893 add initialization method with real data for lct model

cpp/memilio/io/epi_data.h

@@ -65,6 +65,58 @@ class StringDate : public Date
     }
 };
 
+/**
+ * Represents the entries of a confirmed cases data file, e.g., from RKI.
+ * Number of confirmed, recovered and deceased in Germany on a specific date.
+ * ConfirmedCasesNoAgeEntry is a simplified version of ConfirmedCasesDataEntry without agegroups.
+ */
+class ConfirmedCasesNoAgeEntry
+{
+public:
+    double num_confirmed;
+    double num_recovered;
+    double num_deaths;
+    Date date;
+
+    template <class IOContext>
+    static IOResult<ConfirmedCasesNoAgeEntry> deserialize(IOContext& io)
+    {
+        auto obj           = io.expect_object("ConfirmedCasesNoAgeEntry");
+        auto num_confirmed = obj.expect_element("Confirmed", Tag<double>{});
+        auto num_recovered = obj.expect_element("Recovered", Tag<double>{});
+        auto num_deaths    = obj.expect_element("Deaths", Tag<double>{});
+        auto date          = obj.expect_element("Date", Tag<StringDate>{});
+        return apply(
+            io,
+            [](auto&& nc, auto&& nr, auto&& nd, auto&& d) {
+                return ConfirmedCasesNoAgeEntry{nc, nr, nd, d};
+            },
+            num_confirmed, num_recovered, num_deaths, date);
+    }
+};
+
+/**
+ * Deserialize a list of ConfirmedCasesNoAgeEntry from json.
+ * @param jsvalue json value, must be an array of objects, objects must match ConfirmedCasesNoAgeEntry.
+ *  Accordingly, there should be one entry per date with the values for Confirmed, Recovered and Deaths. In addition, no age groups should be specified.
+ * @return List of ConfirmedCasesNoAgeEntry.
+ */
+inline IOResult<std::vector<ConfirmedCasesNoAgeEntry>> deserialize_confirmed_cases_noage(const Json::Value& jsvalue)
+{
+    return deserialize_json(jsvalue, Tag<std::vector<ConfirmedCasesNoAgeEntry>>{});
+}
+
+/**
+ * Read list of ConfirmedCasesNoAgeEntry from a json file.
+ * @param filename name of the json file. File content must be an array of objects, objects must match ConfirmedCasesNoAgeEntry.
+ *  Accordingly, there should be one entry per date with the values for Confirmed, Recovered and Deaths. In addition, no age groups should be specified.
+ * @return List of ConfirmedCasesNoAgeEntry.
+ */
+inline IOResult<std::vector<ConfirmedCasesNoAgeEntry>> read_confirmed_cases_noage(const std::string& filename)
+{
+    return read_json(filename, Tag<std::vector<ConfirmedCasesNoAgeEntry>>{});
+}
+
 /**
  * Represents the entries of a confirmed cases data file, e.g., from RKI.
  * Number of confirmed, recovered and deceased in a region on a specific date.

cpp/models/lct_secir/CMakeLists.txt

@@ -4,6 +4,7 @@ add_library(lct_secir
     model.cpp
     simulation.h    
     parameters.h
+    parameters_io.h
 )
 target_link_libraries(lct_secir PUBLIC memilio)
 target_include_directories(lct_secir PUBLIC

cpp/models/lct_secir/README.md

@@ -2,8 +2,8 @@
 
 This model is based on the Linear Chain Trick. 
 
-The Linear Chain Trick provides the option to use Erlang-distributed sojourn times in the compartments through the use of subcompartments. 
-The normal ODE models have (possibly unrealistic) exponentially distributed sojourn times.
+The Linear Chain Trick provides the option to use Erlang-distributed stay times in the compartments through the use of subcompartments. 
+The normal ODE models have (possibly unrealistic) exponentially distributed stay times.
 The LCT model can still be described by an ordinary differential equation system.
 
 For the concept see 
@@ -57,3 +57,7 @@ The notation of the compartments with indices here stands for subcompartments an
 
 A simple example can be found at [LCT minimal example](../../examples/lct_secir.cpp).
 
+## Initialization 
+
+- The file [parameters_io](parameters_io.h) provides functionality to compute an initial value vector for the LCT-SECIR model based on real data.
+

cpp/models/lct_secir/model.h

@@ -283,6 +283,17 @@ class Model
         return m_initial_values;
     }
 
+    /**
+     * @brief Sets the initial values for the model.
+     *
+     * @param[in] init Vector with initial values for all infection states inclusive subcompartments.
+     */
+    void set_initial_values(Eigen::VectorXd init)
+    {
+        m_initial_values = init;
+        m_N0 = m_initial_values.sum();
+    }
+
     Parameters parameters{}; ///< Parameters of the model.
 
 private:

cpp/tests/CMakeLists.txt

@@ -72,6 +72,7 @@ if(MEMILIO_HAS_JSONCPP)
 set(TESTSOURCES ${TESTSOURCES}
 test_json_serializer.cpp
 test_epi_data_io.cpp
+test_lct_parameters_io.cpp
 )
 endif()
 

cpp/tests/data/cases_all_germany.json

@@ -0,0 +1,92 @@
+[
+    {
+        "Date": "2020-05-24",
+        "Confirmed": 1.2,
+        "Deaths": 0.5,
+        "Recovered": 0
+    },
+    {
+        "Date": "2020-05-25",
+        "Confirmed": 5,
+        "Deaths": 2.0,
+        "Recovered": 2.5
+    },
+    {
+        "Date": "2020-05-26",
+        "Confirmed": 20.2,
+        "Deaths": 5.01,
+        "Recovered": 3.0
+    },
+    {
+        "Date": "2020-05-27",
+        "Confirmed": 25.6,
+        "Deaths": 6,
+        "Recovered": 3.0
+    },
+    {
+        "Date": "2020-05-28",
+        "Confirmed": 27.6,
+        "Deaths": 6,
+        "Recovered": 3.0
+    },
+    {
+        "Date": "2020-05-29",
+        "Confirmed": 30.6,
+        "Deaths": 6,
+        "Recovered": 3.0
+    },
+    {
+        "Date": "2020-05-30",
+        "Confirmed": 30.6,
+        "Deaths": 6,
+        "Recovered": 3.0
+    },
+    {
+        "Date": "2020-05-31",
+        "Confirmed": 35,
+        "Deaths": 6,
+        "Recovered": 3.0
+    },
+    {
+        "Date": "2020-06-01",
+        "Confirmed": 44,
+        "Deaths": 8,
+        "Recovered": 3.0
+    },
+    {
+        "Date": "2020-06-02",
+        "Confirmed": 44.5,
+        "Deaths": 8.999,
+        "Recovered": 6
+    },
+    {
+        "Date": "2020-06-03",
+        "Confirmed": 70,
+        "Deaths": 9,
+        "Recovered": 6
+    },
+    {
+        "Date": "2020-06-04",
+        "Confirmed": 100,
+        "Deaths": 20,
+        "Recovered": 6
+    },
+    {
+        "Date": "2020-06-05",
+        "Confirmed": 100.3,
+        "Deaths": 23.56,
+        "Recovered": 6
+    },
+    {
+        "Date": "2020-06-06",
+        "Confirmed": 115,
+        "Deaths": 24,
+        "Recovered": 6
+    },
+    {
+        "Date": "2020-06-07",
+        "Confirmed": 120.6,
+        "Deaths": 30,
+        "Recovered": 6
+    }
+]

cpp/tests/data/test_empty_file.json

@@ -0,0 +1 @@
+[]

cpp/tests/test_epi_data_io.cpp

@@ -94,6 +94,36 @@ TEST(TestEpiDataIo, read_rki_error_age)
     ASSERT_THAT(print_wrap(result), IsFailure(mio::StatusCode::InvalidValue));
 }
 
+TEST(TestEpiDataIo, read_confirmed_cases_noage)
+{
+    Json::Value js(Json::arrayValue);
+    js[0]["Date"]      = "2021-12-01";
+    js[0]["Confirmed"] = 1;
+    js[0]["Deaths"]    = 2;
+    js[0]["Recovered"] = 3;
+
+    js[1]["Date"]      = "2021-12-02";
+    js[1]["Confirmed"] = 4;
+    js[1]["Deaths"]    = 5;
+    js[1]["Recovered"] = 6;
+
+    auto result = mio::deserialize_confirmed_cases_noage(js);
+    ASSERT_THAT(print_wrap(result), IsSuccess());
+
+    auto rki_data_noage = result.value();
+    ASSERT_EQ(rki_data_noage.size(), 2);
+
+    ASSERT_EQ(rki_data_noage[0].date, mio::Date(2021, 12, 1));
+    ASSERT_EQ(rki_data_noage[0].num_confirmed, 1);
+    ASSERT_EQ(rki_data_noage[0].num_deaths, 2);
+    ASSERT_EQ(rki_data_noage[0].num_recovered, 3);
+
+    ASSERT_EQ(rki_data_noage[1].date, mio::Date(2021, 12, 2));
+    ASSERT_EQ(rki_data_noage[1].num_confirmed, 4);
+    ASSERT_EQ(rki_data_noage[1].num_deaths, 5);
+    ASSERT_EQ(rki_data_noage[1].num_recovered, 6);
+}
+
 TEST(TestEpiDataIo, read_divi)
 {
     Json::Value js(Json::arrayValue);
@@ -301,6 +331,34 @@ TEST(TestEpiDataIo, read_confirmed_cases_data)
     ASSERT_EQ(case_data[2].state_id, boost::none);
 }
 
+TEST(TestEpiDataIo, read_confirmed_cases_noage_data)
+{
+    auto rki_data_noage =
+        mio::read_confirmed_cases_noage(mio::path_join(TEST_DATA_DIR, "cases_all_germany.json")).value();
+
+    ASSERT_EQ(rki_data_noage.size(), 15);
+
+    ASSERT_EQ(rki_data_noage[0].date, mio::Date(2020, 05, 24));
+    ASSERT_EQ(rki_data_noage[0].num_confirmed, 1.2);
+    ASSERT_EQ(rki_data_noage[0].num_deaths, 0.5);
+    ASSERT_EQ(rki_data_noage[0].num_recovered, 0);
+
+    ASSERT_EQ(rki_data_noage[8].date, mio::Date(2020, 06, 01));
+    ASSERT_EQ(rki_data_noage[8].num_confirmed, 44);
+    ASSERT_EQ(rki_data_noage[8].num_deaths, 8);
+    ASSERT_EQ(rki_data_noage[8].num_recovered, 3);
+
+    ASSERT_EQ(rki_data_noage[9].date, mio::Date(2020, 06, 02));
+    ASSERT_EQ(rki_data_noage[9].num_confirmed, 44.5);
+    ASSERT_EQ(rki_data_noage[9].num_deaths, 8.999);
+    ASSERT_EQ(rki_data_noage[9].num_recovered, 6);
+
+    ASSERT_EQ(rki_data_noage[14].date, mio::Date(2020, 06, 07));
+    ASSERT_EQ(rki_data_noage[14].num_confirmed, 120.6);
+    ASSERT_EQ(rki_data_noage[14].num_deaths, 30);
+    ASSERT_EQ(rki_data_noage[14].num_recovered, 6);
+}
+
 TEST(TestEpiDataIO, read_vaccination_data)
 {
     auto vacc_data = mio::read_vaccination_data(mio::path_join(TEST_DATA_DIR, "test_all_ageinf_vacc.json")).value();