015-10-08):
 	- Fixed NEWS file.
 	- Removed empty file.
 
f947f058
 Changes in version 1.99.8 (2015-10-01):
ae77079b
 	- Test "initMutant with oncoSimulSample, 2" occasionally failed.
f947f058
 
0f3a3188
 Changes in version 1.99.7 (2015-09-27):
ae77079b
 	- initMutant available in oncoSimulPop and oncoSimulSample.
0f3a3188
 
e6e95f54
 Changes in version 1.99.6 (2015-09-26):
ae77079b
 	- Improved test coverage and removed stringsAsfactors from tests.
 	- Consistent handling of corner cases in Bozic.
 	- Miscell minor documentation improvements.
e6e95f54
 
1d9018c0
 Changes in version 1.99.5 (2015-06-25):
 	- Fixed bug in initMutant, added tests, and vignette section.
 
5d9775a3
 Changes in version 1.99.4 (2015-06-22):
ae77079b
 	- Plotting true phylogenies.
5d9775a3
 	- 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.
 
f79cc8aa
 Changes in version 1.99.3 (2015-06-19):
 	- More examples to vignette
 	- Using Makevars
 	- More functionality to plot.fitnessEffects
 	- Will Windoze work now?
 
a61af05d
 Changes in version 1.99.2 (2015-06-19):
 	- Fixed typos and other minor in vignett.
 
2db2644d
 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.
a61af05d
 	- Try to compile in Mac: mt RNG must include random in all files.
2db2644d
 
ae77079b
 Changes in version 1.99.01 (2015-06-17):
e693f153
 	- 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.
 
ae77079b
 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)
e693f153
 
ae77079b
 	- 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.
e693f153
 
ae77079b
 	- 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.
e693f153
 
ae77079b
 	- changes in intermediate version 99.1.11 (2015-04-18)
 		- Tests of conversion helpers now really working.
e693f153
 
ae77079b
 	- 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.
e693f153
 
ae77079b
 	- 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.
e693f153
 
ae77079b
 	- changes in intermediate version 99.1.8 (2015-04-03)
 		- added extraTime.
e693f153
 
ae77079b
 	- changes in intermediate version 99.1.7 (2015-04-03)
 		- endTimeEvery removed. Now using minDDrPopSize if needed.
e693f153
 
ae77079b
 	- changes in intermediate version 99.1.6 (2015-03-20)
 		- untilcancer and oncoSimulSample working together
e693f153
 
ae77079b
 	- changes in intermediate version 99.1.5 (2015-03-20)
 		- Using the untilcancer branch
e693f153
 
ae77079b
 	- changes in intermediate version 99.1.4 (2014-12-24)
 		- Added computation of min. of ratio birth/mutation and
                   death/mutation.
e693f153
 
ae77079b
 	- changes in intermediate version 99.1.3 (2014-12-23)
 		- Fixed segfault when hitting wall time and sampling only once.
e693f153
 
ae77079b
 	- changes in intermediate version 99.1.2 (2014-12-16)
 		- Sampling only once
502e447e
 
2f97de14
 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.
e693f153
 
 
 
 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.