Skip to content

chore: Bump pharmsol to 0.24 #251

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Siel merged 9 commits into from
Mar 24, 2026
Merged

chore: Bump pharmsol to 0.24 #251

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
788c1e0
WIP
mhovd Mar 17, 2026
2dc947e
Replace faer_ext operations with faer
mhovd Mar 17, 2026
92e5553
Update error model
mhovd Mar 22, 2026
2cf3d31
Clippy
mhovd Mar 22, 2026
de58a5f
Silence diffsol logs
mhovd Mar 23, 2026
22a7cbf
Update BKE example
mhovd Mar 23, 2026
af85309
Update benchmark
mhovd Mar 23, 2026
0ce2239
Update to pharmsol 0.24
mhovd Mar 24, 2026
3d717ac
All ODE examples are updated to use the new ode! macro
Siel Mar 24, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 2 additions & 3 deletions Cargo.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ exclude = [".github/*", ".vscode/*"]

[dependencies]
csv = "1.3.1"
ndarray = { version = "0.16.1", features = ["rayon"] }
ndarray = { version = "0.17.2", features = ["rayon"] }
serde = "1.0.188"
serde_json = "1.0.66"
sobol_burley = "0.5.0"
Expand All @@ -28,8 +28,7 @@ tracing-subscriber = { version = "0.3.19", features = [
"time",
] }
faer = "0.23.1"
faer-ext = { version = "0.7.1", features = ["nalgebra", "ndarray"] }
pharmsol = "=0.22.1"
pharmsol = "=0.24.1"
rand = "0.9.0"
anyhow = "1.0.100"
rayon = "1.10.0"
Expand Down
13 changes: 6 additions & 7 deletions benches/bimodal_ke.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,16 +8,15 @@ fn create_equation() -> equation::ODE {
equation::ODE::new(
|x, p, _t, dx, b, rateiv, _cov| {
fetch_params!(p, ke, _v);
dx[0] = -ke * x[0] + rateiv[0] + b[0];
dx[0] = -ke * x[0] + rateiv[1] + b[1];
},
|_p, _t, _cov| lag! {},
|_p, _t, _cov| fa! {},
|_p, _t, _cov, _x| {},
|x, p, _t, _cov, y| {
fetch_params!(p, _ke, v);
y[0] = x[0] / v;
y[1] = x[0] / v;
},
(1, 1),
)
}

Expand All @@ -27,10 +26,10 @@ fn create_parameters() -> Parameters {
.add("v", 25.0, 250.0)
}

fn create_error_models() -> Result<ErrorModels> {
Ok(ErrorModels::new().add(
0,
ErrorModel::additive(ErrorPoly::new(0.0, 0.5, 0.0, 0.0), 0.0),
fn create_error_models() -> Result<AssayErrorModels> {
Ok(AssayErrorModels::new().add(
1,
AssayErrorModel::additive(ErrorPoly::new(0.0, 0.5, 0.0, 0.0), 0.0),
)?)
}

Expand Down
16 changes: 6 additions & 10 deletions examples/bestdose.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,29 +7,25 @@ use pmcore::routines::initialization::parse_prior;

fn main() -> Result<()> {
// Example model
let eq = equation::ODE::new(
|x, p, _t, dx, b, _rateiv, _cov| {
let eq = ode! {
diffeq: |x, p, _t, dx, b, _rateiv, _cov| {
// fetch_cov!(cov, t, wt);
fetch_params!(p, ke, _v);
dx[0] = -ke * x[0] + b[0];
},
|_p, _, _| lag! {},
|_p, _, _| fa! {},
|_p, _t, _cov, _x| {},
|x, p, _t, _cov, y| {
out: |x, p, _t, _cov, y| {
fetch_params!(p, _ke, v);
y[0] = x[0] / v;
},
(1, 1),
);
};

let params = Parameters::new()
.add("ke", 0.001, 3.0)
.add("v", 25.0, 250.0);

let ems = ErrorModels::new().add(
let ems = AssayErrorModels::new().add(
0,
ErrorModel::additive(ErrorPoly::new(0.0, 0.20, 0.0, 0.0), 0.0),
AssayErrorModel::additive(ErrorPoly::new(0.0, 0.20, 0.0, 0.0), 0.0),
)?;

// Make settings
Expand Down
16 changes: 6 additions & 10 deletions examples/bestdose_auc.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,29 +10,25 @@ fn main() -> Result<()> {
println!("======================================\n");

// Simple one-compartment PK model
let eq = equation::ODE::new(
|x, p, _t, dx, b, _rateiv, _cov| {
let eq = ode! {
diffeq: |x, p, _t, dx, b, _rateiv, _cov| {
fetch_params!(p, ke, _v);
dx[0] = -ke * x[0] + b[0];
},
|_p, _, _| lag! {},
|_p, _, _| fa! {},
|_p, _t, _cov, _x| {},
|x, p, _t, _cov, y| {
out: |x, p, _t, _cov, y| {
fetch_params!(p, _ke, v);
y[0] = x[0] / v;
},
(1, 1),
);
};

// Minimal parameter ranges
let params = Parameters::new()
.add("ke", 0.001, 3.0)
.add("v", 25.0, 250.0);

let ems = ErrorModels::new().add(
let ems = AssayErrorModels::new().add(
0,
ErrorModel::additive(ErrorPoly::new(0.0, 0.20, 0.0, 0.0), 0.0),
AssayErrorModel::additive(ErrorPoly::new(0.0, 0.20, 0.0, 0.0), 0.0),
)?;

let mut settings = Settings::builder()
Expand Down
16 changes: 6 additions & 10 deletions examples/bestdose_bounds.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,28 +10,24 @@ fn main() -> Result<()> {
println!("==========================================\n");

// Simple one-compartment PK model
let eq = equation::ODE::new(
|x, p, _t, dx, b, _rateiv, _cov| {
let eq = ode! {
diffeq: |x, p, _t, dx, b, _rateiv, _cov| {
fetch_params!(p, ke, _v);
dx[0] = -ke * x[0] + b[0];
},
|_p, _, _| lag! {},
|_p, _, _| fa! {},
|_p, _t, _cov, _x| {},
|x, p, _t, _cov, y| {
out: |x, p, _t, _cov, y| {
fetch_params!(p, _ke, v);
y[0] = x[0] / v;
},
(1, 1),
);
};

let params = Parameters::new()
.add("ke", 0.001, 3.0)
.add("v", 25.0, 250.0);

let ems = ErrorModels::new().add(
let ems = AssayErrorModels::new().add(
0,
ErrorModel::additive(ErrorPoly::new(0.0, 0.20, 0.0, 0.0), 0.0),
AssayErrorModel::additive(ErrorPoly::new(0.0, 0.20, 0.0, 0.0), 0.0),
)?;

let mut settings = Settings::builder()
Expand Down
25 changes: 10 additions & 15 deletions examples/bimodal_ke/main.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,33 +2,28 @@ use anyhow::Result;
use pmcore::prelude::*;

fn main() -> Result<()> {
let eq = equation::ODE::new(
|x, p, _t, dx, b, rateiv, _cov| {
let eq = ode! {
diffeq: |x, p, _t, dx, b, rateiv, _cov| {
// fetch_cov!(cov, t, wt);
fetch_params!(p, ke, _v);
dx[0] = -ke * x[0] + rateiv[0] + b[0];
dx[0] = -ke * x[0] + rateiv[1] + b[1];
},
|_p, _t, _cov| lag! {},
|_p, _t, _cov| fa! {},
|_p, _t, _cov, _x| {},
|x, p, _t, _cov, y| {
out: |x, p, _t, _cov, y| {
fetch_params!(p, _ke, v);
y[0] = x[0] / v;
y[1] = x[0] / v;
},
(1, 1),
);
}
.with_solver(OdeSolver::ExplicitRk(ExplicitRkTableau::Tsit45));

let params = Parameters::new()
.add("ke", 0.001, 3.0)
.add("v", 25.0, 250.0);

let ems = ErrorModels::new()
let ems = AssayErrorModels::new()
.add(
0,
ErrorModel::additive(ErrorPoly::new(0.0, 0.5, 0.0, 0.0), 0.0),
1,
AssayErrorModel::additive(ErrorPoly::new(0.0, 0.5, 0.0, 0.0), 0.0),
)
.unwrap()
.add(1, ErrorModel::None)
.unwrap();

let mut settings = Settings::builder()
Expand Down
25 changes: 11 additions & 14 deletions examples/drusano/main.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@ use anyhow::Result;
use pmcore::prelude::*;
#[allow(unused_variables)]
fn main() -> Result<()> {
let eq = equation::ODE::new(
|x, p, t, dx, b, rateiv, _cov| {
let eq = ode! {
diffeq:|x, p, t, dx, b, rateiv, _cov| {
fetch_params!(
p, v1, cl1, v2, cl2, popmax, kgs, kks, e50_1s, e50_2s, alpha_s, kgr1, kkr1,
e50_1r1, alpha_r1, kgr2, kkr2, e50_2r2, alpha_r2, init_4, init_5, h1s, h2s, h1r1,
Expand Down Expand Up @@ -44,9 +44,7 @@ fn main() -> Result<()> {
let xm0best = get_e2(u_r2, v_r2, w_r2, 1.0 / h1r2, 1.0 / h2r2, alpha_s);
dx[4] = xnr2 * (kgr2 * e - kkr2 * xm0best);
},
|_p, _t, _cov| lag! {},
|_p, _t, _cov| fa! {},
|p, t, cov, x| {
init: |p, t, cov, x| {
fetch_params!(
p, v1, cl1, v2, cl2, popmax, kgs, kks, e50_1s, e50_2s, alpha_s, kgr1, kkr1,
e50_1r1, alpha_r1, kgr2, kkr2, e50_2r2, alpha_r2, init_4, init_5, h1s, h2s, h1r1,
Expand All @@ -59,7 +57,7 @@ fn main() -> Result<()> {
x[3] = 10.0_f64.powf(init_4);
x[4] = 10.0_f64.powf(init_5);
},
|x, p, _t, _cov, y| {
out: |x, p, _t, _cov, y| {
fetch_params!(
p, v1, cl1, v2, cl2, popmax, kgs, kks, e50_1s, e50_2s, alpha_s, kgr1, kkr1,
e50_1r1, alpha_r1, kgr2, kkr2, e50_2r2, alpha_r2, init_4, init_5, h1s, h2s, h1r1,
Expand All @@ -71,8 +69,7 @@ fn main() -> Result<()> {
y[3] = x[3].log10();
y[4] = x[4].log10();
},
(5, 5),
);
};

let params = Parameters::new()
.add("v1", 5.0, 160.0)
Expand Down Expand Up @@ -100,26 +97,26 @@ fn main() -> Result<()> {
.add("h1r1", 5.0, 25.0)
.add("h2r2", 10.0, 22.0);

let ems = ErrorModels::new()
let ems = AssayErrorModels::new()
.add(
0,
ErrorModel::proportional(ErrorPoly::new(0.1, 0.1, 0.0, 0.0), 1.0),
AssayErrorModel::proportional(ErrorPoly::new(0.1, 0.1, 0.0, 0.0), 1.0),
)?
.add(
1,
ErrorModel::proportional(ErrorPoly::new(0.1, 0.1, 0.0, 0.0), 1.0),
AssayErrorModel::proportional(ErrorPoly::new(0.1, 0.1, 0.0, 0.0), 1.0),
)?
.add(
2,
ErrorModel::proportional(ErrorPoly::new(0.1, 0.1, 0.0, 0.0), 1.0),
AssayErrorModel::proportional(ErrorPoly::new(0.1, 0.1, 0.0, 0.0), 1.0),
)?
.add(
3,
ErrorModel::proportional(ErrorPoly::new(0.1, 0.1, 0.0, 0.0), 1.0),
AssayErrorModel::proportional(ErrorPoly::new(0.1, 0.1, 0.0, 0.0), 1.0),
)?
.add(
4,
ErrorModel::proportional(ErrorPoly::new(0.1, 0.1, 0.0, 0.0), 1.0),
AssayErrorModel::proportional(ErrorPoly::new(0.1, 0.1, 0.0, 0.0), 1.0),
)?;

let mut settings = SettingsBuilder::new()
Expand Down
10 changes: 6 additions & 4 deletions examples/iov/main.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,15 +25,17 @@ fn main() -> Result<()> {
fetch_params!(p, _ke0);
y[0] = x[0] / 50.0;
},
(2, 1),
10000,
);
)
.with_nstates(2)
.with_ndrugs(1)
.with_nout(1);

let params = Parameters::new().add("ke0", 0.001, 2.0);

let ems = ErrorModels::new().add(
let ems = AssayErrorModels::new().add(
0,
ErrorModel::additive(ErrorPoly::new(0.0, 0.0, 0.0, 0.0), 0.0000757575757576),
AssayErrorModel::additive(ErrorPoly::new(0.0, 0.0, 0.0, 0.0), 0.0000757575757576),
)?;

let mut settings = Settings::builder()
Expand Down
18 changes: 7 additions & 11 deletions examples/meta/main.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@
use pmcore::{prelude::*, routines::settings};

fn main() {
let eq = equation::ODE::new(
|x, p, t, dx, b, rateiv, cov| {
let eq = ode! {
diffeq: |x, p, t, dx, b, rateiv, cov| {
fetch_cov!(cov, t, wt, pkvisit);
fetch_params!(p, cls, fm, k20, relv, theta1, theta2, vs);
let cl = cls * ((pkvisit - 1.0) * theta1).exp() * (wt / 70.0).powf(0.75);
Expand All @@ -16,10 +16,7 @@ fn main() {
dx[0] = rateiv[0] - ke * x[0] * (1.0 - fm) - fm * x[0] + b[0];
dx[1] = fm * x[0] - k20 * x[1];
},
|_p, _t, _cov| lag! {},
|_p, _t, _cov| fa! {},
|_p, _t, _cov, _x| {},
|x, p, t, cov, y| {
out: |x, p, t, cov, y| {
fetch_cov!(cov, t, wt, pkvisit);
fetch_params!(p, cls, fm, k20, relv, theta1, theta2, vs);
let cl = cls * ((pkvisit - 1.0) * theta1).exp() * (wt / 70.0).powf(0.75);
Expand All @@ -29,8 +26,7 @@ fn main() {
y[0] = x[0] / v;
y[1] = x[1] / v2;
},
(2, 2),
);
};

let params = Parameters::new()
.add("cls", 0.1, 10.0)
Expand All @@ -41,15 +37,15 @@ fn main() {
.add("theta2", 0.1, 10.0)
.add("vs", 1.0, 10.0);

let ems = ErrorModels::new()
let ems = AssayErrorModels::new()
.add(
0,
ErrorModel::proportional(ErrorPoly::new(1.0, 0.1, 0.0, 0.0), 5.0),
AssayErrorModel::proportional(ErrorPoly::new(1.0, 0.1, 0.0, 0.0), 5.0),
)
.unwrap()
.add(
1,
ErrorModel::proportional(ErrorPoly::new(1.0, 0.1, 0.0, 0.0), 5.0),
AssayErrorModel::proportional(ErrorPoly::new(1.0, 0.1, 0.0, 0.0), 5.0),
)
.unwrap();

Expand Down
Loading
Loading