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Fix deprecation errors by replacing reported_cases with data (#700)
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* Fix deprecation error by calling data instead of reported_cases

* Precompile vignette
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@jamesmbaazam
jamesmbaazam authored Jun 27, 2024
1 parent 0b776fd commit 0df415c
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2 changes: 1 addition & 1 deletion data-raw/estimate-infections.R
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ cases <- data.table::rbindlist(list(
))

example_regional_epinow <- regional_epinow(
reported_cases = cases,
data = cases,
generation_time = generation_time_opts(example_generation_time),
delays = delay_opts(example_incubation_period + reporting_delay),
rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
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2 changes: 1 addition & 1 deletion inst/dev/benchmark-functions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ create_profiles <- function(dir = file.path("inst", "stan"),
profiles <- suppressMessages(purrr::map(seeds, \(x) {
set.seed(x)
fit <- estimate_infections(
reported_cases = reported_cases,
data = reported_cases,
generation_time = generation_time_opts(fixed_generation_time),
delays = delay_opts(delays),
rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
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10 changes: 5 additions & 5 deletions touchstone/script.R
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ touchstone::branch_install()
touchstone::benchmark_run(
expr_before_benchmark = { source("touchstone/setup.R") },
default = { epinow(
reported_cases = reported_cases,
data = reported_cases,
generation_time = generation_time_opts(fixed_generation_time),
delays = delay_opts(fixed_delays),
rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
Expand All @@ -24,7 +24,7 @@ touchstone::benchmark_run(
touchstone::benchmark_run(
expr_before_benchmark = { source("touchstone/setup.R") },
uncertain = { epinow(
reported_cases = reported_cases,
data = reported_cases,
generation_time = generation_time_opts(example_generation_time),
delays = delays,
rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
Expand All @@ -40,7 +40,7 @@ touchstone::benchmark_run(
touchstone::benchmark_run(
expr_before_benchmark = { source("touchstone/setup.R") },
no_delays = { epinow(
reported_cases = reported_cases,
data = reported_cases,
generation_time = generation_time_opts(fixed_generation_time),
rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
stan = stan_opts(
Expand All @@ -55,7 +55,7 @@ touchstone::benchmark_run(
touchstone::benchmark_run(
expr_before_benchmark = { source("touchstone/setup.R") },
stationary = { epinow(
reported_cases = reported_cases,
data = reported_cases,
generation_time = generation_time_opts(fixed_generation_time),
delays = delay_opts(fixed_delays),
rt = rt_opts(prior = list(mean = 2, sd = 0.2), gp_on = "R0"),
Expand All @@ -71,7 +71,7 @@ touchstone::benchmark_run(
touchstone::benchmark_run(
expr_before_benchmark = { source("touchstone/setup.R") },
random_walk = { epinow(
reported_cases = reported_cases,
data = reported_cases,
generation_time = generation_time_opts(fixed_generation_time),
delays = delay_opts(fixed_delays),
rt = rt_opts(prior = list(mean = 2, sd = 0.2), rw = 7),
Expand Down
159 changes: 88 additions & 71 deletions vignettes/epinow.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -26,13 +26,8 @@ Here we use the example delay and generation time distributions that come with t
This should be replaced with parameters relevant to the system that is being studied.


```r
``` r
library("EpiNow2")
#>
#> Attaching package: 'EpiNow2'
#> The following object is masked from 'package:stats':
#>
#> Gamma
options(mc.cores = 4)
reported_cases <- example_confirmed[1:60]
reporting_delay <- LogNormal(mean = 2, sd = 1, max = 10)
Expand All @@ -43,21 +38,25 @@ rt_prior <- list(mean = 2, sd = 0.1)
We can then run the `epinow()` function with the same arguments as `estimate_infections()`.


```r
``` r
res <- epinow(reported_cases,
generation_time = generation_time_opts(example_generation_time),
delays = delay_opts(delay),
rt = rt_opts(prior = rt_prior)
)
#> Logging threshold set at INFO for the EpiNow2 logger
#> Writing EpiNow2 logs to the console and: /tmp/RtmpJDlhZu/regional-epinow/2020-04-21.log
#> Writing EpiNow2 logs to the console and: /var/folders/vr/dn4r1_zj417drd1zr9301trw0000gp/T//Rtmpv7UfXL/regional-epinow/2020-04-21.log
#> Logging threshold set at INFO for the EpiNow2.epinow logger
#> Writing EpiNow2.epinow logs to the console and: /tmp/RtmpJDlhZu/epinow/2020-04-21.log
#> WARN [2024-05-10 07:52:36] epinow: There were 11 divergent transitions after warmup. See
#> Writing EpiNow2.epinow logs to the console and: /var/folders/vr/dn4r1_zj417drd1zr9301trw0000gp/T//Rtmpv7UfXL/epinow/2020-04-21.log
#> DEBUG [2024-06-19 18:04:28] epinow: Running in exact mode for 2000 samples (across 4 chains each with a warm up of 250 iterations each) and 81 time steps of which 7 are a forecast
#> WARN [2024-06-19 18:05:49] epinow: There were 1 divergent transitions after warmup. See
#> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them. -
#> WARN [2024-05-10 07:52:36] epinow: Examine the pairs() plot to diagnose sampling problems
#> WARN [2024-06-19 18:05:49] epinow: Examine the pairs() plot to diagnose sampling problems
#> -
```

``` r
res$plots$R
```

Expand All @@ -74,7 +73,7 @@ This is done with the `regional_epinow()` function.
Say, for example, we construct a dataset containing two regions, `testland` and `realland` (in this simple example both containing the same case data).


```r
``` r
cases <- example_confirmed[1:60]
cases <- data.table::rbindlist(list(
data.table::copy(cases)[, region := "testland"],
Expand All @@ -85,49 +84,58 @@ cases <- data.table::rbindlist(list(
To then run this on multiple regions using the default options above, we could use


```r
``` r
region_rt <- regional_epinow(
reported_cases = cases,
data = cases,
generation_time = generation_time_opts(example_generation_time),
delays = delay_opts(delay),
rt = rt_opts(prior = rt_prior),
)
#> Warning: The `reported_cases` argument of `regional_epinow()` is deprecated as of EpiNow2 1.5.0.
#> ℹ Please use the `data` argument instead.
#> ℹ The argument will be removed completely in the next version.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
#> INFO [2024-05-10 07:52:38] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-06-19 18:05:51] Producing following optional outputs: regions, summary, samples, plots, latest
#> Logging threshold set at INFO for the EpiNow2 logger
#> Writing EpiNow2 logs to the console and: /tmp/RtmpJDlhZu/regional-epinow/2020-04-21.log
#> Writing EpiNow2 logs to the console and: /var/folders/vr/dn4r1_zj417drd1zr9301trw0000gp/T//Rtmpv7UfXL/regional-epinow/2020-04-21.log
#> Logging threshold set at INFO for the EpiNow2.epinow logger
#> Writing EpiNow2.epinow logs to: /tmp/RtmpJDlhZu/epinow/2020-04-21.log
#> INFO [2024-05-10 07:52:38] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-05-10 07:52:38] No target directory specified so returning output
#> INFO [2024-05-10 07:52:38] Producing estimates for: testland, realland
#> INFO [2024-05-10 07:52:38] Regions excluded: none
#> INFO [2024-05-10 07:53:40] Completed estimates for: testland
#> INFO [2024-05-10 07:54:29] Completed estimates for: realland
#> INFO [2024-05-10 07:54:29] Completed regional estimates
#> INFO [2024-05-10 07:54:29] Regions with estimates: 2
#> INFO [2024-05-10 07:54:29] Regions with runtime errors: 0
#> INFO [2024-05-10 07:54:29] Producing summary
#> INFO [2024-05-10 07:54:29] No summary directory specified so returning summary output
#> INFO [2024-05-10 07:54:29] No target directory specified so returning timings
#> Writing EpiNow2.epinow logs to: /var/folders/vr/dn4r1_zj417drd1zr9301trw0000gp/T//Rtmpv7UfXL/epinow/2020-04-21.log
#> INFO [2024-06-19 18:05:51] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-06-19 18:05:51] No target directory specified so returning output
#> INFO [2024-06-19 18:05:51] Producing estimates for: testland, realland
#> INFO [2024-06-19 18:05:51] Regions excluded: none
#> DEBUG [2024-06-19 18:05:51] testland: Running in exact mode for 2000 samples (across 4 chains each with a warm up of 250 iterations each) and 81 time steps of which 7 are a forecast
#> WARN [2024-06-19 18:06:27] testland (chain: 1): There were 13 divergent transitions after warmup. See
#> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them. -
#> WARN [2024-06-19 18:06:27] testland (chain: 1): Examine the pairs() plot to diagnose sampling problems
#> -
#> INFO [2024-06-19 18:06:29] Completed estimates for: testland
#> DEBUG [2024-06-19 18:06:29] realland: Running in exact mode for 2000 samples (across 4 chains each with a warm up of 250 iterations each) and 81 time steps of which 7 are a forecast
#> WARN [2024-06-19 18:07:12] realland (chain: 1): There were 12 divergent transitions after warmup. See
#> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them. -
#> WARN [2024-06-19 18:07:12] realland (chain: 1): Examine the pairs() plot to diagnose sampling problems
#> -
#> INFO [2024-06-19 18:07:14] Completed estimates for: realland
#> INFO [2024-06-19 18:07:14] Completed regional estimates
#> INFO [2024-06-19 18:07:14] Regions with estimates: 2
#> INFO [2024-06-19 18:07:14] Regions with runtime errors: 0
#> INFO [2024-06-19 18:07:14] Producing summary
#> INFO [2024-06-19 18:07:14] No summary directory specified so returning summary output
#> INFO [2024-06-19 18:07:15] No target directory specified so returning timings
```

``` r
## summary
region_rt$summary$summarised_results$table
#> Region New infections per day Expected change in daily reports
#> <char> <char> <fctr>
#> 1: realland 2211 (921 -- 4610) Likely decreasing
#> 2: testland 2238 (980 -- 4646) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.87 (0.57 -- 1.2) -0.036 (-0.16 -- 0.076)
#> 2: 0.88 (0.58 -- 1.2) -0.034 (-0.16 -- 0.076)
#> Doubling/halving time (days)
#> <char>
#> 1: -19 (9.2 -- -4.3)
#> 2: -20 (9.1 -- -4.4)
#> 1: realland 2260 (1009 -- 5055) Likely decreasing
#> 2: testland 2237 (952 -- 4767) Likely decreasing
#> Effective reproduction no. Rate of growth Doubling/halving time (days)
#> <char> <char> <char>
#> 1: 0.89 (0.58 -- 1.3) -0.032 (-0.15 -- 0.085) -22 (8.2 -- -4.5)
#> 2: 0.88 (0.58 -- 1.2) -0.032 (-0.15 -- 0.077) -21 (9 -- -4.5)
```

``` r
## plot
region_rt$summary$plots$R
```
Expand All @@ -137,47 +145,56 @@ region_rt$summary$plots$R
If instead, we wanted to use the Gaussian Process for `testland` and a weekly random walk for `realland` we could specify these separately using the `opts_list()` function from the package and `modifyList()` from `R`.


```r
``` r
gp <- opts_list(gp_opts(), cases)
gp <- modifyList(gp, list(realland = NULL), keep.null = TRUE)
rt <- opts_list(rt_opts(), cases, realland = rt_opts(rw = 7))
region_separate_rt <- regional_epinow(
reported_cases = cases,
data = cases,
generation_time = generation_time_opts(example_generation_time),
delays = delay_opts(delay),
rt = rt, gp = gp,
)
#> INFO [2024-05-10 07:54:30] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-06-19 18:07:15] Producing following optional outputs: regions, summary, samples, plots, latest
#> Logging threshold set at INFO for the EpiNow2 logger
#> Writing EpiNow2 logs to the console and: /tmp/RtmpJDlhZu/regional-epinow/2020-04-21.log
#> Writing EpiNow2 logs to the console and: /var/folders/vr/dn4r1_zj417drd1zr9301trw0000gp/T//Rtmpv7UfXL/regional-epinow/2020-04-21.log
#> Logging threshold set at INFO for the EpiNow2.epinow logger
#> Writing EpiNow2.epinow logs to: /tmp/RtmpJDlhZu/epinow/2020-04-21.log
#> INFO [2024-05-10 07:54:30] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-05-10 07:54:30] No target directory specified so returning output
#> INFO [2024-05-10 07:54:30] Producing estimates for: testland, realland
#> INFO [2024-05-10 07:54:30] Regions excluded: none
#> INFO [2024-05-10 07:56:06] Completed estimates for: testland
#> INFO [2024-05-10 07:56:24] Completed estimates for: realland
#> INFO [2024-05-10 07:56:24] Completed regional estimates
#> INFO [2024-05-10 07:56:24] Regions with estimates: 2
#> INFO [2024-05-10 07:56:24] Regions with runtime errors: 0
#> INFO [2024-05-10 07:56:24] Producing summary
#> INFO [2024-05-10 07:56:24] No summary directory specified so returning summary output
#> INFO [2024-05-10 07:56:24] No target directory specified so returning timings
#> Writing EpiNow2.epinow logs to: /var/folders/vr/dn4r1_zj417drd1zr9301trw0000gp/T//Rtmpv7UfXL/epinow/2020-04-21.log
#> INFO [2024-06-19 18:07:15] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-06-19 18:07:15] No target directory specified so returning output
#> INFO [2024-06-19 18:07:15] Producing estimates for: testland, realland
#> INFO [2024-06-19 18:07:15] Regions excluded: none
#> DEBUG [2024-06-19 18:07:15] testland: Running in exact mode for 2000 samples (across 4 chains each with a warm up of 250 iterations each) and 81 time steps of which 7 are a forecast
#> WARN [2024-06-19 18:08:04] testland (chain: 1): There were 1 divergent transitions after warmup. See
#> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them. -
#> WARN [2024-06-19 18:08:04] testland (chain: 1): Examine the pairs() plot to diagnose sampling problems
#> -
#> INFO [2024-06-19 18:08:06] Completed estimates for: testland
#> DEBUG [2024-06-19 18:08:06] realland: Running in exact mode for 2000 samples (across 4 chains each with a warm up of 250 iterations each) and 81 time steps of which 7 are a forecast
#> INFO [2024-06-19 18:08:22] Completed estimates for: realland
#> INFO [2024-06-19 18:08:22] Completed regional estimates
#> INFO [2024-06-19 18:08:22] Regions with estimates: 2
#> INFO [2024-06-19 18:08:22] Regions with runtime errors: 0
#> INFO [2024-06-19 18:08:22] Producing summary
#> INFO [2024-06-19 18:08:22] No summary directory specified so returning summary output
#> INFO [2024-06-19 18:08:23] No target directory specified so returning timings
```

``` r
## summary
region_separate_rt$summary$summarised_results$table
#> Region New infections per day Expected change in daily reports
#> <char> <char> <fctr>
#> 1: realland 2106 (1042 -- 4307) Likely decreasing
#> 2: testland 2128 (843 -- 4774) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.86 (0.6 -- 1.2) -0.038 (-0.11 -- 0.046)
#> 2: 0.86 (0.52 -- 1.3) -0.038 (-0.18 -- 0.081)
#> Doubling/halving time (days)
#> <char>
#> 1: -18 (15 -- -6.3)
#> 2: -18 (8.6 -- -3.8)
#> 1: realland 2026 (1030 -- 4393) Likely decreasing
#> 2: testland 2119 (816 -- 5021) Likely decreasing
#> Effective reproduction no. Rate of growth Doubling/halving time (days)
#> <char> <char> <char>
#> 1: 0.85 (0.6 -- 1.2) -0.041 (-0.11 -- 0.048) -17 (15 -- -6.2)
#> 2: 0.86 (0.5 -- 1.3) -0.038 (-0.19 -- 0.095) -18 (7.3 -- -3.6)
```

``` r
## plot
region_separate_rt$summary$plots$R
```
Expand Down
4 changes: 2 additions & 2 deletions vignettes/epinow.Rmd.orig
View file
Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@ To then run this on multiple regions using the default options above, we could u

```{r regional_epinow, fig.width = 8}
region_rt <- regional_epinow(
reported_cases = cases,
data = cases,
generation_time = generation_time_opts(example_generation_time),
delays = delay_opts(delay),
rt = rt_opts(prior = rt_prior),
Expand All @@ -94,7 +94,7 @@ gp <- opts_list(gp_opts(), cases)
gp <- modifyList(gp, list(realland = NULL), keep.null = TRUE)
rt <- opts_list(rt_opts(), cases, realland = rt_opts(rw = 7))
region_separate_rt <- regional_epinow(
reported_cases = cases,
data = cases,
generation_time = generation_time_opts(example_generation_time),
delays = delay_opts(delay),
rt = rt, gp = gp,
Expand Down

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