Shorten generation_time_opts() to gt_opts() as alias

NAMESPACE

@@ -62,6 +62,7 @@ export(get_pmf)
 export(get_regional_results)
 export(gp_opts)
 export(growth_to_R)
+export(gt_opts)
 export(lognorm_dist_def)
 export(make_conf)
 export(map_prob_change)

NEWS.md

@@ -11,6 +11,7 @@
 ## Documentation
 
 - Updated the documentation of the dots argument of the `stan_sampling_opts()` to add that the dots are passed to `cmdstanr::sample()`. By @jamesmbaazam in #699 and reviewed by @sbfnk.
+- `generation_time_opts()` has been shortened to `gt_opts()` to make it easier to specify. Calls to both functions are equivalent. By @jamesmbaazam in #698 and reviewed by @seabbs and @sbfnk .
 
 # EpiNow2 1.5.2
 

R/epinow.R

@@ -64,7 +64,7 @@
 #' # estimate Rt and nowcast/forecast cases by date of infection
 #' out <- epinow(
 #'   data = reported_cases,
-#'   generation_time = generation_time_opts(generation_time),
+#'   generation_time = gt_opts(generation_time),
 #'   rt = rt_opts(prior = list(mean = 2, sd = 0.1)),
 #'   delays = delay_opts(incubation_period + reporting_delay)
 #' )
@@ -80,7 +80,7 @@
 #' }
 # nolint start: cyclocomp_linter
 epinow <- function(data,
-                   generation_time = generation_time_opts(),
+                   generation_time = gt_opts(),
                    delays = delay_opts(),
                    truncation = trunc_opts(),
                    rt = rt_opts(),

R/estimate_infections.R

@@ -22,9 +22,9 @@
 #'
 #' @param reported_cases Deprecated; use `data` instead.
 #'
-#' @param generation_time A call to [generation_time_opts()] defining the
-#' generation time distribution used. For backwards compatibility a list of
-#' summary parameters can also be passed.
+#' @param generation_time A call to [gt_opts()] (or its alias
+#' [generation_time_opts()]) defining the generation time distribution used.
+#' For backwards compatibility a list of summary parameters can also be passed.
 #'
 #' @param delays A call to [delay_opts()] defining delay distributions and
 #' options. See the documentation of [delay_opts()] and the examples below for
@@ -99,7 +99,7 @@
 #'
 #' # for more examples, see the "estimate_infections examples" vignette
 #' def <- estimate_infections(reported_cases,
-#'   generation_time = generation_time_opts(generation_time),
+#'   generation_time = gt_opts(generation_time),
 #'   delays = delay_opts(incubation_period + reporting_delay),
 #'   rt = rt_opts(prior = list(mean = 2, sd = 0.1)),
 #'   stan = stan_opts(control = list(adapt_delta = 0.95))
@@ -111,7 +111,7 @@
 #' options(old_opts)
 #' }
 estimate_infections <- function(data,
-                                generation_time = generation_time_opts(),
+                                generation_time = gt_opts(),
                                 delays = delay_opts(),
                                 truncation = trunc_opts(),
                                 rt = rt_opts(),

R/opts.R

@@ -3,6 +3,7 @@
 #' @description `r lifecycle::badge("stable")`
 #' Returns generation time parameters in a format for lower level model use.
 #'
+#' @rdname generation_time_opts
 #' @param dist A delay distribution or series of delay distributions . If no
 #'   distribution is given a fixed generation time of 1 will be assumed.
 #'
@@ -40,8 +41,8 @@
 #' )
 #'
 #' # An example generation time
-#' generation_time_opts(example_generation_time)
-generation_time_opts <- function(dist = Fixed(1), ...,
+#' gt_opts(example_generation_time)
+gt_opts <- function(dist = Fixed(1), ...,
                                  disease, source, max = 14, fixed = FALSE,
                                  tolerance = 0.001, weight_prior = TRUE) {
   dot_options <- list(...)
@@ -75,6 +76,10 @@ generation_time_opts <- function(dist = Fixed(1), ...,
   return(dist)
 }
 
+#' @rdname generation_time_opts
+#' @export
+generation_time_opts <- gt_opts
+
 #' Secondary Reports Options
 #'
 #' @description `r lifecycle::badge("stable")`

R/regional_epinow.R

@@ -79,7 +79,7 @@
 #' # for more examples, see the "estimate_infections examples" vignette
 #' def <- regional_epinow(
 #'   data = cases,
-#'   generation_time = generation_time_opts(example_generation_time),
+#'   generation_time = gt_opts(example_generation_time),
 #'   delays = delay_opts(example_incubation_period + example_reporting_delay),
 #'   rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
 #'   stan = stan_opts(
@@ -91,7 +91,7 @@
 #' options(old_opts)
 #' }
 regional_epinow <- function(data,
-                            generation_time = generation_time_opts(),
+                            generation_time = gt_opts(),
                             delays = delay_opts(),
                             truncation = trunc_opts(),
                             rt = rt_opts(),

data-raw/estimate-infections.R

@@ -12,7 +12,7 @@ reported_cases <- example_confirmed[1:60]
 reporting_delay <- LogNormal(mean = 2, sd = 1, max = 10L)
 
 example_estimate_infections <- estimate_infections(reported_cases,
-  generation_time = generation_time_opts(example_generation_time),
+  generation_time = gt_opts(example_generation_time),
   delays = delay_opts(example_incubation_period + reporting_delay),
   rt = rt_opts(prior = list(mean = 2, sd = 0.1)),
   stan = stan_opts(samples = 200, control = list(adapt_delta = 0.95))
@@ -25,8 +25,8 @@ cases <- data.table::rbindlist(list(
 ))
 
 example_regional_epinow <- regional_epinow(
+  generation_time = gt_opts(example_generation_time),
   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)),
   stan = stan_opts(samples = 200, control = list(adapt_delta = 0.95))

inst/dev/benchmark-functions.R

@@ -15,7 +15,7 @@ create_profiles <- function(dir = file.path("inst", "stan"),
     set.seed(x)
     fit <- estimate_infections(
       data = reported_cases,
-      generation_time = generation_time_opts(fixed_generation_time),
+      generation_time = gt_opts(fixed_generation_time),
       delays = delay_opts(delays),
       rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
       stan = stan_opts(

inst/dev/recover-synthetic/rt.R

@@ -12,7 +12,7 @@ obs <- obs_opts(scale = list(mean = 0.1, sd = 0.025), return_likelihood = TRUE)
 # fit model to data to recover realistic parameter estimates and define settings
 # shared simulation settings
 init <- estimate_infections(example_confirmed[1:100],
-  generation_time = generation_time_opts(example_generation_time),
+  generation_time = gt_opts(example_generation_time),
   delays = delay_opts(example_incubation_period + example_reporting_delay),
   rt = rt_opts(prior = list(mean = 2, sd = 0.1), rw = 14),
   gp = NULL, horizon = 0,
@@ -57,7 +57,7 @@ for (method in c("nuts")) {
   # GP
   gp[[method]] <-
     estimate_infections(sim_cases,
-      generation_time = generation_time_opts(example_generation_time),
+      generation_time = gt_opts(example_generation_time),
       delays = delay_opts(example_incubation_period + example_reporting_delay),
       rt = rt_opts(prior = list(mean = 2, sd = 0.25)),
       stan = stanopts,
@@ -72,7 +72,7 @@ for (method in c("nuts")) {
   # Backcalculation
   backcalc[[method]] <-
     estimate_infections(sim_cases,
-      generation_time = generation_time_opts(example_generation_time),
+      generation_time = gt_opts(example_generation_time),
       delays = delay_opts(example_incubation_period + example_reporting_delay),
       rt = NULL,
       stan = stanopts,
@@ -87,7 +87,7 @@ for (method in c("nuts")) {
   # RW (weekly)
   weekly_rw[[method]] <-
     estimate_infections(sim_cases,
-      generation_time = generation_time_opts(example_generation_time),
+      generation_time = gt_opts(example_generation_time),
       delays = delay_opts(example_incubation_period + example_reporting_delay),
       rt = rt_opts(
         prior = list(mean = 2, sd = 0.25),
@@ -106,7 +106,7 @@ for (method in c("nuts")) {
   # RW (every month) + stationary Guassian process
   gp_rw[[method]] <-
     estimate_infections(sim_cases,
-      generation_time = generation_time_opts(example_generation_time),
+      generation_time = gt_opts(example_generation_time),
       delays = delay_opts(example_incubation_period + example_reporting_delay),
       rt = rt_opts(
         prior = list(mean = 2, sd = 0.25), rw = 14, gp_on = "R0"
@@ -125,7 +125,7 @@ for (method in c("nuts")) {
   if (fit_daily) {
     daily_rw[[method]] <-
       estimate_infections(sim_cases,
-        generation_time = generation_time_opts(example_generation_time),
+        generation_time = gt_opts(example_generation_time),
         delays = delay_opts(
           example_incubation_period + example_reporting_delay
         ),

tests/testthat/test-delays.R

@@ -1,4 +1,4 @@
-test_stan_delays <- function(generation_time = generation_time_opts(Fixed(1)),
+test_stan_delays <- function(generation_time = gt_opts(Fixed(1)),
                              delays = delay_opts(),
                              truncation = trunc_opts(),
                              params = c()) {
@@ -21,14 +21,14 @@ test_that("generation times can be specified in different ways", {
   )
   expect_equal(
     test_stan_delays(
-      generation_time = generation_time_opts(Fixed(value = 3)),
+      generation_time = gt_opts(Fixed(value = 3)),
       params = delay_params
     ),
     c(0, 0, 0, 1, 1, 1)
   )
   expect_equal(
     round(test_stan_delays(
-      generation_time = generation_time_opts(
+      generation_time = gt_opts(
         LogNormal(meanlog = 3, sdlog = 1, max = 4)
       ),
       params = delay_params
@@ -69,7 +69,7 @@ test_that("truncation parameters can be specified in different ways", {
 })
 
 test_that("distributions incompatible with stan models are caught", {
-  expect_error(generation_time_opts(
+  expect_error(gt_opts(
     Gamma(2, 2)
   ), "maximum")
   expect_error(delay_opts(