Skip to content

Goodness of fit fix #473

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

Open
plakrisenko wants to merge 2 commits into
base: main
Choose a base branch
from
+3 −2
Open

Goodness of fit fix #473

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
39a487f
fix mean of residuals in plot_goodness_of_fit
plakrisenko Feb 4, 2026
7757a1d
add line break
plakrisenko Feb 4, 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: 3 additions & 2 deletions petab/v1/visualize/plot_residuals.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -199,15 +199,16 @@ def plot_goodness_of_fit(
ax.plot(x, x, linestyle="--", color="gray")
ax.plot(x, intercept + slope * x, "r", label="fitted line")

mse = np.mean(np.abs(residual_df["residual"]))
# assumes that residuals are normalized by default
Copy link
Member

@dweindl dweindl Feb 4, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Don't assume, pass normalize=True to calculate_residuals. And maybe move calculate_residuals and msnr computation closer together, so this becomes clearer.

msnr = np.mean(np.power(residual_df["residual"], 2))
ax.text(
0.1,
0.70,
f"$R^2$: {r_value**2:.2f}\n"
f"slope: {slope:.2f}\n"
f"intercept: {intercept:.2f}\n"
f"p-value: {p_value:.2e}\n"
f"mean squared error: {mse:.2e}\n",
f"mean of squared\nnormalized residuals: {msnr:.2e}\n",
transform=ax.transAxes,
)

Expand Down