
chicane v0.1.1							2019-09-23
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* improved memory handling
* updated model definitions in the vignettes to match manuscript
* add plots representing model fits against observed counts

chicane v0.1.0							2018-08-24
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* First CRAN release

chicane v0.0.3.3						2018-08-09
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* Remove restriction fragments from package
* Slim down extdata folder

chicane v0.0.3.2						2018-06-28
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* Fix fill.in.zeros to replace NAs with zeros across all replicate columns

chicane v0.0.3.1						2018-06-19
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* Add adjustment.terms argument to allow user to adjust for covariates of their choice

chicane v0.0.3.0						2018-06-14
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* Support for parallel processing in cis-interactions model fitting

chicane v0.0.2.10						2018-04-30
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* Expanded test coverage, small code tweaks

chicane v0.0.2.9						2018-04-17
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* Added option for removing counts between adjacent restriction fragments
* Fixed vignette to run without bedtools

chicane v0.0.2.8						2018-04-11
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* Move model fitting try-catch to helper function

chicane v0.0.2.7						2018-04-10
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* Option to store temporary files in specific directory

chicane v0.0.2.6						2018-03-19
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* Added convert.hicup.digest.bed helper function

chicane v0.0.2.5						2018-03-08
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* Vectorize get.id.components function

chicane v0.0.2.4						2018-03-06
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* Bugfix in get.id.components function

chicane v0.0.2.3						2018-03-02
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* Changes to pass CRAN checks 
	- moved gamlss and gamlss.tr to Depends
* Gracefully catch unknown errors

chicane v0.0.2.2						2018-03-01
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* refuse to proceed with data processing if intermediate files already exist
* set data processing examples as \dontrun to get around bedtools dependency on CRAN
* pass keep.files argument through chicane

chicane v0.0.2.1						2018-02-26
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* catch error if model fitting fails after warning


chicane v0.0.2.0						2018-02-15
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* minor test.enrichment bug fix
* catch some --as-cran comments/ warnings
* expanded test coverage


chicane v0.0.1.9						2018-02-14
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* Improvements to test.enrichment:
	- stratified sampling
	- exclude bait-to-bait by default
	- return results as data frame
	- consider proportion of total features 
	- bugfixes

chicane v0.0.1.8 						2018-02-13
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* Revamped data preparation step
* fixed issue where keep.files was not passed through prepare.data


chicane v0.0.1.7						2018-02-12
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* Bare bones enrichment testing


chicane v0.0.1.6						2018-02-05
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* Graceful handling of glm.fitter errors
* Added new level of verbosity


chicane v0.0.1.5						2018-02-02
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* Graceful handling of "no suitable coefficients found" errors
* Pass starting values between distance bins when fitting model 


chicane v0.0.1.4						2018-01-31
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* Retiring some TO DOs
* Minor documentation tweaks


chicane v0.0.1.3						2018-01-30
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* Renamed package
* Added tests for get.trans.count


Dudbridge v0.0.1.2						2018-01-24
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* Error/ warning catching for lack of overdispersion in data
* Added epsilon parameter to be passed to GLM control objects


Dudbridge v0.0.1.1						2018-01-23
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* Switched from VGAM to GAMLSS for truncated distributions
* Added truncated negative binomial
* Added trace and maxit parameters to be passed to GLM/ GAMLSS control objects


Dudbridge v0.0.1.0						2018-01-19
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* Refactored to include run.model.fitting function
* Removed more excess printing


Dudbridge v0.0.0.8						2018-01-19
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* Prettified verbose reports, removed excess printing
* Added smart.split function and incorporated it into split.by.distance

Dudbridge v0.0.0.7						2018-01-18
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* Fixed bug in handling of distance.bins = 1
* Switch to Poisson distribution when negative
  binomial fails to fit


Dudbridge v0.0.0.6						2018-01-17
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* Added truncated negative binomial distribution


Dudbridge v0.0.0.5						2018-01-15
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* Implemented filtering


Dudbridge v0.0.0.4						2018-01-12
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* Option to include zero counts in data (all or cis-only)
* Minor bug fixes and sanity checks


Dudbridge v0.0.0.3						2018-01-09
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* Fixed trans count calculation


Dudbridge v0.0.0.2						2018-01-03
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* Removed other end adjustment from non bait-to-bait model
