Add test for intcox

This commit is contained in:
RunasSudo 2023-04-17 22:12:07 +10:00
parent 46e3b189ce
commit 6ac2d9f055
Signed by: RunasSudo
GPG Key ID: 7234E476BF21C61A
6 changed files with 1223 additions and 7 deletions

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@ -12,6 +12,9 @@ rayon = "1.7.0"
serde = { version = "1.0.160", features = ["derive"] }
serde_json = "1.0.96"
[profile.test]
opt-level = 3
[profile.perf]
inherits = "release"
debug = true

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@ -162,7 +162,7 @@ impl IntervalCensoredCoxData {
}
}
fn fit_interval_censored_cox(data_times: DMatrix<f64>, mut data_indep: DMatrix<f64>, max_iterations: u32, tolerance: f64, reduced: bool, progress_bar: ProgressBar) -> IntervalCensoredCoxResult {
pub fn fit_interval_censored_cox(data_times: DMatrix<f64>, mut data_indep: DMatrix<f64>, max_iterations: u32, tolerance: f64, reduced: bool, progress_bar: ProgressBar) -> IntervalCensoredCoxResult {
// ----------------------
// Prepare for regression
@ -572,11 +572,11 @@ fn profile_log_likelihood_obs(data: &IntervalCensoredCoxData, beta: DVector<f64>
}
#[derive(Serialize, Deserialize)]
struct IntervalCensoredCoxResult {
params: Vec<f64>,
params_se: Vec<f64>,
ll_model: f64,
ll_null: f64,
pub struct IntervalCensoredCoxResult {
pub params: Vec<f64>,
pub params_se: Vec<f64>,
pub ll_model: f64,
pub ll_null: f64,
// TODO: cumulative hazard, etc.
}

1
src/lib.rs Normal file
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@ -0,0 +1 @@
pub mod intcox;

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@ -16,7 +16,7 @@
use clap::{Parser, Subcommand};
mod intcox;
use hpstat::intcox;
#[derive(Parser)]
#[command(about="High-performance statistics implementations")]

87
tests/intcox.rs Normal file
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@ -0,0 +1,87 @@
// hpstat: High-performance statistics implementations
// Copyright © 2023 Lee Yingtong Li (RunasSudo)
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU Affero General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Affero General Public License for more details.
//
// You should have received a copy of the GNU Affero General Public License
// along with this program. If not, see <https://www.gnu.org/licenses/>.
use std::fs;
use indicatif::ProgressBar;
use nalgebra::DMatrix;
use hpstat::intcox::fit_interval_censored_cox;
#[test]
fn test_intcox_zeng_mao_lin() {
// Compare "Bangkok Metropolitan Administration HIV" data from Zeng, Mao & Lin (2016) with IntCens 0.2 output
let contents = fs::read_to_string("tests/zeng_mao_lin.csv").unwrap();
let lines: Vec<String> = contents.trim_end().split("\n").map(|s| s.to_string()).collect();
// Read data into matrices
let mut data_times: DMatrix<f64> = DMatrix::zeros(
2, // Left time, right time
lines.len() - 1 // Minus 1 row for header row
);
// Called "Z" in the paper and "X" in the C++ code
let mut data_indep: DMatrix<f64> = DMatrix::zeros(
lines[0].split(",").count() - 2,
lines.len() - 1 // Minus 1 row for header row
);
// Read data
// FIXME: Parse CSV more robustly
for (i, row) in lines.iter().skip(1).enumerate() {
for (j, item) in row.split(",").enumerate() {
let value = match item {
"inf" => f64::INFINITY,
_ => item.parse().expect("Malformed float")
};
if j < 2 {
data_times[(j, i)] = value;
} else {
data_indep[(j - 2, i)] = value;
}
}
}
// Fit regression
let progress_bar = ProgressBar::hidden();
//let result = fit_interval_censored_cox(data_times, data_indep, 200, 0.00005, false, progress_bar);
let result = fit_interval_censored_cox(data_times, data_indep, 100, 0.0001, false, progress_bar);
// ./unireg --in zeng_mao_lin.csv --out out.txt --r 0.0 --model "(Left_Time, Right_Time) = Needle + Needle2 + LogAge + GenderM + RaceO + RaceW + GenderM_RaceO + GenderM_RaceW" --sep , --inf_char inf --convergence_threshold 0.002
assert!((result.ll_model - -603.205).abs() < 1.0);
assert!((result.params[0] - -0.18636961816695094).abs() < 0.01);
assert!((result.params[1] - 0.080478699024478656).abs() < 0.01);
assert!((result.params[2] - -0.71260450817296639).abs() < 0.01);
assert!((result.params[3] - -0.22937443803422858).abs() < 0.01);
assert!((result.params[4] - -0.14101449484871434).abs() < 0.01);
assert!((result.params[5] - -0.43894526362102332).abs() < 0.01);
assert!((result.params[6] - 0.064533885082884768).abs() < 0.01);
assert!((result.params[7] - 0.20970425315378016).abs() < 0.01);
assert!((result.params_se[0] - 0.41496954829036448).abs() < 0.01);
assert!((result.params_se[1] - 0.15086156546712554).abs() < 0.01);
assert!((result.params_se[2] - 0.36522062865858951).abs() < 0.01);
assert!((result.params_se[3] - 0.32195496906604004).abs() < 0.01);
assert!((result.params_se[4] - 0.3912241733944129).abs() < 0.01);
assert!((result.params_se[5] - 0.41907763222198746).abs() < 0.01);
assert!((result.params_se[6] - 0.45849947730170948).abs() < 0.01);
assert!((result.params_se[7] - 0.48803508171247434).abs() < 0.01);
}

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tests/zeng_mao_lin.csv Normal file

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