replace get functions with examples

epiforecasts · Oct 10, 2023 · 08c0646 · 08c0646
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diff --git a/R/epinow.R b/R/epinow.R
@@ -39,20 +39,11 @@
 #' # set number of cores to use
 #' old_opts <- options()
 #' options(mc.cores = ifelse(interactive(), 4, 1))
-#' # construct example distributions
-#' generation_time <- get_generation_time(
-#'  disease = "SARS-CoV-2", source = "ganyani"
-#' )
-#' incubation_period <- get_incubation_period(
-#'  disease = "SARS-CoV-2", source = "lauer"
-#' )
-#' reporting_delay <- dist_spec(
-#'   mean = convert_to_logmean(2, 1),
-#'   mean_sd = 0.1,
-#'   sd = convert_to_logsd(2, 1),
-#'   sd_sd = 0.1,
-#'   max = 10
-#' )
+#'
+#' # get example delays
+#' generation_time <- example_generation_time
+#' incubation_period <- example_incubation_period
+#' reporting_delay <- example_reporting_delay
 #'
 #' # example case data
 #' reported_cases <- example_confirmed[1:40]

diff --git a/R/estimate_infections.R b/R/estimate_infections.R
@@ -74,22 +74,10 @@
 #' # get example case counts
 #' reported_cases <- example_confirmed[1:60]
 #'
-#' # set up example generation time
-#' generation_time <- get_generation_time(
-#'   disease = "SARS-CoV-2", source = "ganyani", fixed = TRUE
-#' )
-#' # set delays between infection and case report
-#' incubation_period <- get_incubation_period(
-#'   disease = "SARS-CoV-2", source = "lauer", fixed = TRUE
-#' )
-#' # delays between infection and case report, with uncertainty
-#' incubation_period_uncertain <- get_incubation_period(
-#'   disease = "SARS-CoV-2", source = "lauer"
-#' )
-#' reporting_delay <- dist_spec(
-#'   mean = convert_to_logmean(2, 1), mean_sd = 0,
-#'   sd = convert_to_logsd(2, 1), sd_sd = 0, max = 10
-#' )
+#' # get example delays
+#' generation_time <- example_generation_time
+#' incubation_period <- example_incubation_period
+#' reporting_delay <- example_reporting_delay
 #'
 #' # for more examples, see the "estimate_infections examples" vignette
 #' def <- estimate_infections(reported_cases,

diff --git a/R/opts.R b/R/opts.R
@@ -35,8 +35,8 @@
 #'  dist_spec(mean = 3, sd = 2, mean_sd = 1, sd_sd = 0.5, max = 15)
 #' )
 #'
-#' # A generation time sourced from the literature
-#' dist <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
+#' # An example generation time
+#' dist <- example_generation_time
 #' generation_time_opts(dist)
 generation_time_opts <- function(dist = dist_spec(mean = 1), ...,
                                  disease, source, max = 15L, fixed = FALSE,

diff --git a/R/regional_epinow.R b/R/regional_epinow.R
@@ -65,19 +65,10 @@
 #' old_opts <- options()
 #' options(mc.cores = ifelse(interactive(), 4, 1))
 #'
-#' # construct example distributions
-#' generation_time <- get_generation_time(
-#'  disease = "SARS-CoV-2", source = "ganyani"
-#' )
-#' incubation_period <- get_incubation_period(
-#'  disease = "SARS-CoV-2", source = "lauer"
-#' )
-#' reporting_delay <- dist_spec(
-#'   mean = convert_to_logmean(2, 1),
-#'   mean_sd = 0.1,
-#'   sd = convert_to_logsd(2, 1),
-#'   sd_sd = 0.1, max = 15
-#' )
+#' # use example distributions
+#' generation_time <- example_generation_time
+#' incubation_period <- example_incubation_period
+#' reporting_delay <- example_reporting_delay
 #'
 #' # uses example case vector
 #' cases <- example_confirmed[1:60]

diff --git a/R/report.R b/R/report.R
@@ -32,17 +32,10 @@
 #' # define example cases
 #' cases <- example_confirmed[1:40]
 #'
-#' # set up example delays
-#' generation_time <- get_generation_time(
-#'  disease = "SARS-CoV-2", source = "ganyani"
-#' )
-#' incubation_period <- get_incubation_period(
-#'  disease = "SARS-CoV-2", source = "lauer"
-#' )
-#' reporting_delay <- dist_spec(
-#'   mean = convert_to_logmean(2, 1), mean_sd = 0.1,
-#'   sd = convert_to_logsd(2, 1), sd_sd = 0.1, max = 10
-#' )
+#' # get example delays
+#' generation_time <- example_generation_time
+#' incubation_period <- example_incubation_period
+#' reporting_delay <- example_reporting_delay
 #'
 #' # Instead of running them model we use example
 #' # data for speed in this example.

diff --git a/R/simulate_infections.R b/R/simulate_infections.R
@@ -46,18 +46,11 @@
 #' # get example case counts
 #' reported_cases <- example_confirmed[1:50]
 #'
-#' # set up example generation time
-#' generation_time <- get_generation_time(
-#'  disease = "SARS-CoV-2", source = "ganyani"
-#' )
+#' # use example generation times provided with the package
+#' generation_time <- example_generation_time
 #' # set delays between infection and case report
-#' incubation_period <- get_incubation_period(
-#'  disease = "SARS-CoV-2", source = "lauer"
-#' )
-#' reporting_delay <- dist_spec(
-#'   mean = convert_to_logmean(2, 1), mean_sd = 0.1,
-#'   sd = convert_to_logsd(2, 1), sd_sd = 0.1, max = 15
-#' )
+#' incubation_period <- example_incubation_period
+#' reporting_delay <- example_reporting_delay
 #'
 #' # fit model to data to recover Rt estimates
 #' est <- estimate_infections(reported_cases,

diff --git a/README.Rmd b/README.Rmd
@@ -107,21 +107,14 @@ reporting_delay <- estimate_delay(
 If data was not available we could instead make an informed estimate of the likely delay (*this is a synthetic example and not applicable to real world use cases and we have not included uncertainty to decrease runtimes*),
 
 ```{r}
-reporting_delay <- dist_spec(
-  mean = convert_to_logmean(2, 1), sd = convert_to_logsd(2, 1), max = 10,
-  dist = "lognormal"
-)
+reporting_delay <- example_reporting_delay
 ```
 
-Here we define the incubation period and generation time based on literature estimates for Covid-19 (see [here](https://github.com/epiforecasts/EpiNow2/tree/main/data-raw) for the code that generates these estimates). *Note that these distributions may not be applicable for your use case and that we have not included uncertainty here to reduce the runtime of this example but in most settings this is not recommended.*
+Here we define the incubation period and generation time based on example literature estimates for Covid-19 (see [here](https://github.com/epiforecasts/EpiNow2/tree/main/data-raw) for the code that generates these estimates). *These distributions are unlikely to be applicable for your use case and do not have uncertainty associated with them. We strongly recommend investigating what might be the best distributions to use in any given use case.*
 
 ```{r}
-generation_time <- get_generation_time(
-  disease = "SARS-CoV-2", source = "ganyani", max = 10, fixed = TRUE
-)
-incubation_period <- get_incubation_period(
-  disease = "SARS-CoV-2", source = "lauer", max = 10, fixed = TRUE
-)
+generation_time <- example_generation_time
+incubation_period <- example_incubation_period
 ```
 
 ### [epinow()](https://epiforecasts.io/EpiNow2/reference/epinow.html) 

diff --git a/data-raw/estimate-infections.R b/data-raw/estimate-infections.R
@@ -6,24 +6,11 @@ options(mc.cores = 4)
 # get example case counts
 reported_cases <- example_confirmed[1:60]
 
-# set up example generation time
-generation_time <- get_generation_time(
-  disease = "SARS-CoV-2", source = "ganyani", fixed = TRUE
-)
-# set delays between infection and case report
-incubation_period <- get_incubation_period(
-  disease = "SARS-CoV-2", source = "lauer", fixed = TRUE
-)
-# delays between infection and case report, with uncertainty
-incubation_period_uncertain <- get_incubation_period(
-  disease = "SARS-CoV-2", source = "lauer"
-)
-reporting_delay <- dist_spec(
-  mean = convert_to_logmean(2, 1), mean_sd = 0,
-  sd = convert_to_logsd(2, 1), sd_sd = 0, max = 10
-)
+#' # use example distributions
+generation_time <- example_generation_time
+incubation_period <- example_incubation_period
+reporting_delay <- example_reporting_delay
 
-# default settings but assuming that delays are fixed rather than uncertain
 example_estimate_infections <- estimate_infections(reported_cases,
   generation_time = generation_time_opts(generation_time),
   delays = delay_opts(incubation_period + reporting_delay),

diff --git a/inst/dev/recover-synthetic/rt.R b/inst/dev/recover-synthetic/rt.R
@@ -6,14 +6,10 @@ source(here::here("inst", "dev", "recover-synthetic", "plot.R"))
 old_opts <- options()
 options(mc.cores = 4)
 
-# set up example generation time
-generation_time <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
-# set delays between infection and case report
-incubation_period <- get_incubation_period(disease = "SARS-CoV-2", source = "lauer")
-reporting_delay <- dist_spec(
-  mean = convert_to_logmean(2, 1), mean_sd = 0.1,
-  sd = convert_to_logsd(2, 1), sd_sd = 0.1, max = 15
-)
+#' get example delays
+generation_time <- example_generation_time
+incubation_period <- example_incubation_period
+reporting_delay <- example_reporting_delay
 
 obs <- obs_opts(scale = list(mean = 0.1, sd = 0.025), return_likelihood = TRUE)
 

diff --git a/man/epinow.Rd b/man/epinow.Rd
diff --git a/man/estimate_infections.Rd b/man/estimate_infections.Rd
diff --git a/man/generation_time_opts.Rd b/man/generation_time_opts.Rd
diff --git a/man/regional_epinow.Rd b/man/regional_epinow.Rd
diff --git a/man/report_cases.Rd b/man/report_cases.Rd
diff --git a/man/simulate_infections.Rd b/man/simulate_infections.Rd
diff --git a/tests/testthat/test-epinow.R b/tests/testthat/test-epinow.R
@@ -1,13 +1,9 @@
 skip_on_cran()
 
-
-generation_time <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani", max_value = 15)
-incubation_period <- get_incubation_period(disease = "SARS-CoV-2", source = "lauer", max_value = 15)
-reporting_delay <- dist_spec(
-  mean = convert_to_logmean(2, 1), mean_sd = 0.1,
-  sd = convert_to_logsd(2, 1), sd_sd = 0.1,
-  max = 10
-)
+# get example delays
+generation_time <- example_generation_time
+incubation_period <- example_incubation_period
+reporting_delay <- example_reporting_delay
 
 reported_cases <- EpiNow2::example_confirmed[1:30]
 

diff --git a/tests/testthat/test-estimate_infections.R b/tests/testthat/test-estimate_infections.R
@@ -2,13 +2,12 @@
 
 futile.logger::flog.threshold("FATAL")
 
+# get example delays
+generation_time <- example_generation_time
+incubation_period <- example_incubation_period
+reporting_delay <- example_reporting_delay
+
 reported_cases <- EpiNow2::example_confirmed[1:30]
-generation_time <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani", max_value = 10)
-incubation_period <- get_incubation_period(disease = "SARS-CoV-2", source = "lauer", max_value = 10)
-reporting_delay <- dist_spec(
-  mean = convert_to_logmean(2, 1), mean_sd = 0.1,
-  sd = convert_to_logsd(2, 1), sd_sd = 0.1, max = 10
-)
 
 default_estimate_infections <- function(..., add_stan = list(), delay = TRUE) {
   futile.logger::flog.threshold("FATAL")

diff --git a/tests/testthat/test-models/estimate_infections.R b/tests/testthat/test-models/estimate_infections.R
@@ -1,11 +1,7 @@
 
-reported_cases <- EpiNow2::example_confirmed[1:30]
-generation_time <- get_generation_time(
-  disease = "SARS-CoV-2", source = "ganyani", max_value = 10
-)
-incubation_period <- get_incubation_period(
-  disease = "SARS-CoV-2", source = "lauer", max_value = 10
-)
+#' get example delays
+generation_time <- example_generation_time
+incubation_period <- example_incubation_period
 
 # static model
 fit <- estimate_infections(