Merge branch 'develop' into amici_petab_problem

include/amici/edata.h

@@ -390,6 +390,13 @@ class ExpData : public SimulationParameters {
      */
     realtype const* getObservedEventsStdDevPtr(int ie) const;
 
+    /**
+     * @brief Set all observations and their standard deviations to NaN.
+     *
+     * Useful, e.g., after calling ExpData::setTimepoints.
+     */
+    void clear_observations();
+
     /**
      * @brief Arbitrary (not necessarily unique) identifier.
      */

include/amici/model.h

@@ -704,6 +704,12 @@ class Model : public AbstractModel, public ModelDimensions {
 
     /**
      * @brief Set simulation start time.
+     *
+     * Output timepoints are absolute timepoints, independent of
+     * \f$ t_{0} \f$.
+     * For output timepoints \f$ t <  t_{0} \f$, the initial state will be
+     * returned.
+
      * @param t0 Simulation start time
      */
     void setT0(double t0);

include/amici/simulation_parameters.h

@@ -175,7 +175,14 @@ class SimulationParameters {
      */
     std::vector<int> plist;
 
-    /** starting time */
+    /**
+     * @brief Starting time of the simulation.
+     *
+     * Output timepoints are absolute timepoints, independent of
+     * \f$ t_{start} \f$.
+     * For output timepoints \f$ t <  t_{start} \f$, the initial state will be
+     * returned.
+     */
     realtype tstart_{0.0};
 
     /**

src/edata.cpp

@@ -338,6 +338,18 @@ realtype const* ExpData::getObservedEventsStdDevPtr(int ie) const {
     return nullptr;
 }
 
+void ExpData::clear_observations() {
+    std::fill(observed_data_.begin(), observed_data_.end(), getNaN());
+    std::fill(
+        observed_data_std_dev_.begin(), observed_data_std_dev_.end(), getNaN()
+    );
+    std::fill(observed_events_.begin(), observed_events_.end(), getNaN());
+    std::fill(
+        observed_events_std_dev_.begin(), observed_events_std_dev_.end(),
+        getNaN()
+    );
+}
+
 void ExpData::applyDimensions() {
     applyDataDimension();
     applyEventDimension();