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: -  : 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 220.127.116.11 (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.