Skip to content

Use natural parameters when specifying uncertain distributions #893

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
merged 18 commits into from
Dec 17, 2024
Merged

Use natural parameters when specifying uncertain distributions #893

Changes from 1 commit
Commits
Show all changes
18 commits
Select commit Hold shift + click to select a range
457d4ac
Use natural parameters in all examples
jamesmbaazam Dec 12, 2024
9b9dbf1
Add NEWS item
jamesmbaazam Dec 12, 2024
ed39b8d
Remove statement about warning
jamesmbaazam Dec 12, 2024
19be97e
Remove use of Fixed() for specifying fixed parameters
jamesmbaazam Dec 12, 2024
36cff84
Redocument
jamesmbaazam Dec 12, 2024
172743a
Fix missing comma
jamesmbaazam Dec 12, 2024
e049f74
Change uncertain parameters to numeric
jamesmbaazam Dec 13, 2024
bd75998
Revert to using mean and sd
jamesmbaazam Dec 13, 2024
4960f7f
Use numeric instead of uncertain parameters
jamesmbaazam Dec 13, 2024
a34e03d
Revert indentation
jamesmbaazam Dec 13, 2024
d5c7612
Use natural parameters to specify uncertain distributions
jamesmbaazam Dec 13, 2024
78f0800
Redoc after revert to mean and sd for numeric parameters
jamesmbaazam Dec 13, 2024
3a534bc
Update NEWS
jamesmbaazam Dec 13, 2024
6b0140f
Fix example in collapse.dist_spec
jamesmbaazam Dec 13, 2024
07e94bc
Align code with text
jamesmbaazam Dec 13, 2024
d9265c3
Use natural params of Gamma in vignette example
jamesmbaazam Dec 13, 2024
2f2b3bb
Update LogNormal example
jamesmbaazam Dec 17, 2024
89e89a7
Generate docs
jamesmbaazam Dec 17, 2024
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
Prev Previous commit
Next Next commit
Remove statement about warning
  • Loading branch information
@jamesmbaazam
jamesmbaazam committed Dec 13, 2024
commit ed39b8de40ea2396fbd87470eec121616bd2083f
4 changes: 0 additions & 4 deletions vignettes/estimate_infections_workflow.Rmd.orig
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -102,10 +102,6 @@ which looks like this when plotted
```{r plot_uncertain_gamma}
plot(uncertain_gamma)
```

Note the warning about parameters.
We used the mean and standard deviation to define this distribution with uncertain parameters, but it would be better to use the "natural" parameters of the gamma distribution, shape and rate, for example using the values estimate and reported back after calling the previous command.

There are various ways the specific delay distributions mentioned below might be obtained.
Often, they will come directly from the existing literature reviewed by the user and studies conducted elsewhere.
Sometimes it might be possible to obtain them from existing databases, e.g. using the [epiparameter](https://github.com/epiverse-trace/epiparameter) R package.
Expand Down