# synergyfinder 3.3.3 (2022-01-05)
# Author: shuyu.zheng@helsinki.fi
## New features

* Enable the setting of color bar range in plotting functions for heatmap, contour, and 3D surface plots.
* Enable the setting of z-axis range in plotting functions for 3D surface plots.
* Enable the setting of axis lines and ticks in plotting functions for contour and 3D surface plots.
* Check the number of drugs-cell combo in each block. If there are more than one combo in some blocks. The ReshapeData stops and raises an error message.

## Debug

* The input data with replicates and missing values caused errors while calculating synergy scores. Now this bug is fixed.

# synergyfinder 2.99.0/2.4.8 (2021-03-10)
## Author: shuyu.zheng@helsinki.fi
## Major Update

* Upgrade all existing functions to be compitible with multiple (more than 2) drugs combination data
* Add functions for drug sensitivity score (CSS, RI) calucluation.
* Add ploting functions for barometer, S-S plot, bar plot for multiple drug combinations.

# synergyfinder 2.5.2/2.4.2 (2021-01-07)
## Author: shuyu.zheng@helsinki.fi
## Changes

* "CorrectBaseLine": Use the minimu value (instead of mean) of the fitted single drug response as the baseline.

# synergyfinder 2.3.5/2.2.5 (2020-12-01)
## Author: shuyu.zheng@helsinki.fi
## Changes

* Enable the "ZIP" function to handle the N x 2 or 2 x N drug combination matrices.
* Add "seed" parameter into function "ReshapeData" for generating the noise, if "noise = TRUE".

# synergyfinder 2.1.2/2.0.2 (2019-11-08)
## Author: shuyu.zheng@helsinki.fi
## Changes

* Fix the bug caused by changes in 2.1.1

# synergyfinder 2.1.1/2.0.1 (2019-10-30)
## Author: shuyu.zheng@helsinki.fi
## New features

* Add "file.type" option in the "PlotSynergy" and "PlotDoseResponse" functions to specify the format of files when saving plots.
* Add "file.name" parameter to plot functions. User can specify the name of the saved files.

## Changes

* Delete the "warning" exceptions in "FitDoseResponse" function.

# synergyfinder 1.99.1/2.0.1 (2019-06-14)
## Author: shuyu.zheng@helsinki.fi
## New features

* Add data pre-process functions: AddNoise, ImputeNA to handle more data.
* Make column names of input data compatible with "camel" and "snake" style.
* Add one more method ("part") for correcting base line.
* User can set adjusted in PlotDoseResponse function to plot original matrix.

## Changes

* Updated algorithms in Loewe and ZIP functions.
* Move correction argument from syngergy functions to ReshapeData function.
* Delete Emin and Emax argument in CalculateSynergy function.
* fixed the col.range and row.range in PlotSynergy function.

# synergyfinder 1.5.1

## New features

* change license to Mozilla Public License 2.0
* update the citation information
* fix for non-square dose response matrix

# synergyfinder 1.3.0

## New features

* new kriging function in PlotSynergy function

# synergyfinder 0.99.2

## New features

* Fixed the no convergence issue when fitting single drugs.
* Fixed the Emin and Emax to 0 and 100 in PlotDoseResponse function.
* User can set Emin and Emax for fitting single drugs.
* Choose drug combination pair in PlotDoseResponse function.
* Choose drug combination pair in PlotSynergy function.
* Set legend starting and ending point in PlotSynergy function.

# synergyfinder 0.99.1

## New features

* Fixed the issues in PlotSynergy function when the matrix is not 6*6.
* Fixed the wrong labels of 3D synergy plot.
* Fixed the index issues in Loewe function.

# synergyfinder 0.99.0

## New features

* Four synergy score methods are implemented.

