@@ -1,3 +1,8 @@

+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).

@@ -1,3 +1,7 @@

+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).

@@ -1,4 +1,4 @@

-Changes in version 4.1.1 (2023-02-20):

+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).

@@ -1,3 +1,7 @@

+Changes in version 4.1.1 (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.

@@ -1,3 +1,6 @@

+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

@@ -1,3 +1,23 @@

+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.

@@ -1,3 +1,7 @@

+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.

@@ -1,3 +1,11 @@

+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.

@@ -1,3 +1,7 @@

+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.

@@ -1,3 +1,8 @@

+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.

@@ -1,3 +1,7 @@

+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.

@@ -1,3 +1,6 @@

+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.

@@ -1,3 +1,6 @@

+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.

@@ -1,3 +1,7 @@

+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

@@ -1,3 +1,6 @@

+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.

@@ -1,3 +1,6 @@

+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

@@ -1,3 +1,14 @@

+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

@@ -1,3 +1,6 @@

+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.

@@ -1,3 +1,7 @@

+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.

@@ -1,3 +1,9 @@

+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.

@@ -1,3 +1,7 @@

+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.

@@ -1,3 +1,7 @@

+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.

@@ -1,3 +1,12 @@

+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.

@@ -1,3 +1,6 @@

+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.

@@ -1,5 +1,6 @@

-Changes in version 2.99.6 (2020-12-13):

+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

@@ -1,3 +1,6 @@

+Changes in version 2.99.6 (2020-12-13):

+	- No longer v.1 functionality.

+

 Changes in version 2.99.5 (2020-12-18):

 	- Random timeouts when building in tokay2 (Windows, BioC); fixing

 	seed in vignette.

@@ -1,9 +1,15 @@

+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.

-	- Clean up of C++ code.

 Changes in version 2.99.2 (2020-12-11):

 	- Failed on test on Mac.

@@ -1,8 +1,9 @@

-Changes in version 2.99.3 (2020-12-13):

+Changes in version 2.99.4 (2020-12-17):

 	- 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.

+	- Clean up of C++ code.

 Changes in version 2.99.2 (2020-12-11):

 	- Failed on test on Mac.

@@ -1,3 +1,9 @@

+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.

@@ -1,3 +1,6 @@

+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.

@@ -1,69 +1,165 @@

-Changes in version 2.19.2 (2020-06-03):

+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 2.19.1 (2020-05-05):

+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

-

-Changes in version 2.19.0 (2020-05-05):

-	- Bumped version to match current Biocdevel.

-

-Changes in version 2.17.92 (2020-04-27):

-	- Fixed test.Z-magellan failure in Mac.

-

-Changes in version 2.17.91 (2020-04-24):

 	- Fixed Wrestrict warnings in Windows from MAGELLAN's sources.

-	

-Changes in version 2.17.9 (2020-03-16):

+	- 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.

-	

-Changes in version 2.17.8 (2020-02-02):

 	- 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 2.17.7 (2020-01-30):

+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).

-

-Changes in version 2.17.6 (2020-01-22):

 	- Further additions of MAGELLAN's functionality and Additive

-	model to rfitness

-

-Changes in version 2.17.5 (2019-12-19):

+	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

-	

-Changes in version 2.17.4 (2019-12-19):

 	- 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 2.17.3 (2019-12-17):

+Changes in version 2.17.991 (2019-12-18):

 	- Compiles with fno-common (for gcc 10).

-	

-Changes in version 2.17.2 (2019-12-17):

 	- Fixed error "length(x) = 5 > 1' in coercion to 'logical(1)'"

-	

-Changes in version 2.17.1 (2019-11-24):

 	- rfitness: clarified log=TRUE and truncate_at_0 after log.

 	- Magellan_stats: really return a vector.

-	

-Changes in version 2.17.0 (2019-10-25):

-	- Bumped version for BioC-3.11

-	

-Changes in version 2.15.2 (2019-08-14):

 	- Trying to prevent fscanf warning in FitnessLandscape/input.c

-Changes in version 2.15.1 (2019-06-06):

+	- 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 2.15.0 (2019-06-06):

+

+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

@@ -1,3 +1,6 @@

+Changes in version 2.19.2 (2020-06-03):

+	- Updated ctb: added Magellan and exprTk and clarified contributions.

+

 Changes in version 2.19.1 (2020-05-05):

 	- Occasional failures of @test.sample-prob.R#42

 	in Windows 386

@@ -1,3 +1,10 @@

+Changes in version 2.19.1 (2020-05-05):

+	- Occasional failures of @test.sample-prob.R#42

+	in Windows 386

+

+Changes in version 2.19.0 (2020-05-05):

+	- Bumped version to match current Biocdevel.

+

 Changes in version 2.17.92 (2020-04-27):

 	- Fixed test.Z-magellan failure in Mac.

@@ -1,3 +1,6 @@

+Changes in version 2.17.92 (2020-04-27):

+	- Fixed test.Z-magellan failure in Mac.

+

 Changes in version 2.17.91 (2020-04-24):

 	- Fixed Wrestrict warnings in Windows from MAGELLAN's sources.

@@ -1,3 +1,6 @@

+Changes in version 2.17.91 (2020-04-24):

+	- Fixed Wrestrict warnings in Windows from MAGELLAN's sources.

+	

 Changes in version 2.17.9 (2020-03-16):

 	- With R-devel, stringsAsFactors = FALSE by default. Fix

 	tests

@@ -1,3 +1,8 @@

+Changes in version 2.17.9 (2020-03-16):

+	- With R-devel, stringsAsFactors = FALSE by default. Fix

+	tests

+	- POM documentation.

+	

 Changes in version 2.17.8 (2020-02-02):

 	- With newest R-devel (01-28) getting

 	  "the condition has length > 1": fixed.

@@ -1,3 +1,7 @@

+Changes in version 2.17.8 (2020-02-02):

+	- With newest R-devel (01-28) getting

+	  "the condition has length > 1": fixed.

+	

 Changes in version 2.17.7 (2020-01-30):

 	- Removed dependency on nem, to be deprecated. Adding nem's

 	code (file nem_transitive_reduction.R).

@@ -1,3 +1,11 @@

+Changes in version 2.17.7 (2020-01-30):

+	- Removed dependency on nem, to be deprecated. Adding nem's

+	code (file nem_transitive_reduction.R).

+

+Changes in version 2.17.6 (2020-01-22):

+	- Further additions of MAGELLAN's functionality and Additive

+	model to rfitness

+

 Changes in version 2.17.5 (2019-12-19):

 	- Oooops: forgot Makevars.win

@@ -1,3 +1,6 @@

+Changes in version 2.17.5 (2019-12-19):

+	- Oooops: forgot Makevars.win

+	

 Changes in version 2.17.4 (2019-12-19):

 	- fno-common: better way of dealing with verbose in magellan.

@@ -1,3 +1,6 @@

+Changes in version 2.17.4 (2019-12-19):

+	- fno-common: better way of dealing with verbose in magellan.

+

 Changes in version 2.17.3 (2019-12-17):

 	- Compiles with fno-common (for gcc 10).

@@ -1,6 +1,8 @@

+Changes in version 2.17.3 (2019-12-17):

+	- Compiles with fno-common (for gcc 10).

+	

 Changes in version 2.17.2 (2019-12-17):

 	- Fixed error "length(x) = 5 > 1' in coercion to 'logical(1)'"

-	- Compiles with fno-common (for gcc 10).

 Changes in version 2.17.1 (2019-11-24):

 	- rfitness: clarified log=TRUE and truncate_at_0 after log.

@@ -1,5 +1,6 @@

 Changes in version 2.17.2 (2019-12-17):

 	- Fixed error "length(x) = 5 > 1' in coercion to 'logical(1)'"

+	- Compiles with fno-common (for gcc 10).

 Changes in version 2.17.1 (2019-11-24):

 	- rfitness: clarified log=TRUE and truncate_at_0 after log.

@@ -1,3 +1,6 @@

+Changes in version 2.17.2 (2019-12-17):

+	- Fixed error "length(x) = 5 > 1' in coercion to 'logical(1)'"

+	

 Changes in version 2.17.1 (2019-11-24):

 	- rfitness: clarified log=TRUE and truncate_at_0 after log.

 	- Magellan_stats: really return a vector.

@@ -1,3 +1,10 @@

+Changes in version 2.17.1 (2019-11-24):

+	- rfitness: clarified log=TRUE and truncate_at_0 after log.

+	- Magellan_stats: really return a vector.

+	

+Changes in version 2.17.0 (2019-10-25):

+	- Bumped version for BioC-3.11

+	

 Changes in version 2.15.2 (2019-08-14):

 	- Trying to prevent fscanf warning in FitnessLandscape/input.c

@@ -1,3 +1,6 @@

+Changes in version 2.15.2 (2019-08-14):

+	- Trying to prevent fscanf warning in FitnessLandscape/input.c

+

 Changes in version 2.15.1 (2019-06-06):

 	- Added MAGELLAN's sources and functionality from MAGELLAN.

@@ -1,3 +1,9 @@

+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.

+	

 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

@@ -1,3 +1,8 @@

+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

@@ -1,3 +1,9 @@

+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

@@ -1,3 +1,6 @@

+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

@@ -1,3 +1,19 @@

+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

@@ -1,3 +1,16 @@

+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

@@ -1,3 +1,16 @@

+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)

@@ -1,3 +1,6 @@

+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++.

@@ -1,3 +1,11 @@

+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).

@@ -1,3 +1,14 @@

+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

@@ -4,22 +4,23 @@ Changes in version 2.6.0 (for BioC 3.5):

 	  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.

-	- Citation shows Bioinformatics paper.

+	- 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.

-	- fixation of a genotype/gene as stopping mechanism.

 	- sampledGenotypes in user code.

 	- clonePhylog et al: deal with never any descendant.

 	- samplePop can handle failed simulations graciously.

-	- accessible genotypes now done in C++.

-	- simOGraph can also output rT data frames.

-	- 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.