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strvalidator

Process Control and Internal Validation of Forensic STR Kits

An open source platform for validation and process control. Tools to analyze data from internal validation of forensic short tandem repeat (STR) kits are provided. The tools are developed to provide the necessary data to conform with guidelines for internal validation issued by the European Network of Forensic Science Institutes (ENFSI) DNA Working Group, and the Scientific Working Group on DNA Analysis Methods (SWGDAM). A front-end graphical user interface is provided. More information about each function can be found in the respective help documentation.

strvalidator

STR-validator is a free and open source R-package intended for process control and internal validation of forensic STR DNA typing kit. Its graphical user interface simplifies the analysis of data exported from e.g. GeneMapper software, without extensive knowledge about R. It provides functions to import, view, edit, and export data. After analysis the results, generated plots, heat-maps, and data can be saved in a project for easy access. Currently, analysis modules for stutter, balance, dropout, mixture, concordance, typing result, precision, pull-up, and analytical thresholds are available. In addition there are functions to analyse the GeneMapper bins- and panels files. EPG like plots can be generate from data. STR-validator can greatly increase the speed of validation by reducing the time and effort needed to analyse the validation data. It allows exploration of the characteristics of DNA typing kits according to ENFSI and SWGDAM recommendations. This facilitates the implementation of probabilistic interpretation of DNA results.

STR-validator was written and is maintained by Oskar Hansson, senior forensic scientist at Oslo University Hospital (OUS), Section for Forensic Genetics. The work initially received external funding from the European Union seventh Framework Programme (FP7/2007-2013) under grant agreement no 285487 (EUROFORGEN-NoE) but development and maintenance is now performed as a part of my position at OUS, and on personal spare time.

More information can be found at: https://sites.google.com/site/forensicapps/strvalidator

Info and user community at Facebook: https://www.facebook.com/pages/STR-validator/240891279451450?ref=tn_tnmn https://www.facebook.com/groups/strvalidator/

The source code is hosted at GitHub: https://github.com/OskarHansson/strvalidator

Please report bugs to: https://github.com/OskarHansson/strvalidator/issues

News

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

Reference manual

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install.packages("strvalidator")

2.1.0 by Oskar Hansson, 6 months ago

https://sites.google.com/site/forensicapps/strvalidator

Report a bug at https://github.com/OskarHansson/strvalidator/issues

Browse source code at https://github.com/cran/strvalidator

Authors: Oskar Hansson

Documentation:   PDF Manual  

GPL-2 license

Imports ggplot2, gWidgets2, gridExtra, grid, gtable, plyr, scales, gWidgets2RGtk2, RGtk2, data.table, grDevices, graphics, stats, utils, MASS

Suggests ResourceSelection, testthat

Depended on by pcrsim.

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