NEWS.rmd

---
title: "Release History of the airGR Package"
output: 
  html_document:
    keep_md: true
---




### 1.0.9.24 Release Notes (2017-08-18) 

#### New features

- An article describing the airGR package has been published. Its reference has been added and will be displayed with <code>citation("airGR")</code>. 

- Added <code>CreateIniStates()</code> function in order to help user to format <code>IniStates</code> argument for <code>CreateRunOptions()</code>.

- Added (<code>Param_Sets_GR4J</code>) dataset. It contains the generalist parameter sets for the GR4J model.


#### Bug fixes

- Fixed bug in <code>RunModel_GR4H()</code>: in <code>frun_GR4H</code> fortran subroutine, <code>St(2)</code> is now set to 0 (and not <code>St(1)</code>) when <code>St(2) < 0</code>. 

- Fixed bug in <code>plot.OutputsModel()</code> for the regime plot when the period is less than 1 year.

- Fixed bug in <code>plot.OutputsModel()</code> when there is no common data to plot the cumulative frequency or the correlation QQ.

- Fixed bug in <code>plot.OutputsModel()</code> for y-axis labelling of flows time series when <code>log_scale = TRUE</code> and <code>BasinArea</code> used.


#### Deprectated and defunct

- The <code>RunSnowModule</code> argument is now deprecated in <code>CreateRunOptions()</code>.


#### Major user-visible changes

- <code>RunModel_GR4J()</code>, <code>RunModel_GR5J()</code> and <code>RunModel_GR6J()</code> (and <code>CemaNeige_GR&#42;J()</code>) now return Ps, Pn and true exchanges. 

- <code>CreateInputsModel()</code> now returns an error when <code>DatesR</code> contains duplicated values.

- <code>RunModel_GR5J</code> now returns <code>StateEnd</code> in the same order as the other models. 


#### Minor user-visible changes

- <code>plot.OutputsModel()</code> now returns a warning message when the length of Qobs is different from the length of Qsim. 

- The X1, X3 (and X6) parameters from GR4H, GR4J, GR2M, GR5J (and GR6J) are now set to 1e-2 when they are fixed to lower values. <code>RunModel&#42;()</code> functions now return a warning message. <code>RunModel&#42;()</code> functions now return a warning when X4 < 0.5 and set it to 0.5.

- The commands <code>?L0123001</code>, <code>?L0123002</code> and <code>?L0123003</code> now return the documentation page related to <code>BasinObs</code>.

- Many functions of the package were cleant or slightly modified, with no effect on their outputs. 

- The documentation and help of several functions were improved.


#### CRAN-comparibility updates

- "airGR.c" file registers native routines.

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### 1.0.5.12 Release Notes (2017-01-23) 


#### New features

- <code>DataAltiExtrapolation_Valery()</code> and <code>CreateInputsModel()</code> now present a PrecipScale argument which allows rescaling precipitation when it is interpolated on the elevation layers when CemaNeige is used.


#### Bug fixes

- Fixed bug in <code>DataAltiExtrapolation_Valery()</code>. The elevation gradients for air temperature returned by <code>CreateInputsModel()</code> are improved.


#### User-visible changes

- <code>DataAltiExtrapolation_Valery()</code> has been improved. <code>DataAltiExtrapolation_Valery()</code> now runs faster (and by consequence <code>CreateInputsModel()</code> too, when CemaNeige is used).

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### 1.0.4 Release Notes (2017-01-18) 

#### New features

- <code>RunModel_CemaNeige()</code>, <code>RunModel_CemaNeigeGR4J()</code>, <code>RunModel_CemaNeigeGR5J()</code> and <code>RunModel_CemaNeigeGR6J()</code> now return air temperature for each elevation layer. 


#### Deprectated and defunct

- S3 plot method defined for <code>OutputsModel</code> objects. It means that the <code>plot_OutputsModel()</code> function is deprecated and his use has been replaced by the use of <code>plot.OutputsModel()</code> or <code>plot()</code>.

- In <code>plot.OutputsModel()</code> the <code>PlotChoice</code> argument is deprecated and has been renamed <code>which</code>.


#### User-visible changes

- <code>plot.OutputsModel()</code> displays air temperature time series for each layer when <code>CemaNeige</code> is used (argument <code>which = "Temp"</code> or <code>"all"</code>).

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### 1.0.3 Release Notes (2016-12-09) 

#### New features

- <code>ErrorCrit&#42;()</code> functions gain a warnings argument to replace the verbose action and the verbose argument now prints the criterion value(s).


#### Bug fixes

- Fixed bug in <code>CreateCalibOptions()</code> when <code>StartParamList</code> or <code>StartParamDistrib</code> arguments are used.


#### User-visible changes

- <code>CreateInputsModel()</code> now returns an error if <code>NLayers <= 0</code> when <code>CemaNeige</code> is used.

- <code>plot_OutputsModel()</code> now displays raw values on the y-axis when the discharge time series is represented with log scale (formerly, log values of discharges were displayed on the y-axis).


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### 1.0.2 Release Notes (2016-11-03) 


#### New features

- <code>SeriesAggreg()</code> gains a TimeLag argument that corresponds to a numeric value indicating a time lag (in seconds) for the time series aggregation (useful to aggregate hourly time series to the daily time step for instance).
  In addition, the function now accepts input dates in both POSIXt formats (POSIXct and POSIXlt). The output is in POSIXct format.
  
- <code>plot_OutputsModel()</code> gains a <code>log_scale</code> argument in order to plot the flow with a log scale.

- A tutorial is available online on the following link: from http://webgr.irstea.fr/airGR.
  It can also be displayed with the <code>vignette("airGR")</code> command
  

#### Bug fixes

- The value <code>sort</code> for the <code>transfo</code> argument of <code>CreateInputsCrit()</code> was not taken into account. It is now fixed. 


#### Deprectated and defunct

- <code>CreateCalibOptions()</code> loses the OptimParam argument that was redundant with the <code>FixedParam</code> argument. The <code>Calibration_Michel()</code> was modified to take into account this change by using directly <code>FixedParam</code>, but this is transparent to the user. 

- <code>CreateCalibOptions()</code> loses the StartParam argument that was not used. 

  
#### Major user-visible changes

- The <code>RunModel_GR6J()</code> and <code>RunModel_CemaNeigeGR6J()</code> models were modified back to versions previous to 1.0.1 to prevent from unwanted efficiency criteria deterioration related to the calibration with <code>Calibration_Michel()</code>. 
  The actual model codes were not modified but the <code>TransfoParam_GR6J()</code> and <code>CreateCalibOptions()</code> functions were modified regarding the X5 parameter. 
  It is strongly advised to use airGR 1.0.2 for the <code>RunModel_GR6J()</code> and <code>RunModel_CemaNeigeGR6J()</code> functions if you are using <code>Calibration_Michel()</code>, as they are much more efficient. 
  In case you were using your own calibration algorithm, you will not notice any difference. 


#### Minor user-visible changes

- <code>CreateInputsModel()</code> and <code>DataAltiExtrapolation_Valery()</code> functions now allow both POSIXt formats (POSIXct and POSIXlt).


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### 1.0.1 Release Notes (2016-04-21) 

#### Deprectated and defunct

- The <code>Calibration_HBAN()</code> and <code>DataAltiExtrapolation_HBAN()</code> functions have respectively been renamed as <code>Calibration_Michel()</code> and <code>DataAltiExtrapolation_Valery()</code> after the names of their creators.

- The <code>Calibration_optim()</code> function has been removed from the package.

- The silent mode is now defined by the <code>verbose = TRUE</code> argument (formerly <code>quiet = FALSE</code>) in the following functions :
<code>Calibration()</code>, <code>Calibration_Michel()</code>, <code>CreateInputsModel()</code>, <code>CreateRunOptions()</code>, <code>DataAltiExtrapolation_Valery()</code>, <code>ErrorCrit()</code>, <code>ErrorCrit_KGE()</code>, <code>ErrorCrit_KGE2()</code>, <code>ErrorCrit_NSE()</code>, <code>ErrorCrit_RMSE()</code>, <code>plot_OutputsModel()</code>, <code>SeriesAggreg()</code>.


#### Major user-visible changes
- The GR5J model has been modified: previously, two unit hydrographs were used, now only one is remaining.
  As a consequence, simulations from the GR5J (<code>RunModel_GR5J()</code> function) and CemaNeige (<code>RunModel_CemaNeigeGR5J()</code> function) models will be different.

- An important proportion of the transformations of the parameters have been modified (<code>TransfoParam&#42;()</code> functions). Since this modifies the local search, calibration results will be different .

- The quantiles of the parameters have been recalculated with the new transformations (<code>CreateCalibOptions()</code> function). Since these quantiles constitute the starting point of the calibration algorithm, calibration results will be different.


#### Minor user-visible changes

- The FORTRAN model core codes have been modified:
	- optimisation of the codes for fastening of computation;
	- simplification of the internal variables for easier reading and understanding.
	
- The list of the contributors and authors is now full.

- The references of the package has been updated; they are returned by the following R-command <code>citation("airGR")</code>.

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### 0.8.1.2 Release Notes (2015-08-21) 

#### Bug fixes

- Bug fxed in <code>CreateInputsModel()</code> related to the handling of missing values.

- Bug fxed in <code>CreateRunOptions()</code> preventing the correct use of the <code>IniResLevels</code> argument (to manually set the filling rate of the production and routing stores).


#### Minor user-visible changes

- Removal of an unnecessary warning when <code>IndPeriod_WarmUp = 0</code>.


#### CRAN-comparibility updates

- Modification of namespace file to ensure proper use under linux whithout compilation issues.


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### 0.8.0.2 Release Notes (2015-04-15) 


#### New features

- Three new hydrological models: <code>RunModel_GR4H() function for </code> GR4H (hourly), <code>RunModel_GR2M()</code>  function for GR2M (monthly) and <code>RunModel_GR1A()</code>  function for GR1A (yearly).

- New function <code>SeriesAggreg()</code> to easily aggreg timesteps.


#### Bug fixes

- Fixed bug in <code>ErrorCrit_RMSE()</code> which led to incorrect calibration (the criterion was maximised instead of minimised).


#### Major user-visible changes

- Update of the functions <code>CreateRunOptions()</code>, <code>CreateCalibOptions()</code> and <code>plot_OutputsModel()</code> to handle the new models.

- Modification of CemaNeige FORTRAN code to add an update of Gratio after the SnowPack update (no impact on snow simulation).


#### Minor user-visible changes

- Improvement of the <code>plot_OutputsModel()</code> function to allow a selection among available plots.

- Minor update in <code>ErrorCrit_KGE()</code> and <code>ErrorCrit_KGE2()</code> to handle case when only one values in not NA.

- Update of the scripts in airGR-advanced-example to match the structures of the <code>BasinData</code> objects.

- Correction of formatting issue in airGR-advanced-example regarding the "List_HypsoData.txt" file.


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### 0.7.4 Release Notes (2014-11-01) 

#### User-visible changes

- Stable version stemming from version 0.7.3.

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### 0.7.3 Release Notes (2014-XX-XX) 

#### Minor user-visible changes

- Improvements allowing the arrival of new models.

- Improvements of the argument verifications in <code>CreateInputsModel()</code>, <code>CreateRunOptions()</code>, <code>CreateInputsCrit()</code>, <code>CreateCalibOptions()</code>.

- Improvements of all the <code>ErrorCrit()</code> functions to better account for the cases with constant flow values or local zeros.

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### 0.7.2 Release Notes (2014-07-14) 

#### New features

- New argument in many functions (<code>quiet = TRUE</code> or <code>FALSE</code>) to choose if the warnings should be suppressed or not.


#### Bug fixes

- Fixed bug in <code>CreateCalibOptions()</code> to handle models with only one parameter.


#### Major user-visible changes

- CemaNeige users must now specify one <code>MeanAnSolidPrecip</code> for each elevation layer. The <code>CreateRunOptions()</code> function is impacted.

- CemaNeige users can now specify the mean elevation of the input series (before it was always considered equal to the catchment median elevation). 
  The impacted functions are <code>CreateInputsModel()</code> and <code>DataAltiExtrapolation_HBAN()</code>.


#### Minor user-visible changes

- Improvement of the <code>plot_OutputsModel</code> function (to handle 0 in Qobs and Qsim).

- Improved documentation.

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### 0.7.1 Release Notes (2014-07-14) 

#### Bug fixes

- Fixed bug in <code>Calibration_HBAN()</code>. The function was not working properly with models having only one parameter.


#### Deprectated and defunct

- The <code>CalibrationAlgo_&#42;()</code> functions were renamed into<code>Calibration_&#42;()</code>.


#### Major user-visible changes

- New architecture with better format verification procedure (using classes) and simpler setting of default configuration.

- New architecture where the model, calibration and error functions are in the arguments of the functions
  (the exotic use of "generic function" created by the users has been removed).

- Improved documentation and examples.



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### 0.7.0 Release Notes (2014-06-06) 

#### Experimental features

- unfinished version used for development purpose.

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### 0.6.2 Release Notes (2014-02-12) 

#### Bug fixes

- RC11 bug correction: the automatic selection of the warm-up period was not working properly when no data was available from warm-up (i.e. when the user had set the run to start at the very first index).

- RC10 bug correction: the <code>CalibrationAlgo_HBAN()</code> function was not working in the very rare case when the diagonal search was activated and lead to a set outside the authorised range.

- RC9 bug correction: the <code>CalibrationAlgo_HBAN()</code> function was not working properly with models having only one parameter.

- RC8 bug correction of the <code>ModelDefaultIniOptions()</code> function (this bug was introduced in the RC7 and caused an error when <code>IndPeriod_WarmUp = NULL</code>

- RC7 bug correction of the <code>ModelDefaultIniOptions()</code> function (the automatic selection of one year for warm-up was not handling properly missing data).

- RC6 correction of the help files (the description of CemaNeige parameters were inverted).

- RC5 differs from previous releases in the way the data are read and stored (in a list instead of individual vectors).
  The package is similar, only the examples of Main and the files in MyScriptBlocks have changed.
  All basin data are now stored inside a list named <code>BasinData</code>. This will greatly ease the future use of Rdata files (instead of txt files) as storage format for the time series of observation.  

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### 0.6.1 Release Notes (2014-02-12) 


#### New features

- Additional functions for results plotting (the <code>{zoo}</code> package is required for some of them).

- Add multi-objective calibration using <code>nsga2()</code> (the <code>{mco}</code> package is required).

#### Major user-visible changes

- The definition of the generic function is now made in a much simpler way (e.g. see <code>DefineFunctions_Model()</code> or <code>DefineFunctions_ErrorCrit()</code>).


#### Minor user-visible changes

- Code improvements to reduce the computation time.

- Clearer instructions for the adding and modification of a model.

- Improvements of the documentation.

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### 0.6.0 Release Notes (2014-02-12) 

#### New features

- The field Multiplier has been added in the ErrorCrit() outputs, to indicate whether the criterion is an error (to minimise) or and efficiency (to maximise).
  This allows to provide real efficiency values in the outputs e.g. NSE[Q] instead of (-1)  &times; NSE[Q].


#### Deprectated and defunct

- <code>EfficiencyCrit()</code> have been replaced by <code>ErrorCrit()</code> to avoid misunderstanding (by default, the algorithms minimise the error criterion).

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### 0.5.2 Release Notes (2014-02-05) 


#### Deprectated and defunct

- The <code>SelectPer</code> arguments are replaced by <code>IndPeriod</code> to ease understanding.

- The <code>PE</code> arguments are replaced by <code>PotEvap()</code> to ease understanding.

- The <code>Fsol</code> arguments are replaced by <code>FracSolidPrecip</code> to ease understanding.


#### Major user-visible changes

- R 2.15 in not supported by default.

- The check that <code>SelectPer_Run()</code> is continuous is now made in the <code>CheckArg()</code> functions.

- Check of the model functioning time step.

- Name of the calibration criterion provided in <code>OutputsAlgo()</code>.


#### Minor user-visible changes

- Missing values in FORTRAN are now -999.999 instead of -9.999.


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### 0.5.1  Release Notes (2014-01-27) 


#### New features

- New <code>EfficiencyCrit_NSE_sqrtQ()</code> function to compute NSE criterion on sqrt flows


#### Bug fixes

- Incorrect arguments in the call to <code>RunModelAndCrit</code> from <code>CalibrationAlgo_optim_stats</code> and <code>CalibrationAlgo_nlminb_stats</code>.

- <code>CalibrationAlgo_nlminb_stats</code> argument was wrongly defined in <code>DefineFunctions_CalibrationAlgo()</code> (<code>optim</code> instead of <code>nlminb</code>).

- Format checking for <code>RunOptions</code> was incorrectly made in <code>CheckArg()</code> function.