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Merged
merged 18 commits into from
Dec 17, 2024
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Use natural parameters when specifying uncertain distributions #893

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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
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Remove use of Fixed() for specifying fixed parameters
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@jamesmbaazam
jamesmbaazam committed Dec 13, 2024
commit 19be97ebb89e99ccc261261971c593e7e008673c
4 changes: 2 additions & 2 deletions R/epinow.R
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Expand Up @@ -57,8 +57,8 @@
#' # set an example reporting delay. In practice this should use an estimate
#' # from the literature or be estimated from data
#' reporting_delay <- LogNormal(
#' meanlog = Fixed(2),
#' sdlog = Fixed(1),
#' meanlog = 2,
#' sdlog = 1,
#' max = 10
#' )
#'
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4 changes: 2 additions & 2 deletions R/estimate_infections.R
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Expand Up @@ -102,8 +102,8 @@
#' # set an example reporting delay. In practice this should use an estimate
#' # from the literature or be estimated from data
#' reporting_delay <- LogNormal(
#' meanlog = Fixed(2),
#' sdlog = Fixed(1),
#' meanlog = 2,
#' sdlog = 1,
#' max = 10
#' )
#'
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4 changes: 2 additions & 2 deletions R/regional_epinow.R
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Expand Up @@ -81,8 +81,8 @@
#' delays = delay_opts(example_incubation_period + example_reporting_delay),
#' rt = rt_opts(
#' prior = LogNormal(
#' meanlog = Fixed(2),
#' sdlog = Fixed(0.2)
#' meanlog = 2,
#' sdlog = 0.2
#' ),
#' stan = stan_opts(
#' samples = 100, warmup = 200
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4 changes: 2 additions & 2 deletions R/simulate_infections.R
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Expand Up @@ -278,8 +278,8 @@ simulate_infections <- function(estimates, R, initial_infections,
#' generation_time = generation_time_opts(example_generation_time),
#' delays = delay_opts(example_incubation_period + example_reporting_delay),
#' rt = rt_opts(prior = LogNormal(
#' meanlog = Fixed(2),
#' sdlog = Fixed(0.1)
#' meanlog = 2,
#' sdlog = 0.1
#' ),
#' rw = 7
#' ),
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12 changes: 6 additions & 6 deletions vignettes/EpiNow2.Rmd.orig
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Expand Up @@ -51,8 +51,8 @@ To demonstrate, we choose a lognormal distribution with mean 2, standard deviati

```{r}
reporting_delay <- LogNormal(
meanlog = Fixed(2),
sdlog = Fixed(1),
meanlog = 2,
sdlog = 1,
max = 10
)
reporting_delay
Expand Down Expand Up @@ -99,8 +99,8 @@ estimates <- epinow(
generation_time = gt_opts(example_generation_time),
delays = delay_opts(example_incubation_period + reporting_delay),
rt = rt_opts(prior = LogNormal(
meanlog = Fixed(2),
sdlog = Fixed(0.2)
meanlog = 2,
sdlog = 0.2
)),
stan = stan_opts(cores = 4, control = list(adapt_delta = 0.99)),
verbose = interactive()
Expand Down Expand Up @@ -157,8 +157,8 @@ estimates <- regional_epinow(
delays = delay_opts(example_incubation_period + reporting_delay),
rt = rt_opts(
prior = LogNormal(
meanlog = Fixed(2),
sdlog = Fixed(0.2)
meanlog = 2,
sdlog = 0.2
),
rw = 7
),
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8 changes: 4 additions & 4 deletions vignettes/epinow.Rmd.orig
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Expand Up @@ -39,14 +39,14 @@ library("EpiNow2")
options(mc.cores = 4)
reported_cases <- example_confirmed[1:60]
reporting_delay <- LogNormal(
meanlog = Fixed(2),
sdlog = Fixed(1),
meanlog = 2,
sdlog = 1,
max = 10
)
delay <- example_incubation_period + reporting_delay
rt_prior <- LogNormal(
meanlog = Fixed(2),
sdlog = Fixed(0.1)
meanlog = 2,
sdlog = 0.1
)
```

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8 changes: 4 additions & 4 deletions vignettes/estimate_infections_options.Rmd.orig
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Expand Up @@ -74,8 +74,8 @@ Note that the mean and standard deviation must be converted to the log scale, wh

```{r reporting_delay}
reporting_delay <- LogNormal(
meanlog = Fixed(2),
sdlog = Fixed(1),
meanlog = 2,
sdlog = 1,
max = 10
)
reporting_delay
Expand All @@ -102,8 +102,8 @@ Lastly we need to choose a prior for the initial value of the reproduction numbe

```{r initial_r}
rt_prior <- LogNormal(
meanlog = Fixed(2),
sdlog = Fixed(0.1)
meanlog = 2,
sdlog = 0.1
)
```

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2 changes: 1 addition & 1 deletion vignettes/estimate_infections_workflow.Rmd.orig
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Expand Up @@ -205,7 +205,7 @@ It can be changed using the `rt_opts()` function.
For example, if the user believes that at the very start of the data the reproduction number was 2, with uncertainty in this belief represented by a standard deviation of 1, they would use

```{r results = 'hide'}
rt_prior <- LogNormal(meanlog = Fixed(2), sdlog = Fixed(1))
rt_prior <- LogNormal(meanlog = 2, sdlog = 1)
rt_opts(prior = rt_prior)
```

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