chore: update pharmsol to 0.29.1

Cargo.toml

@@ -28,7 +28,7 @@ tracing-subscriber = { version = "0.3.19", features = [
     "time",
 ] }
 faer = "0.24.0"
-pharmsol = { version = "=0.29.0" }
+pharmsol = "0.29.1"
 anyhow = "1.0.100"
 rayon = "1.10.0"
 rand = "0.10.1"

benches/bimodal_ke.rs

@@ -10,11 +10,8 @@ fn create_equation() -> equation::ODE {
         params: [ke, v],
         states: [central],
         outputs: [outeq_1],
-        routes: [
-            infusion(input_1) -> central,
-        ],
         diffeq: |x, _t, dx| {
-            dx[central] = -ke * x[central];
+            dx[central] = infusion[input_1] - ke * x[central];
         },
         out: |x, _t, y| {
             y[outeq_1] = x[central] / v;

examples/bestdose/main.rs

@@ -17,9 +17,7 @@ params = ke, v
 states = central
 outputs = outeq_0
 
-bolus(input_0) -> central
-
-dx(central) = -ke * central
+dx(central) = bolus(input_0) - ke * central
 out(outeq_0) = central / v
 "#;
 

examples/bimodal_ke/main.rs

@@ -9,11 +9,8 @@ fn main() -> Result<()> {
         params: [ke, v],
         states: [central],
         outputs: [outeq_1],
-        routes: [
-            infusion(input_1) -> central,
-        ],
         diffeq: |x, _t, dx| {
-            dx[central] = -ke * x[central];
+            dx[central] = infusion[input_1] - ke * x[central];
         },
         out: |x, _t, y| {
             y[outeq_1] = x[central] / v;

examples/bimodal_ke_backend_compare.rs

@@ -15,9 +15,7 @@ params = ke, v
 states = central
 outputs = outeq_1
 
-infusion(input_1) -> central
-
-dx(central) = -ke * central
+dx(central) = infusion(input_1) - ke * central
 
 out(outeq_1) = central / v
 "#;
@@ -78,11 +76,8 @@ fn macro_equation() -> equation::ODE {
         params: [ke, v],
         states: [central],
         outputs: [outeq_1],
-        routes: [
-            infusion(input_1) -> central,
-        ],
         diffeq: |x, _t, dx| {
-            dx[central] = -ke * x[central];
+            dx[central] = infusion[input_1] - ke * x[central];
         },
         out: |x, _t, y| {
             y[outeq_1] = x[central] / v;

examples/chain_algorithms.rs

@@ -12,9 +12,8 @@ fn main() -> Result<()> {
         params: [ke, v],
         states: [central],
         outputs: [outeq_1],
-        routes: [bolus(input_1) -> central],
         diffeq: |x, _t, dx| {
-            dx[central] = -ke * x[central];
+            dx[central] = bolus[input_1] - ke * x[central];
         },
         out: |x, _t, y| {
             y[outeq_1] = x[central] / v;

examples/drusano/main.rs

@@ -11,19 +11,15 @@ fn main() -> Result<()> {
         covariates: [ic_t],
         states: [drug_1_amount, drug_2_amount, total_bacteria, resistant_1, resistant_2],
         outputs: [outeq_1, outeq_2, outeq_3, outeq_4],
-        routes: [
-            bolus(input_1) -> drug_1_amount,
-            bolus(input_2) -> drug_2_amount,
-        ],
         diffeq: |x, _t, dx| {
 
             let e50_2r1 = e50_2s;
             let e50_1r2 = e50_1s;
             let h2r1 = h2s;
             let h1r2 = h1s;
 
-            dx[drug_1_amount] = -cl1 * x[drug_1_amount] / v1;
-            dx[drug_2_amount] = -cl2 * x[drug_2_amount] / v2;
+            dx[drug_1_amount] = bolus[input_1] - cl1 * x[drug_1_amount] / v1;
+            dx[drug_2_amount] = bolus[input_2] - cl2 * x[drug_2_amount] / v2;
 
             let xns = x[total_bacteria];
             let xnr1 = x[resistant_1];
@@ -32,20 +28,17 @@ fn main() -> Result<()> {
 
             let u_s = x[drug_1_amount] / (v1 * e50_1s);
             let v_s = x[drug_2_amount] / (v2 * e50_2s);
-            let w_s = alpha_s * u_s * v_s / (e50_1s * e50_2s);
-            let xm0best = get_e2(u_s, v_s, w_s, 1.0 / h1s, 1.0 / h2s, alpha_s);
+            let xm0best = estimate_effect_2(u_s, v_s, alpha_s, 1.0 / h1s, 1.0 / h2s);
             dx[total_bacteria] = xns * (kgs * e - kks * xm0best);
 
             let u_r1 = x[drug_1_amount] / (v1 * e50_1r1);
             let v_r1 = x[drug_2_amount] / (v2 * e50_2r1);
-            let w_r1 = alpha_r1 * u_r1 * v_r1 / (e50_1r1 * e50_2r1);
-            let xm0best = get_e2(u_r1, v_r1, w_r1, 1.0 / h1r1, 1.0 / h2r1, alpha_s);
+            let xm0best = estimate_effect_2(u_r1, v_r1, alpha_r1, 1.0 / h1r1, 1.0 / h2r1);
             dx[resistant_1] = xnr1 * (kgr1 * e - kkr1 * xm0best);
 
             let u_r2 = x[drug_1_amount] / (v1 * e50_1r2);
             let v_r2 = x[drug_2_amount] / (v2 * e50_2r2);
-            let w_r2 = alpha_r2 * u_r2 * v_r2 / (e50_1r2 * e50_2r2);
-            let xm0best = get_e2(u_r2, v_r2, w_r2, 1.0 / h1r2, 1.0 / h2r2, alpha_s);
+            let xm0best = estimate_effect_2(u_r2, v_r2, alpha_r2, 1.0 / h1r2, 1.0 / h2r2);
             dx[resistant_2] = xnr2 * (kgr2 * e - kkr2 * xm0best);
         },
         init: |_t, x| {

examples/meta/main.rs

@@ -11,14 +11,11 @@ fn main() -> Result<()> {
         covariates: [wt, pkvisit],
         states: [central, metabolite],
         outputs: [outeq_1, outeq_2],
-        routes: [
-            infusion(input_1) -> central,
-        ],
         diffeq: |x, _t, dx| {
             let cl = cls * ((pkvisit - 1.0) * theta1).exp() * (wt / 70.0).powf(0.75);
             let v = vs * ((pkvisit - 1.0) * theta2).exp() * (wt / 70.0);
             let ke = cl / v;
-            dx[central] = -ke * x[central] * (1.0 - fm) - fm * x[central];
+            dx[central] = infusion[input_1] - ke * x[central] * (1.0 - fm) - fm * x[central];
             dx[metabolite] = fm * x[central] - k20 * x[metabolite];
         },
         out: |x, _t, y| {

examples/neely/main.rs

@@ -7,9 +7,6 @@ fn main() -> Result<()> {
         covariates: [wt, pkvisit],
         states: [central, peripheral, metabolite_1, metabolite_2],
         outputs: [outeq_1, outeq_2, outeq_3],
-        routes: [
-            infusion(input_1) -> central,
-        ],
         diffeq: |x, _t, dx| {
             let cl = cls * ((pkvisit - 1.0) * theta1).exp() * (wt / 70.0).powf(0.75);
             let q = qs * (wt / 70.0).powf(0.75);
@@ -19,7 +16,7 @@ fn main() -> Result<()> {
             let k12 = q / v;
             let k21 = q / vp;
 
-            dx[central] = -ke * x[central] * (1.0 - fm1 - fm2)
+            dx[central] = infusion[input_1] - ke * x[central] * (1.0 - fm1 - fm2)
                 - (fm1 + fm2) * x[central]
                 - k12 * x[central]
                 + k21 * x[peripheral];

examples/two_eq_lag/main.rs

@@ -6,11 +6,8 @@ fn main() -> Result<()> {
         params: [ka, ke, tlag, v],
         states: [gut, central],
         outputs: [outeq_0],
-        routes: [
-            bolus(input_0) -> gut,
-        ],
         diffeq: |x, _t, dx| {
-            dx[gut] = -ka * x[gut];
+            dx[gut] = bolus[input_0] - ka * x[gut];
             dx[central] = ka * x[gut] - ke * x[central];
         },
         lag: |_t| {

examples/vanco.rs

@@ -5,11 +5,8 @@ fn main() -> Result<()> {
         params: [ke, kcp, kpc],
         states: [central, peripheral],
         outputs: [peripheral_amount],
-        routes: [
-            bolus(dose) -> central,
-        ],
         diffeq: |x, _t, dx| {
-            dx[central] = -ke * x[central] - kcp * x[central] + kpc * x[peripheral];
+            dx[central] = bolus[dose] - ke * x[central] - kcp * x[central] + kpc * x[peripheral];
             dx[peripheral] = -kpc * x[peripheral] + kcp * x[central];
         },
         init: |_t, x| {

src/lib.rs

@@ -88,7 +88,7 @@ pub mod prelude {
 
     // Items required by downstream code that are not part of `pharmsol::prelude`.
     pub use pharmsol::equation::{EquationTypes, Predictions};
-    pub use pharmsol::optimize::effect::get_e2;
+    pub use pharmsol::optimize::effect::{estimate_effect_2, estimate_effect_3};
     pub use pharmsol::{ODE, SDE};
 
     // Organized submodules mirroring pharmsol's grouping.

tests/bestdose_tests.rs

@@ -18,11 +18,8 @@ fn bolus_model() -> ODE {
         params: [ke, v],
         states: [central],
         outputs: [outeq_0],
-        routes: [
-            bolus(input_0) -> central,
-        ],
         diffeq: |x, _t, dx| {
-            dx[central] = -ke * x[central];
+            dx[central] = bolus[input_0] - ke * x[central];
         },
         out: |x, _t, y| {
             y[outeq_0] = x[central] / v;
@@ -37,11 +34,8 @@ fn infusion_model() -> ODE {
         params: [ke, v],
         states: [central],
         outputs: [outeq_0],
-        routes: [
-            infusion(input_0) -> central,
-        ],
         diffeq: |x, _t, dx| {
-            dx[central] = -ke * x[central];
+            dx[central] = infusion[input_0] - ke * x[central];
         },
         out: |x, _t, y| {
             y[outeq_0] = x[central] / v;