From 443dc0b89b3ff7ade4babda39e3973c0ec040566 Mon Sep 17 00:00:00 2001
From: unknown <olivier.delaigue@ANPI1430.antony.irstea.priv>
Date: Thu, 9 Nov 2017 11:59:58 +0100
Subject: [PATCH] v1.0.9.59 minor revisions in the NEWS file
---
DESCRIPTION | 4 +-
NEWS.md | 455 ----------------------------------------------------
NEWS.rmd | 18 +--
3 files changed, 11 insertions(+), 466 deletions(-)
delete mode 100644 NEWS.md
diff --git a/DESCRIPTION b/DESCRIPTION
index 1c3b053c..f50ab11d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: airGR
Type: Package
Title: Suite of GR Hydrological Models for Precipitation-Runoff Modelling
-Version: 1.0.9.58
-Date: 2017-11-07
+Version: 1.0.9.59
+Date: 2017-11-09
Authors@R: c(
person("Laurent", "Coron", role = c("aut", "trl")),
person("Charles", "Perrin", role = c("aut", "ths")),
diff --git a/NEWS.md b/NEWS.md
deleted file mode 100644
index e3235de3..00000000
--- a/NEWS.md
+++ /dev/null
@@ -1,455 +0,0 @@
-# Release History of the airGR Package
-
-
-
-
-### 1.0.9.47 Release Notes (2017-09-13)
-
-#### 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 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*J()</code>) now return Ps, Pn and actual exchanges. See the model Fortran codes for more details about the calculation of these variables.
-
-- <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*()</code> functions now return a warning message. <code>RunModel*()</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.
-
-____________________________________________________________________________________
-
-
-### 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).
-
-____________________________________________________________________________________
-
-
-### 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>).
-
-____________________________________________________________________________________
-
-
-### 1.0.3 Release Notes (2016-12-09)
-
-#### New features
-
-- <code>ErrorCrit*()</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).
-
-
-____________________________________________________________________________________
-
-
-### 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).
-
-
-____________________________________________________________________________________
-
-
-### 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*()</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>.
-
-____________________________________________________________________________________
-
-
-### 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.
-
-
-____________________________________________________________________________________
-
-
-### 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.
-
-
-____________________________________________________________________________________
-
-
-### 0.7.4 Release Notes (2014-11-01)
-
-#### User-visible changes
-
-- Stable version stemming from version 0.7.3.
-
-____________________________________________________________________________________
-
-
-### 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.
-
-____________________________________________________________________________________
-
-
-### 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.
-
-____________________________________________________________________________________
-
-
-### 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.
-
-
-#### Deprecated and defunct
-
-- The <code>CalibrationAlgo_*()</code> functions were renamed into<code>Calibration_*()</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.
-
-
-
-____________________________________________________________________________________
-
-
-### 0.7.0 Release Notes (2014-06-06)
-
-#### Experimental features
-
-- unfinished version used for development purpose.
-
-____________________________________________________________________________________
-
-
-### 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.
-
-____________________________________________________________________________________
-
-
-### 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.
-
-____________________________________________________________________________________
-
-
-### 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) × NSE[Q].
-
-
-#### Deprecated and defunct
-
-- <code>EfficiencyCrit()</code> have been replaced by <code>ErrorCrit()</code> to avoid misunderstanding (by default, the algorithms minimise the error criterion).
-
-____________________________________________________________________________________
-
-
-### 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.
-
-
-____________________________________________________________________________________
-
-
-### 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.
-
-
diff --git a/NEWS.rmd b/NEWS.rmd
index 9bb0d9b8..2043fe2c 100644
--- a/NEWS.rmd
+++ b/NEWS.rmd
@@ -14,28 +14,28 @@ output:
-### 1.0.9.58 Release Notes (2017-11-07)
+### 1.0.9.59 Release Notes (2017-11-09)
#### 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>CreateIniStates()</code> function in order to help user to format the <code>IniStates</code> argument for <code>CreateRunOptions()</code>.
-- Added (<code>Param_Sets_GR4J</code>) dataset. It contains generalist parameter sets for the GR4J model.
+- Added the <code>Param_Sets_GR4J</code> dataset. It contains generalist parameter sets for the GR4J model.
-- Three vignettes have been added. They are relatives to different calibration methods (including the generalist parameters sets of the GR4J model).
+- Three vignettes have been added. They are relative to different calibration methods (including the generalist parameters sets of 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>RunModel_GR4H()</code>: in <code>frun_GR4H</code> Fortran subroutine, <code>St(2)</code> is now set to 0 (instead of <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.
+- Fixed bug in <code>plot.OutputsModel()</code> for the y-axis labelling of flows time series when <code>log_scale = TRUE</code> and <code>BasinArea</code> is used.
#### Deprectated and defunct
@@ -56,7 +56,7 @@ output:
- <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*()</code> functions now return a warning message. <code>RunModel*()</code> functions now return a warning when X4 < 0.5 and set it to 0.5.
+- The X1 parameter from GR4H, GR4J, GR2M, GR5J and GR6J, the X3 parameter from GR4H, GR4J, GR5J and GR6J and the X6 parameter from GR6J are now set to 1e-2 when they are fixed to lower values. <code>RunModel*()</code> functions now return a warning message in this case. <code>RunModel*()</code> functions now return a warning when X4 < 0.5 and its value is set 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>.
@@ -215,9 +215,9 @@ ________________________________________________________________________________
#### Bug fixes
-- Bug fxed in <code>CreateInputsModel()</code> related to the handling of missing values.
+- Fixed bug in <code>CreateInputsModel()</code> that was 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).
+- Fixed bug in <code>CreateRunOptions()</code> that prevented 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
--
GitLab