diff --git a/DESCRIPTION b/DESCRIPTION
index e10e064f7f5e1db420d3e8de431d031b601956ac..501042c6dc0980e8e029b59260ca5cd1a10c78e8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,17 +1,17 @@
Package: airGR
Type: Package
Title: Suite of GR Hydrological Models for Precipitation-Runoff Modelling
-Version: 1.0.11.0
-Date: 2018-07-18
+Version: 1.0.11.1
+Date: 2018-08-09
Authors@R: c(
- person("Laurent", "Coron", role = c("aut", "trl")),
- person("Charles", "Perrin", role = c("aut", "ths")),
- person("Olivier", "Delaigue", role = c("aut", "cre"), email = "airGR@irstea.fr"),
- person("Guillaume", "Thirel", role = c("aut")),
+ person("Laurent", "Coron", role = c("aut", "trl"), comment = c(ORCID = "0000-0002-1503-6204")),
+ person("Charles", "Perrin", role = c("aut", "ths"), comment = c(ORCID = "0000-0001-8552-1881")),
+ person("Olivier", "Delaigue", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7668-8468"), email = "airGR@irstea.fr"),
+ person("Guillaume", "Thirel", role = c("aut"), comment = c(ORCID = "0000-0002-1444-1830")),
person("Claude", "Michel", role = c("aut", "ths")),
- person("Vazken", "Andréassian", role = c("ctb", "ths")),
- person("François", "Bourgin", role = c("ctb"), comment = "'Parameter estimation' vignettes"),
- person("Pierre", "Brigode", role = c("ctb")),
+ person("Vazken", "Andréassian", role = c("ctb", "ths"), comment = c(ORCID = "0000-0001-7124-9303")),
+ person("François", "Bourgin", role = c("ctb"), comment = c(ORCID = "0000-0002-2820-7260", vignette = "'Parameter estimation' vignettes")),
+ person("Pierre", "Brigode", role = c("ctb"), comment = c(ORCID = "0000-0001-8257-0741")),
person("Nicolas", "Le Moine", role = c("ctb")),
person("Thibaut", "Mathevet", role = c("ctb")),
person("Safouane", "Mouelhi", role = c("ctb")),
diff --git a/NEWS.html b/NEWS.html
index 0928177629730981507b4bdc4ef042d063a4f913..aa7af84248575d539cad680e8123835593a4c720 100644
--- a/NEWS.html
+++ b/NEWS.html
@@ -76,6 +76,9 @@ img {
.tabbed-pane {
padding-top: 12px;
}
+.html-widget {
+ margin-bottom: 20px;
+}
button.code-folding-btn:focus {
outline: none;
}
@@ -203,23 +206,48 @@ div.tocify {
</div>
-<div id="release-notes-2017-09-13" class="section level3">
-<h3>1.0.9.47 Release Notes (2017-09-13)</h3>
+<div id="release-notes-2018-06-29" class="section level3">
+<h3>1.0.10.11 Release Notes (2018-06-29)</h3>
+<div id="bug-fixes" class="section level4">
+<h4>Bug fixes</h4>
+<ul>
+<li>Fixed bug in <code>RunModel_GR2M</code>. The function now returns the total precipitation (P) instead of the net rainfall (P1).</li>
+</ul>
+</div>
+<div id="major-user-visible-changes" class="section level4">
+<h4>Major user-visible changes</h4>
+<ul>
+<li><p><code>RunModel_GR2M</code> now returns more explicit precipitation outputs names.</p></li>
+<li><p><code>CreateInputsCrit</code> now returns a warning message when the KGE (or KGE’) is used with a log transformation on flows.</p></li>
+<li><p>The article reference is corrected.</p></li>
+</ul>
+</div>
+<div id="minor-user-visible-changes" class="section level4">
+<h4>Minor user-visible changes</h4>
+<ul>
+<li>The documentation and help of several functions were improved.</li>
+</ul>
+<hr />
+</div>
+</div>
+<div id="release-notes-2017-11-10" class="section level3">
+<h3>1.0.9.64 Release Notes (2017-11-10)</h3>
<div id="new-features" class="section level4">
<h4>New features</h4>
<ul>
<li><p>An article describing the airGR package has been published. Its reference has been added and will be displayed with <code>citation(“airGRâ€)</code>.</p></li>
-<li><p>Added <code>CreateIniStates()</code> function in order to help user to format <code>IniStates</code> argument for <code>CreateRunOptions()</code>.</p></li>
-<li><p>Added (<code>Param_Sets_GR4J</code>) dataset. It contains generalist parameter sets for the GR4J model.</p></li>
+<li><p>Added <code>CreateIniStates()</code> function in order to help user to format the <code>IniStates</code> argument for <code>CreateRunOptions()</code>.</p></li>
+<li><p>Added the <code>Param_Sets_GR4J</code> dataset. It contains generalist parameter sets for the GR4J model.</p></li>
+<li><p>Three vignettes have been added. They are relative to different calibration methods (including the generalist parameters sets of the GR4J model).</p></li>
</ul>
</div>
-<div id="bug-fixes" class="section level4">
+<div id="bug-fixes-1" class="section level4">
<h4>Bug fixes</h4>
<ul>
-<li><p>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>.</p></li>
+<li><p>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>.</p></li>
<li><p>Fixed bug in <code>plot.OutputsModel()</code> for the regime plot when the period is less than 1 year.</p></li>
<li><p>Fixed bug in <code>plot.OutputsModel()</code> when there is no common data to plot the cumulative frequency or the correlation QQ.</p></li>
-<li><p>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.</p></li>
+<li><p>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.</p></li>
</ul>
</div>
<div id="deprectated-and-defunct" class="section level4">
@@ -228,7 +256,7 @@ div.tocify {
<li>The <code>RunSnowModule</code> argument is now deprecated in <code>CreateRunOptions()</code>.</li>
</ul>
</div>
-<div id="major-user-visible-changes" class="section level4">
+<div id="major-user-visible-changes-1" class="section level4">
<h4>Major user-visible changes</h4>
<ul>
<li><p><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.</p></li>
@@ -236,18 +264,18 @@ div.tocify {
<li><p><code>RunModel_GR5J</code> now returns <code>StateEnd</code> in the same order as the other models.</p></li>
</ul>
</div>
-<div id="minor-user-visible-changes" class="section level4">
+<div id="minor-user-visible-changes-1" class="section level4">
<h4>Minor user-visible changes</h4>
<ul>
<li><p><code>plot.OutputsModel()</code> now returns a warning message when the length of Qobs is different from the length of Qsim.</p></li>
-<li><p>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.</p></li>
+<li><p>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.</p></li>
<li><p>The commands <code>?L0123001</code>, <code>?L0123002</code> and <code>?L0123003</code> now return the documentation page related to <code>BasinObs</code>.</p></li>
<li><p>Many functions of the package were cleant or slightly modified, with no effect on their outputs.</p></li>
<li><p>The documentation and help of several functions were improved.</p></li>
</ul>
</div>
-<div id="cran-comparibility-updates" class="section level4">
-<h4>CRAN-comparibility updates</h4>
+<div id="cran-compatibility-updates" class="section level4">
+<h4>CRAN-compatibility updates</h4>
<ul>
<li>“airGR.c†file registers native routines.</li>
</ul>
@@ -262,7 +290,7 @@ div.tocify {
<li><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.</li>
</ul>
</div>
-<div id="bug-fixes-1" class="section level4">
+<div id="bug-fixes-2" class="section level4">
<h4>Bug fixes</h4>
<ul>
<li>Fixed bug in <code>DataAltiExtrapolation_Valery()</code>. The elevation gradients for air temperature returned by <code>CreateInputsModel()</code> are improved.</li>
@@ -307,7 +335,7 @@ div.tocify {
<li><code>ErrorCrit*()</code> functions gain a warnings argument to replace the verbose action and the verbose argument now prints the criterion value(s).</li>
</ul>
</div>
-<div id="bug-fixes-2" class="section level4">
+<div id="bug-fixes-3" class="section level4">
<h4>Bug fixes</h4>
<ul>
<li>Fixed bug in <code>CreateCalibOptions()</code> when <code>StartParamList</code> or <code>StartParamDistrib</code> arguments are used.</li>
@@ -329,10 +357,10 @@ div.tocify {
<ul>
<li><p><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.</p></li>
<li><p><code>plot_OutputsModel()</code> gains a <code>log_scale</code> argument in order to plot the flow with a log scale.</p></li>
-<li><p>A tutorial is available online on the following link: from <a href="http://webgr.irstea.fr/airGR" class="uri">http://webgr.irstea.fr/airGR</a>. It can also be displayed with the <code>vignette(“airGRâ€)</code> command</p></li>
+<li><p>A tutorial is available online on the following link: from <a href="http://webgr.irstea.fr/airGR" class="uri">http://webgr.irstea.fr/airGR</a>. It can also be displayed with the <code>vignette(“airGRâ€)</code> command.</p></li>
</ul>
</div>
-<div id="bug-fixes-3" class="section level4">
+<div id="bug-fixes-4" class="section level4">
<h4>Bug fixes</h4>
<ul>
<li>The value <code>sort</code> for the <code>transfo</code> argument of <code>CreateInputsCrit()</code> was not taken into account. It is now fixed.</li>
@@ -345,13 +373,13 @@ div.tocify {
<li><p><code>CreateCalibOptions()</code> loses the StartParam argument that was not used.</p></li>
</ul>
</div>
-<div id="major-user-visible-changes-1" class="section level4">
+<div id="major-user-visible-changes-2" class="section level4">
<h4>Major user-visible changes</h4>
<ul>
<li>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.</li>
</ul>
</div>
-<div id="minor-user-visible-changes-1" class="section level4">
+<div id="minor-user-visible-changes-2" class="section level4">
<h4>Minor user-visible changes</h4>
<ul>
<li><code>CreateInputsModel()</code> and <code>DataAltiExtrapolation_Valery()</code> functions now allow both POSIXt formats (POSIXct and POSIXlt).</li>
@@ -369,7 +397,7 @@ div.tocify {
<li><p>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>.</p></li>
</ul>
</div>
-<div id="major-user-visible-changes-2" class="section level4">
+<div id="major-user-visible-changes-3" class="section level4">
<h4>Major user-visible changes</h4>
<ul>
<li><p>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.</p></li>
@@ -377,7 +405,7 @@ div.tocify {
<li><p>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.</p></li>
</ul>
</div>
-<div id="minor-user-visible-changes-2" class="section level4">
+<div id="minor-user-visible-changes-3" class="section level4">
<h4>Minor user-visible changes</h4>
<ul>
<li>The Fortran model core codes have been modified:
@@ -393,21 +421,21 @@ div.tocify {
</div>
<div id="release-notes-2015-08-21" class="section level3">
<h3>0.8.1.2 Release Notes (2015-08-21)</h3>
-<div id="bug-fixes-4" class="section level4">
+<div id="bug-fixes-5" class="section level4">
<h4>Bug fixes</h4>
<ul>
-<li><p>Bug fxed in <code>CreateInputsModel()</code> related to the handling of missing values.</p></li>
-<li><p>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).</p></li>
+<li><p>Fixed bug in <code>CreateInputsModel()</code> that was related to the handling of missing values.</p></li>
+<li><p>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).</p></li>
</ul>
</div>
-<div id="minor-user-visible-changes-3" class="section level4">
+<div id="minor-user-visible-changes-4" class="section level4">
<h4>Minor user-visible changes</h4>
<ul>
<li>Removal of an unnecessary warning when <code>IndPeriod_WarmUp = 0</code>.</li>
</ul>
</div>
-<div id="cran-comparibility-updates-1" class="section level4">
-<h4>CRAN-comparibility updates</h4>
+<div id="cran-compatibility-updates-1" class="section level4">
+<h4>CRAN-compatibility updates</h4>
<ul>
<li>Modification of namespace file to ensure proper use under linux whithout compilation issues.</li>
</ul>
@@ -423,20 +451,20 @@ div.tocify {
<li><p>New function <code>SeriesAggreg()</code> to easily aggreg timesteps.</p></li>
</ul>
</div>
-<div id="bug-fixes-5" class="section level4">
+<div id="bug-fixes-6" class="section level4">
<h4>Bug fixes</h4>
<ul>
<li>Fixed bug in <code>ErrorCrit_RMSE()</code> which led to incorrect calibration (the criterion was maximised instead of minimised).</li>
</ul>
</div>
-<div id="major-user-visible-changes-3" class="section level4">
+<div id="major-user-visible-changes-4" class="section level4">
<h4>Major user-visible changes</h4>
<ul>
<li><p>Update of the functions <code>CreateRunOptions()</code>, <code>CreateCalibOptions()</code> and <code>plot_OutputsModel()</code> to handle the new models.</p></li>
<li><p>Modification of CemaNeige Fortran code to add an update of Gratio after the SnowPack update (no impact on snow simulation).</p></li>
</ul>
</div>
-<div id="minor-user-visible-changes-4" class="section level4">
+<div id="minor-user-visible-changes-5" class="section level4">
<h4>Minor user-visible changes</h4>
<ul>
<li><p>Improvement of the <code>plot_OutputsModel()</code> function to allow a selection among available plots.</p></li>
@@ -459,7 +487,7 @@ div.tocify {
</div>
<div id="release-notes-2014-xx-xx" class="section level3">
<h3>0.7.3 Release Notes (2014-XX-XX)</h3>
-<div id="minor-user-visible-changes-5" class="section level4">
+<div id="minor-user-visible-changes-6" class="section level4">
<h4>Minor user-visible changes</h4>
<ul>
<li><p>Improvements allowing the arrival of new models.</p></li>
@@ -477,20 +505,20 @@ div.tocify {
<li>New argument in many functions (<code>quiet = TRUE</code> or <code>FALSE</code>) to choose if the warnings should be suppressed or not.</li>
</ul>
</div>
-<div id="bug-fixes-6" class="section level4">
+<div id="bug-fixes-7" class="section level4">
<h4>Bug fixes</h4>
<ul>
<li>Fixed bug in <code>CreateCalibOptions()</code> to handle models with only one parameter.</li>
</ul>
</div>
-<div id="major-user-visible-changes-4" class="section level4">
+<div id="major-user-visible-changes-5" class="section level4">
<h4>Major user-visible changes</h4>
<ul>
<li><p>CemaNeige users must now specify one <code>MeanAnSolidPrecip</code> for each elevation layer. The <code>CreateRunOptions()</code> function is impacted.</p></li>
<li><p>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>.</p></li>
</ul>
</div>
-<div id="minor-user-visible-changes-6" class="section level4">
+<div id="minor-user-visible-changes-7" class="section level4">
<h4>Minor user-visible changes</h4>
<ul>
<li><p>Improvement of the <code>plot_OutputsModel</code> function (to handle 0 in Qobs and Qsim).</p></li>
@@ -501,7 +529,7 @@ div.tocify {
</div>
<div id="release-notes-2014-07-14-1" class="section level3">
<h3>0.7.1 Release Notes (2014-07-14)</h3>
-<div id="bug-fixes-7" class="section level4">
+<div id="bug-fixes-8" class="section level4">
<h4>Bug fixes</h4>
<ul>
<li>Fixed bug in <code>Calibration_HBAN()</code>. The function was not working properly with models having only one parameter.</li>
@@ -513,7 +541,7 @@ div.tocify {
<li>The <code>CalibrationAlgo_*()</code> functions were renamed into<code>Calibration_*()</code>.</li>
</ul>
</div>
-<div id="major-user-visible-changes-5" class="section level4">
+<div id="major-user-visible-changes-6" class="section level4">
<h4>Major user-visible changes</h4>
<ul>
<li><p>New architecture with better format verification procedure (using classes) and simpler setting of default configuration.</p></li>
@@ -535,13 +563,13 @@ div.tocify {
</div>
<div id="release-notes-2014-02-12" class="section level3">
<h3>0.6.2 Release Notes (2014-02-12)</h3>
-<div id="bug-fixes-8" class="section level4">
+<div id="bug-fixes-9" class="section level4">
<h4>Bug fixes</h4>
<ul>
<li><p>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).</p></li>
<li><p>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.</p></li>
<li><p>RC9 bug correction: the <code>CalibrationAlgo_HBAN()</code> function was not working properly with models having only one parameter.</p></li>
-<li><p>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></p></li>
+<li><p>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>.</p></li>
<li><p>RC7 bug correction of the <code>ModelDefaultIniOptions()</code> function (the automatic selection of one year for warm-up was not handling properly missing data).</p></li>
<li><p>RC6 correction of the help files (the description of CemaNeige parameters were inverted).</p></li>
<li><p>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.</p></li>
@@ -558,13 +586,13 @@ div.tocify {
<li><p>Add multi-objective calibration using <code>nsga2()</code> (the <code>{mco}</code> package is required).</p></li>
</ul>
</div>
-<div id="major-user-visible-changes-6" class="section level4">
+<div id="major-user-visible-changes-7" class="section level4">
<h4>Major user-visible changes</h4>
<ul>
<li>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>).</li>
</ul>
</div>
-<div id="minor-user-visible-changes-7" class="section level4">
+<div id="minor-user-visible-changes-8" class="section level4">
<h4>Minor user-visible changes</h4>
<ul>
<li><p>Code improvements to reduce the computation time.</p></li>
@@ -600,7 +628,7 @@ div.tocify {
<li><p>The <code>Fsol</code> arguments are replaced by <code>FracSolidPrecip</code> to ease understanding.</p></li>
</ul>
</div>
-<div id="major-user-visible-changes-7" class="section level4">
+<div id="major-user-visible-changes-8" class="section level4">
<h4>Major user-visible changes</h4>
<ul>
<li><p>R 2.15 in not supported by default.</p></li>
@@ -609,7 +637,7 @@ div.tocify {
<li><p>Name of the calibration criterion provided in <code>OutputsAlgo()</code>.</p></li>
</ul>
</div>
-<div id="minor-user-visible-changes-8" class="section level4">
+<div id="minor-user-visible-changes-9" class="section level4">
<h4>Minor user-visible changes</h4>
<ul>
<li>Missing values in Fortran are now -999.999 instead of -9.999.</li>
@@ -622,10 +650,10 @@ div.tocify {
<div id="new-features-9" class="section level4">
<h4>New features</h4>
<ul>
-<li>New <code>EfficiencyCrit_NSE_sqrtQ()</code> function to compute NSE criterion on sqrt flows</li>
+<li>New <code>EfficiencyCrit_NSE_sqrtQ()</code> function to compute NSE criterion on sqrt flows.</li>
</ul>
</div>
-<div id="bug-fixes-9" class="section level4">
+<div id="bug-fixes-10" class="section level4">
<h4>Bug fixes</h4>
<ul>
<li><p>Incorrect arguments in the call to <code>RunModelAndCrit</code> from <code>CalibrationAlgo_optim_stats</code> and <code>CalibrationAlgo_nlminb_stats</code>.</p></li>