Add Walter's IOV examples

* walter's IOV examples

* re-enable the iov example. Remove non-needed bench

* re-write examples using the new settings

* using new version of pharmsol. New debugging tools when having zero likelihoods for a subject

* working on vanco

* Clean dataset

* Fix data

* using new version of pharmsol

* Update main.rs

* remove files not needed on the main repo

* rename examples and some data files

---------

Co-authored-by: Markus <markushh@uio.no>

Cargo.toml

@@ -33,7 +33,7 @@ tracing-subscriber = { version = "0.3.17", features = [
 config = { version = "0.15", features = ["preserve_order"] }
 faer = "0.19.3"
 faer-ext = { version = "0.2.0", features = ["nalgebra", "ndarray"] }
-pharmsol = "0.7.2"
+pharmsol = "0.7.6"
 rand = "0.9.0"
 anyhow = "1.0.86"
 
@@ -45,9 +45,6 @@ opt-level = 3
 [dev-dependencies]
 criterion = { version = "0.5" }
 
-[[bench]]
-name = "fibonacci"
-harness = false
 
 [[bench]]
 name = "bimodal_ke"

examples/iov/main.rs

@@ -0,0 +1,65 @@
+use anyhow::Ok;
+use pmcore::prelude::{
+    settings::{Parameters, Prior, Settings},
+    *,
+};
+fn main() -> Result<()> {
+    let sde = equation::SDE::new(
+        |x, p, _t, dx, _rateiv, _cov| {
+            // automatically defined
+            fetch_params!(p, ke0);
+            // let ke0 = 1.2;
+            dx[1] = -x[1] + ke0;
+            let ke = x[1];
+            // user defined
+            dx[0] = -ke * x[0];
+        },
+        |p, d| {
+            fetch_params!(p, _ke0);
+            d[1] = 0.1;
+        },
+        |_p| lag! {},
+        |_p| fa! {},
+        |p, _t, _cov, x| {
+            fetch_params!(p, ke0);
+            x[1] = ke0;
+        },
+        |x, p, _t, _cov, y| {
+            fetch_params!(p, _ke0);
+            y[0] = x[0] / 50.0;
+        },
+        (2, 1),
+        10000,
+    );
+
+    let mut settings = Settings::new();
+
+    let params = Parameters::builder()
+        .add("ke0", 0.001, 2.0, false)
+        .build()
+        .unwrap();
+    settings.set_parameters(params);
+    settings.set_cycles(100000);
+    settings.set_error_poly((0.0, 0.0, 0.0, 0.0));
+    settings.set_error_type(ErrorType::Add);
+    settings.set_error_value(0.0000757575757576);
+    settings.set_output_path("examples/iov/output");
+    settings.set_prior(Prior {
+        sampler: "sobol".to_string(),
+        points: 100,
+        seed: 347,
+        file: None,
+    });
+    settings.set_output_write(true);
+
+    setup_log(&settings)?;
+
+    let data = data::read_pmetrics("examples/iov/test.csv").unwrap();
+    let mut algorithm = dispatch_algorithm(settings, sde, data).unwrap();
+    algorithm.initialize().unwrap();
+    while !algorithm.next_cycle().unwrap() {}
+    let result = algorithm.into_npresult();
+    result.write_outputs().unwrap();
+
+    Ok(())
+}