Version 2.4.0
------------------------------------------------------------------------------
* The graphical user interface (GUI) was optimized for gWidgets2tcltk. The GUI
  is now a lot more compact to improve the user experience on small computer screens. The
  GUI has been rearranged such that dropdown menues for selecting datasets expands to the
  right. Expansion to the widest string was automatic under RGtk2, but tcltk had a fixed width often too narrow to show the full names. 
* Now uses DT (https://rstudio.github.io/DT/) to view datasets as interactive tables with export functions.
* New functions:
  - plotEPG2/plotEPG2_gui/sample_tableToList
  Interactive EPG plot and converter function (adapted from package euroformix by Øyvind Bleka)
* Removed functions (deprecated in 2.3.0):
  - tableBalance/tableBalance_gui
  - tableCapillary/tableCapillary_gui
  - tablePrecision/tablePrecision_gui
  - tableStutter/tableStutter_gui
* Added gWidgets2tcltk (> 1.0.6)to imports as gWidgets2RGtk2 was removed from CRAN 2021-11-08. This version fixes a bug: https://github.com/jverzani/gWidgets2tcltk/commit/9388900afc57454b6521b00a187ca4a16829df53 The workaround (https://stackoverflow.com/questions/54285836/how-to-retrieve-checkbox-state-in-gwidgets2tcltk-works-in-gwidgets2rgtk2) for the above bug was removed for all *_gui functions.
* All code run through styler_1.7.0
* Bug fixes and improvements with the most significant listed below:
  - editData_gui, strvalidator
  Added export buttons to DT table shown by view button.
  - ggsave_gui
  Reworked to avoid 'dispose' error https://github.com/jverzani/gWidgets2/issues/103
  - import_gui
  Filename as suggested name for dataset for single file import.
  - calculateHeight/modelDropout_gui
  Added information about limitations of the calculation of average peak height H, when dropout is present.
  - editData_gui
  Fixed dataset info when NULL. Added view button. Now defaults to limit to 100 rows.
  - strvalidator
  Fixed warning when selecting multiple objects for export. Added 'datatables' and 'plotly' to supported classes in view function.
  Fixed workspace not refreshed when no supported objects in environment and after loading a previous project.
  - calculateStutter_gui
  Fixed 'Replace false stutters' table not working under gWidgets2tcltk. 
  - calculateStatistics/calculateStatistics_gui
  Added parameter 'decimals' for rounding of result.
  - en_GB.txt/es_ES.txt/it_IT.txt
  Updated with new strings related to changes. Cleared strings for removed functions.
  - calculateStatistics_gui
  Fixed "missing value where TRUE/FALSE needed" due to no matching 'target' or 'count' column names in the default (most recent) data.frame.
  Fixed saved gui state cleared when opening with pre set parameters.
  - columns
  Fixed "Found if() conditions comparing class() to string.
  - getStrings
  Fixed Warning message: In !is.na(result) && !is.na(gui):'length(x) = 780 > 1' in coercion to 'logical(1)'
  - calculateMixture, calculateHeight_gui, calculateHeight, calculateAT, calculateAT6,
  calculateDropout, modelDropout_gui, plotContamination_gui, calculateLb
  Fixed url-> doi in references.
  - plotSlope_gui
  Fixes issue #19 "Error in exists(name, envir = env, inherits = FALSE)"

Version 2.3.0
------------------------------------------------------------------------------
* Implemented language support.
* Italian and Spanish language files.
* New functions:
  - calculateStatistics/calculateStatistics_gui
  General funcion to calculate summary statistics.
* Deprecated functions:
  - tableBalance/tableBalance_gui
  - tableCapillary/tableCapillary_gui
  - tablePrecision/tablePrecision_gui
  - tableStutter/tableStutter_gui
  Use calculateStatistics/calculateStatistics_gui instead.
* Bug fixes and improvements with the most significant listed below:
  - auditTrail
  Added timestamp attribute.
  - listObjects
  Added parameters "sort" and "decreasing". Now returns NULL if no result.
  - getKit
  Better description of parameter 'what'.
  - calculateDropout_gui
  Changed LDT to AT for analytical threshold in gui.
  - strvalidator
  Made Decsription in Projects tab hidden and inactive as default.
  Fixed potential "memory leak" by adding parent = emptyenv() to new.env()
  - plotSlope_gui
  Fixed narrow dropdown with hidden argument ellipsize = "none".
  - plotStutter_gui, plotPrecision_gui
  Added controls of main, x, y and facet titles.
  - readBinsFile
  Fixed failed detection of "virtual" when trailing tabs, leading to error in combineBinsAndPanels.
  - plotKit_gui
  Made the scrollable checkbox expand with the window.
  - tablePrecision_gui
  Further adjustments to gui.
  - export_gui
  Compacted and tweaked gui for tcltk.
  - export
  Added support for comma separated names.
  - calculateMixture_gui
  Compacted gui and expand text field under tcltk.
  - tablePrecision_gui
  Fixed strange behaviour when selecting from tables (double click/drag and drop).
  - tablePrecision_gui
  Improved tables with set initial height.
  Fixed save field not expanded (tcltk).
  - calculateResultType_gui
  Fixed Error in paste(parent$ID, parent$env$num.subwin... (tcltk)
* Intended to fix Travis error:
  Moved gWidgets2tcltk to suggests in DESCRIPTION. Removed gWidgets2RGtk2.

 Version 2.2.0
------------------------------------------------------------------------------
* The package is now optimized for both the tcltk and the RGtk2 graphical user
 interface packages through the gWidgets2 APIs gWidgets2tcltk and gWidgets2RGtk2.
 In English: installing strvalidator should be easier, especially in restricted IT environments.
* The graphical user interface STR-validator and functions have been compacted to work better on laptops with small screens.
* The welcome tab has been updated and now includes important direct links.
* Cleaning code formatting with styler package.
* New functionality and changes:
  - calculateLb/calculateLb_gui
  New option to calculate locus balance as peak height ratio.
  - import_gui
  More intuitive layout.
  - modelDropout_gui
  Added option to use log10 y scale on plots.
  - auditTrail
  No longer print messages to console.
* Bug fixes and improvements with the most significant listed below:
  - strvalidator (the main GUI, STR-validator)
  Fixed behaviour of project list and description field in Projects tab.
  - calculateT
  Fixed "Error: $operator..." when ResourceSelection is not installed.
  - modelDropout_gui
  Fixed "save object" triggered when plotting if object was previously saved (RGtk2).
* Fixed settings not saved after running some functions. 
  
Version 2.1.0
------------------------------------------------------------------------------
* New functions
  - calculateT
  - calculateAllT
  - calculateAllT_gui
  - plotGroups_gui
* New tests
  - test-calculateAllT
  New file for testing of the function calculateAllT (indirectly tests calculateT).
* Bug fixes and improvements with the most significant listed below:
  - auditTrail
  Now logs R version.
  - cropData_gui
  Fixed error replacing NA's.
  - modelDropout_gui
  Converts dependent and explanatory values to numeric if necessary.
  - export_gui
  Fixed initial export error and improved error message.
  - modelDropout_gui
  Added option to dump model data for manual inspection and verification.
  Changed default P(D) to 0.01 (previous 0.05).
  - plotKit_gui
  Fixed x title and size not saved.
  - ggsave_gui
  Fixed initial save error and improved error message.

Version 2.0.0
------------------------------------------------------------------------------
* The package now use gWidgets2 instead of gWidgets (changes in all "_gui" functions).
  - Improved GUI speed by 10-100% (https://github.com/jverzani/gWidgets2).
* Improved audit trail logging.
  - New function auditTrail used internally to log audit trail from functions.
  - Extensive logging, now handles multiple runs of the same function.
* Bug fixes and improvements with the most significant listed below:
  - strvalidator (the main GUI)
  Button 'Delete' in tab 'Workspace' now support multiple selections.
  Across all tabs the 'Edit' button was changed to 'View'.
  The 'Edit' button is available in the 'Tools' tab.
  - import
  Prefix now works as intended (previously worked as 'contain').
  - import_gui
  Implemented last used directory as default
  Partly changed layout.
  - export_gui
  Implemented last used directory as default.
  Now closes after export.
  - ggsave_gui
  Implemented last used directory.
  Minor GUI improvements.
  - tableBalance_gui
  Added 'kit' attribute to result.
  - tableStutter / tableStutter_gui
  Added attributes to result.
* Exported functions (previously internal)
  - export
  - export_gui

Version 1.9.0
------------------------------------------------------------------------------
* New functions
  - addOrder (implemented in addDye_gui)
* Bug fixes and improvements with the most significant listed below:
  - addDye_gui
  New options to add marker 'Dye', 'Color', 'R.Color', and 'Order'.
  - addData
  Fixed data saved as attribute (new.data)
  - plotStutter_gui
  Added option to drop unused levels.
  - plotDistribution_gui
  Changed y axis title from 'Probability' to 'Density'.
  - modelDropout_gui
  Added reference "Estimating the probability of allelic drop-out...".
  - cropData_gui
  New options "containing", "not containing".
  Added attributes to result.
  - calculateAT6
  Fixes "Error in calculateHeight: 'kit' can't be NULL if sex.rm=TRUE
  - plotDistribution_gui
  Added controls for x and y axis range.
  No longer required to select a group if column Group is present.
  - combine_gui
  Changed to rbind.fill to handle filling in missing columns.
  Check for column names no longer require identical order.

Version 1.8.0
------------------------------------------------------------------------------
* New built in datasets intended for tutorials and tests:
  - Fusion example data for dropout analysis (Thanks to Dixie Peters).
  set6 (dataset)
  ref61 (Marker order is different from set6. Includes a Y marker with NA.)
  ref62 (Marker order is same as set6. Includes a Y marker with NA.)
  - ESSplex SE QS example data for inhibition analysis.
  set7 (dataset)
  ref7 (reference dataset)
* New functions
  - plotContamination_gui
  - calculateCopies
  - calculateCopies_gui
  - calculateHb
  - calculateHb_gui
  - tableHb
  - tableHb_gui
* Removed functions
  - calculateBalance
  - calculateBalance_gui
* Replaced functions:
  - calculateHeterozygous -> calculateCopies (faster and more functions)
  - calculateHeterozygous_gui -> calculateCopies_gui (faster and more functions)
  - calculateBalance -> calculateHb (faster and more robust)
  - calculateBalance_gui -> calculateHb_gui (faster and more robust)
* Bug fixes and improvements with the most significant listed below:
  - addColor
  Fixed dataset saved to attributes.
  Fixed attribute 'kit' saved with wrong name.
  - calculateDropout
  Fixed dataset saved to attributes.
  Implemented new filterProfile function to remove sex markers and quality sensors.
  - calculateHb
  Fixed dataset saved to attributes.
  - calculateHeight
  Fixed parameter 'word' not saved to attributes.
  Fixed error when homozygotes are given as double notation in reference dataset.
  - calculatePeaks
  Rewritten for efficiency using the data.table package.
  Added factors to Group for correct order when creating plot.
  - calculatePeaks_gui
  Changed some labels, added tooltips, changed one widget.
  - filterProfile
  Now retains information in 'File.Name' and 'File.Time' when adding markers.
  Fixed attribute 'kit' saved with wrong name.
  New options to filter sex markers and quality sensors.
  - filterProfile_gui
  Kit dropdown always active and now passes 'kit' to command line function.
  New options to filter sex markers and quality sensors.
  - calculateLb
  Implemented the new filterProfile.
  Fixed 'data' saved as attribute.
  - calculateHeight
  Implemented the new filterProfile, with word boundary option.
  - plotDistribution_gui
  Fixed factor levels in 'Group' drop-down after change in calculatePeaks.
  - tableHb_gui
  Removed 'Lb' as a required column.
  - calculateConcordance / calculateConcordance_gui
  Added option 'list.all' to return missing samples in the result.
  - calculateSlope / calculateSlope_gui
  Implemented the new filterProfile, with word boundary option.
  - calculateHeight_gui
  Completely rewritten using data.table for better performance.
  Calculates total peak height (TPH) and number of peaks (Peaks) by default.
  Given a reference dataset, average peak height (H) and profile proportion (Proportion) are calculated.
  Fixed options 'sex.rm' and 'qs.rm' not saved.
  - addData
  Now handles empty dataset by returning unchanged.
  Fixed detection and conversion of data.table.
  - calculateDropout_gui
  Implemented the new calculateHeight.
  - calculateLb_gui
  Implemented the new calculateHeight.
  - calculateBalance_gui
  Added missing argument to attribute list (per.dye).
  Implemented the new calculateHeight.
  - calculateAT6
  Implemented the new calculateHeight.
  - maskAT
  Fixed error if NA in reference profiles (Y markers in female profiles).
  - tableBalance / tableBalance_gui
  Rewritten to use data.table for increased efficiency.
  Now calculates summary statistics for both Hb and Lb data.
  - calculateMixture
  Fixed name matching bug. Now works as shown in check subsetting.
* Added attributes for the following functions:
  - calculateResultType / calculateResultType_gui
  - calculatePeaks_gui
  - calculatePeaks
* New tests
  - test-calculateHeight
  Uppdated with tests for complete negative samples.
  Uppdated with test for homozygous double notation.
  - test-calculateConcordance
  Added test for option 'list.all'.

Version 1.7.0
------------------------------------------------------------------------------
* Updated kit file to support quality sensors (new column) and added:
  Investigator 24plex GO! Kit
  Investigator ESSplex Plus Kit
  Investigator ESSplex SE QS Kit
  Updated panel for 'Investigator ESSplex SE Plus Kit' from v1 to v4.
  Defined 'Yindel' and 'DYS391' as sex markers for 'GlobalFiler'.
* Bug fixes and improvements with the most significant listed below:
  - calculateAT / calculateAT_gui
  Implemented method AT7 assuming log normal-distribution of noise.
  Changed some column names.
  - calculateAT_gui
  Fixed bug in plot sample masking range (ESX17 hardcoded).
  Now all excluded peaks are marked in plot (not only high peaks).
  Prepare button and drop-down menu now disabled while processing.
  -detectKit
  Now check for and removes NA in markers to handle SamplePlotSizingTable.
  - plotDistribution_gui
  Fixed update of drop-down and information when selecting a new dataset without selected column.
  Implemented log option and number of bins. Changed layout.
  Default binwidth changed from 1 to 'empty', which will use default 'bins=30'.
  - calculateSpike
  Implemented accurate method.
  Fixed multiple peaks in same dye triggers treshold by adding additional check
  that number of unique dyes must be > threshold.
  - addSize
  Fixed message returing string + 'TRUE'.
  - saveObject
  Fixed object not saved if an object existed and the new object is renamed.
  - columns / columns_gui
  Added option to extract a substring.
  - plotStutter_gui
  Enabling of plot buttons after changing some plot options.
  Fixed some plot error and implemented check for missing values.
  - calculatePullup/calculatePullup_gui
  Now handles missing alleles in the reference dataset (e.g. sex markers).
  New option 'limit' that by default removes ratios > 1, unlikely pull-ups.
  - plotPullup_gui
  Enabling of plot buttons after changing some plot options.
  Implemented check for missing values.
  - heightToPeak
  Fixed error when no peaks in sample.
  - plotDropout_gui
  New option 'Round to digits' (x-tick labels).
  - editData_gui
  Limit number of rows now FALSE by default + tooltip.
  - calculateAT
  Handles missing ILS dye.
  - getKit
  Added support for quality sensors.
  - calculateLb / calculateLb_gui
  Added option to remove quality sensors.
  Fixed missing markers after removing OL alleles when only OL alles were observed.
  Fixed problem with replacing NAs.
  - calculateDropout / calculateDropout_gui
  Added option to remove sex markers and quality sensors.
  - calculateHeight / calculateHeight_gui
  Added option to remove sex markers and quality sensors.
  Fixed attribute saved dataset.
  - generateEPG / generateEPG_gui
  Fixed bug in plotting of marker ranges.
  - makeKit_gui
  Fixed bug removing space within marker names.
  Added support for quality sensors.
* New functions
  - calculateSlope
  - calculateSlope_gui
  - plotSlope_gui
  - removeSpike
  - removeSpike_gui
  - removeArtefact
  - removeArtefact_gui
* Name changes.
  - blockAT
  Changed to maskAT to better reflect the function.
  Parameter names changed from 'block*' to 'mask*'.
  - calculateAT / calculateAT_gui
  Parameter names changed from 'block*' to 'mask*'.
* Minor changes
  - plotDropout_gui
  Removed units on automatic titles.
  - calculateAT_gui
  Removed check for reference samples if masking is active (does no harm).
* Added button to create new project in the 'Workspace' tab.
* Added attributes for the following functions:
  - columns/columns_gui
  - calculatePullup/calculatePullup_gui
* Added expand=TRUE to 'save as' textbox:
  - addDye_gui
  - addMarker_gui
  - calculateRatio_gui
  - calculateDropout_gui
  - calculateCapillary_gui
  - calculateHeterozygous_gui
  - calculateAT6_gui
  - calculateAT_gui
  - calculateBalance_gui
  - calculateStutter_gui
  - calculateResultType_gui
  - calculatePeaks_gui
  - calculatePullup_gui
  - calculateHeight_gui
  - columns_gui
  - cropData_gui
  - editData_gui
  - filterProfile_gui
  - modelDropout_gui
  - plotDistribution_gui
  - plotResultType_gui
  - plotBalance_gui
  - plotStutter_gui
  - plotPeaks_gui
  - plotDropout_gui
  - plotPullup_gui
  - plotCapillary_gui
  - slim_gui
  - tableCapillary_gui
  - trim_gui

Version 1.6.0
------------------------------------------------------------------------------
* STR-validator now requires R version >= 3.1.3 and ggplot2 version >= 2.0.0
* Updated kit file. Added 'Fusion 6C', removed 'ESI17'.
  Kit sorted roughly according to vendor and release.
* Bug fixes and improvements with the most significant listed below:
  - calculateDropout / calculateDropout_gui
  Handles the case when a reference allele is NA (skip to next marker).
  Reverted fix in 1.5.2.9000 and instead removed all NA rows from reference prior to analysis.
  - calculateDropout_gui
  Added automatic calculation of average peak height 'H'.
  - calculateDropout
  Fixed reference sample name subsetting bug. Confirmed with new test #09.
  Some 'warnings' changed to 'stop'.
  Better information in stop messages.
  - readPanelsFile
  Convert all color names to lower case. Fixes kit plot D16 bug in Fusion 6C.
  - calculateBalance / calculateBalance_gui
  Added option to calculate Hb by LMW/HMW, and updated test-calculateBalance accordingly.
  - calculateBalance_gui
  Added automatic calculation of average peak height 'H'.
  Added option for exact matching, and drop sex markers, fixed word option not saved.
  - plotBalance_gui
  Added new plot options 'Hb vs. Marker' and 'Lb vs. Marker'.
  Added options to plot all data 'Facet per marker and wrap by dye'. 
  Implemented by dye.
  Better default values reduce risk of plot error.
  - editData_gui
  Added option to limit number of rows.
  Added option to show attributes.
  - plotDistribution_gui
  NA's now removed prior to plotting and subtracted from number of observations.
  - cropData_gui
  Option to remove NA (earlier NA was automatically removed).
  Fixed 'Info' not updated when selecting a column.
  - import / import_gui
  New parameter 'na.strings' to specify what gets converted to NA.
  - addData / addData_gui
  New parameter to specify columns to add.
  - heightToPeak
  Improved implementation.
  - checkSubset_gui
  'Marker' is no longer a required column.
  - filterProfile / filterProfile_gui
  New parameter 'exact' for sample name matching.
  - checkSubset / checkSubset_gui
  New parameter 'exact' for sample name matching.
  - columns / columns_gui
  Now possible to add new column without combining with an existing column.
  - ggsave_gui
  Updated to work with ggplot2 2.0. Fixes error 'dev' function not found.
  - generateEPG / generateEPG_gui
  Rewrote funtion and fixed dye channel bug introduced in ggplot2 2.0.
* New functions:
  - scrambleAlleles
  Scrambles alleles in a dataset to anonymise the profile.
  - colConvert
  - calculateSpike / calculateSpike_gui
  Detection of spikes in profiles.
  - calculateAllele
  Counts the number of each allele per marker over the entire dataset.
  - calculateLb / calculateLb_gui
  Implemented locus balance calculations using data.table wich is much faster.
  Does not require a reference dataset. Calculates as proportion, normalised,
  or centred quantities (sum to 0). Global or by dye.
  - calculateRatio / calculateRatio_gui / plotRatio_gui
  Implemented calculation of locus ratios and plotting of the result.
* New exported function:
  - detectKit
* New tests:
  test-filterProfile
    - Test for unfiltered data.
  test-calculateDropout
    - Test for reference subsetting bug.
  test-calculateLb
    - Tests for new function.
* Removed global variables for ggplot2 in 'globals.R', added importFrom in functions.
* Functions removed:
  - compact
* Added attributes for the following functions:
  - addColor/addDye_gui
  - addData/addData_gui
  - addMarker/addMarker_gui
  - addSize/addSize_gui
  - calculateAT/calculateAT_gui
  - calculateBalance/calculateBalance_gui
  - calculateDropout/calculateDropout_gui
  - calculateHeight/calculateHeight_gui
  - calculateStutter/calculateStutter_gui
  - filterProfile/filterProfile_gui
  - heightToPeak
  - import/import_gui
  - slim/slim_gui
  - tableBalance/tableBalance_gui
  - trim/trim_gui

Version 1.5.2
------------------------------------------------------------------------------
* Bug fixes and improvements with the most significant listed below:
  - calculateAT6 / calculateAT6_gui
  Now use 'standard error of the regression' (or 'sigma') instead of 'standard error of the intercept'.
  - slim / slim_gui
  Fixed error when 'stack' and 'slim' is empty or "" (replaced by 'NULL').
  Now handle no columns to slim/stack (return unchanged data.frame).
  - Plot AT confidence interval now matches the one-sided used in calculateAT6.
* Corrections in documentation or GUI:
  - calculateBalance / calculateBalance_gui
  Parameter description for 'hb=2' changed to 'Max2(Ph)/Max1(Ph)'.
  Changes drop-down menu to 'Smaller peak / larger peak'.
  - modelDropout_gui
  More information in the detailes.
* Use of 'importFrom' as required in R 3.3.0 pre-release.
* Now fully enforces the version numbering convention (http://r-pkgs.had.co.nz/release.html)
 x.y.z.9XXX, where x is a major release, y is a minor release, z is a bug fix, 
 and 9XXX is a in-development version. Development versions will be synchronised to
 GitHub (https://github.com/OskarHansson/strvalidator) and possibly made available at
 the website (https://sites.google.com/site/forensicapps/strvalidator) as file
 for manual download and installation (binary package).

Version 1.5.1
------------------------------------------------------------------------------
* AT function now calculate global AT per dye.
* Bug fixes and improvements with the most significant listed below:
  - Fixed bug in calculateAT (hardcoded dyes)
  - Changed from two-sided critical t-value to one-sided in calculateAT6.

Version 1.5.0
------------------------------------------------------------------------------
* New functions to estimate analytical threshold (tab 'AT').
* New function to perform actions (concatenate, add, multiply, subtract,
  divide) on columns in a dataset (tab 'Tools').
* New plot option 'Histogram' in funtion plotDistribution_gui.
* Bug fixes and improvements with the most significant listed below:
  - Fixed bug in calculatePullup (https://github.com/OskarHansson/strvalidator/issues/8) partial column name match.
  - Fixed bug in calculateBalance (https://github.com/OskarHansson/strvalidator/issues/9) error when NA.
  - Fixed bug in plotDropout_gui (https://github.com/OskarHansson/strvalidator/issues/10) colors in dotplot hardcoded as ESX17.
  - checkSubset, editData_gui, and trim
  Now accept columns named 'Sample.File.Name' or the first occurance of any
  column name containing '*Sample*' as alternative to 'Sample.Name'.
  - colNames
  New option to require number suffix on repeated columns improve autodetection
  for the 'import' and 'slim' function. 
  - editData
  Fixed bug column name changes not saved (introduced in 1.4.0)
  - filterProfile / filterProfile_gui
  Now have and option 'invert' to filter peaks NOT in the reference profile
  - import / import_gui
  Function parameter name changed from 'file.name' to 'import.file',
  New options to autotrim and autolim the imported data,
  New options to import file name and time stamp.
  - calculateBalance_gui
  Option to drop sex markers.
  - plotBalance_gui
  Implemented check for plot facet error caused by all NA'.
  - slim / slim_gui
  Fixed problems with partial column name matching.
  Function parameter name changed from 'keepAllFixed' to 'keep.na',
* Changed parameter names to the same naming convention (period.separated)
  for checkDataset.
* New functions:
  - blockAT
  - calculateAT
  - calculateAT_gui
  - calculateAT6
  - calculateAT6_gui
  - plotAT_gui
  - columns
  - columns_gui
* Removed unused function: loadPackage.
* New tests:
  test-filterProfile
    - Test for parameter 'invert'.


Version 1.4.0
------------------------------------------------------------------------------
* GUI changes: Tab 'Edit' changed to 'Tools'.
* New function to analyse and plot pull-up (bleed-through) peaks (tab 'Pull-up').
* New function to generate EPG like plot to visualise profiles (tab 'Tools').
* New structure of kit file to support multiple sex markers.
* Changed all parameter names to the same naming convention (period.separated)
  for all functions except for in checkDataset and getKit (will be changed in the future).
* Minor bug fixes and improvements with the most significant listed below:
  addColor
  - Fixed error NA Dye for e.g. Yfiler Plus.
  addSize_gui
  - Fixed bug (https://github.com/OskarHansson/strvalidator/issues/7).
  calculateBalance
  - Fixed error when NA's in markerPeakHeightSum.
  calculateBalance_gui / calculateDropout_gui
  - Added kit dropdown and kit attribute to result.
  editData_gui
  - Now copy attribute list to new object upon 'Save As'.
  getKit
  - what='Gender' changed to 'Sex.Marker' and now return vector.
  makeKit_gui
  - Fixed "Error in read.table..." when 'Save' is pressed without data.
  - Fixed "Error in basename(x) : a character vector argument expected"
  - Changed single gender marker to general sex markers (multiple).
  modelDropout_gui
  - Added option to use average peak height 'H'.
  plotStutter_gui
  - Option to drop sex markers.
* New functions:
  - calculatePullup
  - calculatePullup_gui
  - plotPullup_gui
  - generateEPG
  - generateEPG_gui


Version 1.3.1
------------------------------------------------------------------------------
* Now handles window focus correctly.
* Explicit export of functions in NAMESPACE.
* Minor bug fixes and improvements with the most significant listed below:
  calculateBalance_gui
  - Added 'word' option (word boundary) for subsetting of samples.
  calculateHeight / calculateHeight_gui
  - New parameter 'exclude' for allele designations to exclude from dataset.
  - Now also calculate the total peak height.
  calculateMixture
  - Check for uniqueness between reference datasets.
  - Fixed bug in drop-out of minor in if: AA:AB | (A-B)/(A+B). 
  calculateMixture_gui
  - Fixed bug in 'Check subsetting' showing extra combinations in many cases.
  getDb
  - Fixed error when package is not loaded.
  getKit
  - Fixed error if kit=NULL and what!=NA.
  - what="Offset" and what="Repeat" now returns identical data frames.
  ggsave_gui
  - Fixed wrong size to pixel conversion.
  plotPrecision_gui
  - Filter rows with Allele=NA (Fixes issue #6).
  strvalidator
  - 'View' button in 'Workspace' tab can now be used on plot objects.
  - Fixed error message when no projects in projects folder.
* Renamed or replaced functions:
  - calculateH -> calculateHeight
  - calculateH_gui -> calculateHeight_gui
  - test-calculateH -> test-calculateHeight
* Updated tests:
  test-calculateHeight
    - Tests for parameter 'exclude'.
    - Tests for TPH - total peak height.

Version 1.3.0
------------------------------------------------------------------------------
* This version includes a new project manager tab and improved workspace functions.
* New analysis modules for concordance and mixture analysis.
* Version number now visible in STR-validator GUI.
* Help buttons available throughout the GUI, and improved documentation.
* Numerous bug fixes and improvements with the most significant listed below:
  calculateBalance_gui
  - Added check and error message for 'NA' in 'Dye'.
  calculateStutter_gui
  - Added detection of kit and add attribute 'kit' to result.
  detectKit
  - Added support for 'kit' attribute.
  export
  - Fixed 'NA' bug when recycling names.
  getKit
  - Added option to return kit index.
  modelDropout_gui
  - Changed notation on plot to be more correct.
  plotCapillary_gui
  - Fixed boxplot error.
  saveObject (internal function)
  - Added syntactically valid name check.
  - Added 'remove' and 'suggested' parameter.
  tableCapillary, tableCapillary_gui
  - Added scope=RUN.
* New example datasets:
  - 'set5', 'ref51', and 'ref52' (ESX17 example data for mixture analysis).
* New functions:
  - calculateConcordance, calculateConcordance_gui, calculateMixture, calculateMixture_gui.
* Renamed or replaced functions:
  - concatenate_gui -> combine_gui
* New tests:
  - test-calculateConcordance, test-calculateMixture.



Version 1.2.0
------------------------------------------------------------------------------
* Kit definition file 'kit.txt'.
    - Added support for 'Fusion'.
    - Added support for 'GlobalFiler'.
* Allele frequency database file 'database.txt'.
    - Removed column 'AM'.
* Numerous bug fixes and improvements with the most significant listed below:
  addColor/addDye_gui
    - Option to ignore case in marker names.
  - Added 'orange' and 'purple'.
  addSize/addSize_gui
  - Option to ignore case in marker names.
  - Option 'bins' and option to calculate an estimate of size.
  - Fixed bug, kit always "ESX17" (issue#4 @ GitHub).
  calculateBalance/calculateBalance_gui
    - New column 'TPH' (Total locus Peak Height) in result table.
  plotBalance_gui
  - 'position_jitter height' now fixed to zero, previously 'default'.
  - Implemented new column 'TPH' for X-axis when plot Lb.
  - Fixed bug when no observation in an entire dye channel.
  plotDistribution_gui
  - Fixed boxplot bug.
  plotDropout_gui
  - 'position_jitter height' now fixed to zero, previously 'default'.
  plotStutter_gui
  - 'position_jitter height' now fixed to zero, previously 'default'.
  - Fixed same color scale for all sub plots in complex plots.
  - Fixed different y max for complex plot, when supposed to be fixed.
  - Fixed bug when no observation in an entire dye channel.
  trim
  - Made more robust and handles '+' and '-' in sample names.
* New experimental functions for capillary balance analysis:
  - Functions: calculateCapillary, calculateCapillary_gui, plotCapillary_gui, tableCapillary, and tableCapillary_gui.
  - Internal lane standard definition file (ils.txt).
* New function:
  - checkDataset.
* Updated test:
  test-calculateBalance
    - Updated in response to new column 'TPH' and NA in 'MPH' if homozygous.
* New tests:
  - test-addSize, test-tableBalance, test-trim.
* New file:
  - database_readme.


Version 1.1.0
------------------------------------------------------------------------------
* NB! Version 1.1.0 include an important bug fix for estimating a prediction
range for the stochastic threshold (see bug fixes in 'modelDropout').
* Updated for compatibility with 'testthat' version 0.8.
* Kit definition file 'kit.txt'.
    - Added support for 'PowerPlex ESX 16'.
    - Added support for 'Investigator ESSplex Plus'.
    - Fixed errors in 'virtual alleles' for 'Investigator ESSplex SE Plus Kit'
      D2S1338 14 (1->0), D2S441 11.3 (0->1), FGA 30.2 (1->0), FGA 46.2 (0->1).
* New functions for process control (plotting distributions).
* Added package 'gWidgetsRGtk2' in suggestests.
* Numerous bug fixes and improvements made to the following functions.
  The most significant changes are listed below:
  addDye_gui
    - 'Sample.Name' column not required in dataset (only 'Marker' is required).
  calculateBalance/calculateBalance_gui
    - Removed 'perSample' parameter. Use 'tableBalance' for summary statistics.
  calculateH/calculateH_gui
    - New option to add directly to dataframe.
    - New option to replace NA's.
  ggsave_gui
    - Removed unsupported unit 'px', but added info for size in pixels.
  guessProfile/guessProfile_gui
    - Option to remove off-ladder ('OL') alleles.
  modelDropout_gui
    - Removed erroneously implemented prediction interval for T.
    - Implemented conserative T estimate.
  plotBalance_gui
    - Fixed plot bugs.
    - Implemented theme.
  plotDropout_gui
    - Fixed NA in title for ecdp.
    - Fixed heatmap by 'H' loosing samples with equal 'H'.
  plotPrecision_gui
    - Implemented new dot/box plot and plot all data (insted of min/max).
    - Implemented theme and colour.
  plotStutter_gui
    - Fixed plot bugs.
    - Implemented theme.
  slim/slim_gui
    - Fixed minor bug when only one column in 'fix' (issue#3 @ GitHub).
  strvalidator (Main GUI)
    - Added 'Summarize' balance data button in 'Balance' tab.
    - Added 'Add Size' button in 'Edit' tab.
    - Added 'Plot' button for plotting distributions in 'Result' tab.
    - Added 'Summarize' precision data button in 'Precision' tab.
* Example dataset 'Set2' and 'Ref2', changed 'Amelogenin' to 'AMEL'.
* New functions: addSize, addSize_gui, plotDistribution_gui, tableBalance,
    tableBalance_gui, tablePrecision, tablePrecision_gui, 
* Removed functions: calculatePrecision, calculatePrecision_gui.
* Renamed or replaced functions: test-All.R -> testthat.R.


Version 1.0.0
------------------------------------------------------------------------------
* NB! Version 1.0.0 includes many fixes and it is recommended to re-import
   and re-analyse previous data.
* New kit file structure pre-loaded with ESI17, ESI17Fast, ESX17, ESX17Fast,
    Y23, Identifiler, NGM, ESSPlexSE (fixed virtual alleles), NGMSElect, SGMPlus
* New functions for creating new kit definitions and edit the kit definition file.
* New functions for analysis of 'bins' and 'panels' files.
* New functions for process control (e.g. contamination).
* New 'database.txt' file including allele frequency databases:
    "SGM Norway", R. Andreassen et al. / Forensic Science International 170 (2007) 59-61
    "ESX 17 Hill", C.R. Hill et al. / Forensic Science International: Genetics 5 (2011) 269-275
* New function for saving plots as various formats.
* Numerous bug fixes and improvements made to the following functions.
  The most significant changes are listed below:
  calculateBalance/calculateBalance_gui
    - Alleles are now filtered and only peaks matching reference are considered.
    - Added calculation of 'delta' i.e. difference in repeat number.
    - Fixed bug when two peaks have identical height.
    - Added a second definition of Hb (HMW/LMW).
    - Additional data checks.
  calculateDropout/calculateDropout_gui
    - Now complies with the recommendations from the ISFG DNA commission.
    - Implemented a scoring threshold (LDT).
    - Multiple scoring methods implemented.
  filterProfile/filterProfile_gui
    - Possible to use 'ref' without 'Sample.Name' column i.e. one profile for all.
    - Does not discard columns anymore.
    - Fixed bug when adding missing loci.
  getKit
    - Changed to support new kit file structure.
    - New parameter 'what' for specifying the information returned.
  import
    - Changed name on some parameters.
    - Progress messages added.
    - Strings "NA" and "" now replaced with NA.
    - All data is imported as character data.
  modelDropout_gui
    - Implemented modelling from several dropout scoring methods.
    - Removed subset modelling because a subset must be scored again.
    - Changed logistic regression in accordance to ref. 2012.
    - Implemented 'Hosmer-Lemeshow test'.
    - Improved control over plot.
  plotBalance_gui
    - New plot option 'Hb by Delta'.
    - Correctly handles different number of markers per dye.
    - Better control over plot elements, and fixed zoom.
  plotDropout_gui
    - New plot options 'plot by sample name' and empirical cumulative distribution plot.
    - Correctly handles different number of markers per dye.
    - Better control over plot elements, and fixed zoom.
  plotStutter
    - Correctly handles different number of markers per dye.
    - Better control over plot elements, and fixed zoom.
  slim
    - Re-written for better performance.
  tableStutter/tableStutter_gui
    - User defined quantile.
  trim/trim_gui
    - Supports dataframe without 'Sample.Name' column.
    - Fixed bug when samples=NULL, and invertS=TRUE.
  calculatePeaks (former countPeaks)
    - Completely re-written.
* Various bug fixes and improvements in functions:
    addData, calculateResultType, colNames, cropData_gui, detectKit,
    editData_gui, export_gui, addColor, sortMarker.
* New functions: addMarker, addMarker_gui, calculateOL, calculateOL_gui,
    calculateOverlap, calculateOverlap_gui, calculatePeaks_gui,
    calculatePrecision, calculatePrecision_gui, calculateResultType_gui,
    combineBinsAndPanels, getDb, ggsave_gui, loadPackage, makeKit_gui,
    plotKit_gui, plotPeaks_gui, plotPrecision_gui, plotResultType_gui,
    readBinsFile, readPanelsFile.
* Removed functions: addKitInfo, calculateMx (dev. version), dyeToColor,
    calculateMean, calculateSummary, combineRef, getDropoutData
* Renamed or replaced functions: addDye -> addColor, sortMarkers -> sortMarker,
    countPeaks -> calculatePeaks, modelDropout -> modelDropout_gui.
* Renamed files: kits.txt -> kit.txt
* Files moved: inst\tests\ -> tests\testthat\
* Added tests for calculateOL


Version 0.3.0
------------------------------------------------------------------------------

* Save GUI state option added.
* Removed dependency on pcrsim.
* Numerous bug fixes and some clean-up.
* New functions: colNames, cropData_gui, dyeToColor, export, export_gui,
    saveObject, tableStutter_gui
* Functions removed: savePlot_gui
* Added external data: set3.txt, ref3.txt
* Added datasets: set4, ref4


Version 0.2.0
------------------------------------------------------------------------------

* Graphical user interface added: strvalidator - Main GUI.
* New functions: calculateHeterozygous, concatenate_gui, detectKit, 
    editData_gui, guessProfile, guessProfile_gui, listObjects,
    savePlot_gui.
* GUI wrappers added for most functions: addData_gui, addDye_gui,
    calculateBalance_gui, calculateDropoout_gui, calculateH_gui,
    calculateHeterozygous_gui, calculateStutter_gui, checkSubset_gui,
    filterProfile_gui, import_gui, modelDropout_gui, plotBalance_gui,
    plotDropout_gui, plotStutter_gui, slim_gui, trim_gui.
* Functions removed: addZvalue, addZygosity, getDropoutData,
* Functions renamed: importGM -> import
* Added globals.R to suppress NOTES when checking package.

Version 0.1
------------------------------------------------------------------------------

* Initial release