

Version 1.9.2
----------------------------
o featdata renamed to featData

o associated methods also renamed:
    + adductdata() -> adductData()
    + iddata() -> idData()
    + mzdata() -> mzData()
    + Qdata() -> QData()
    + rtdata() -> rtData()

o new method combineData():
    + merges columns from combinedTable() and featData()


Version 1.9.1
----------------------------
o Changes to metabData():
    + Major changes to duplicate feature handling
    + bug fix to existing duplicate filtering code
    + duplicate argument reworked to accept a list of parameters
    + option to merge duplicate feature rows added
    + duplicate features are filtered or merged before missingness filter
    + new rowID column added to metabData objects


o new function opts.duplicate():
    + lists default parameters for duplicate feature handling in metabData()
    + new duplicate feature merging option (opts.duplicate(resolve = "merge"))

o Minor Change to evaluateParams():
    + "score" column changed to "totalScore" (for clarity)




Version 1.7.1
----------------------------
o Addition of filtered features to metabData objects and filtered method

o Bug Fix in metabData():
  + zero values now treated as missing in Q calculations (zero = TRUE)

o Bug Fix in calcScores()/ evaluateParams():
  + rtrange calculations now account for missing values

o Bug Fix in reduceTable()/ reduceTableParam():
  + method argument included with "mzrt" option

o small logic fix in labelRows() / reduceTable()
  + previous version caused duplicate feature matches in rare cases



Version 1.5.2
-----------------------
o Bug Fix in fit_model():
  + rtx & rty parameter issue resolved

Version 1.5.1
-----------------------
o New function updateTables():
  + user changes to combinedTable report
  + inclusion of non-intersected features

o Changes in metabCombiner():
  + handling of missing features enabled (i.e. when update() is used)
  + new argument "impute"
  + rtOrder argument bug fix

o Changes in metabCombine():
  + new arguments "union" & "impute"

o Changes in fit_model/ fit_gam()/ fit_loess():
  + new arguments rtx & rty

o Changes in batchCombine():
  + new argument "union"
  + expected multiple (2 or more) datasets as input
  + end message added

o Changes in labelRows()/ reduceTable()/ labelRowParam()/ reduceTableParam():
  + new argument 'useID'
  + 'resolveConflicts' and 'remove' set to TRUE in reduceTable()

o Changes to metabData objects:
  + "extra"" column count added to show() message

o Package functions updated to handle "group 0"

Version 1.3.2
---------------------
o Changes to labelRows():
  + new resolveConflicts + rtOrder arguments
  + column names duplication of {labels, subgroup, alt} eliminated

o Changes to metabCombiner()/ metabCombine():
  + resolveConflicts method applied to metabCombiner object
  + new rtOrder argument

Version 1.3.1
----------------------
o Changes to fit_gam()/ fit_loess():
  + message() used in place of cat()

o Changes to metabCombiner() & combinedTable / featdata slots:
  + new rowID column added

o Changes to calcScores() / evaluateParams() / labelRows()/ reduceTable():
  + new rowID checks

o Changes to write2file():
  + combinedTable & featdata merged by rowID column (metabCombiner inputs)

Version 1.1.4 (2021-5-18)
-------------------------------
o Multi-dataset support and batchCombine added to metabCombiner package.

o Changes to metabCombiner-class:
  + new slots "featdata", "datasets", "xy"

o New metabCombiner object methods:
  + datasets, x, y, featdata, iddata, mzdata, rtdata, Qdata, adductdata

o New reduceTable()/ reduceTableParam() function

o New batchCombine() function

o Changes to object methods (getExtra, getSamples, nonmatched):
  + default data argument value changed to NULL
  + if data = NULL, returns full list pertaining to object slot

o Changes to data.R:
  + new object "metabBatches"

o Changes to metabCombiner():
  + xdata & ydata arguments accept metabCombiner objects as inputs
  + featdata constructed alongside combinedTable
  + new arguments: xid, yid, means
  + faster combinedTable construction

o Changes to labelRows()/ labelRowsParam():
  + new argument "maxRTerr""

o Changes to plot_fit():
  + bug fix for outlier highliting
  + new "legend" argument

o Changes to write2file():
  + merges combinedTable with featdata (metabCombiner object inputs)
  + faster data parsing with tidyr::unite

o CITATION added

o numerous changes to documentation, parameter & error checking

Version 1.1.3 (2021-1-13)
-------------------------------
o new metabCombine() wrapper function

o new parameter list functions for loading main function defaults

o Changes to labelRows():
  + "conflict" argument replaced with "delta", with default value (0.2)
  + default value of "minScore" argument increased to 0.5

o Changes to calcScores():
  + default argument values set: A (75), B (10), C (0.25)

o Changes to fit_loess():
  + new argument "control"
  - "iterLoess" parameter removed

o Changes to selectAnchors():
  + default "tolrtq" value changed: 0.5 -> 0.3

Version 1.1.2 (2020-12-28)
-------------------------------
o Changes to fit_gam()/ fit_loess():
  + new "outlier" argument
  + altered argument names: "frac" -> "prop", "ratio" -> "coef"
  + documentation and minor code changes

o Changes to plot_fit():
  + new outlier argument
  - remove.outliers argument removed

o new test case for fit_gam()

Version 1.1.1 (2020-12-02)
-------------------------------
o Bug Fixes:
  + combinedTable check for missing group values
  + calcScores / evaluateParams groups argument fix
  + warning for column names with bracket characters "{ ( [ ] ) }"
  + QCol bug in metabData

o New Functionality
  + getExtra method added to metabCombiner objects (Issue #11)

Version 1.0.0 (2020-10-20)
------------------------------
o Accepted to Bioconductor

o Changes to metabData():
  + matrixStats package used with notable improvements to metabData()
  + rtmin or rtmax out of bounds warning replaced with error

Changes in version 0.99.0 (2020-09-11)
------------------------------------------
+ Submitted to Bioconductor




