fixes to small issues introduced by PR #305 (#336)

R/estimate_truncation.R

@@ -229,7 +229,7 @@ estimate_truncation <- function(obs, max_truncation, trunc_max = 10,
   out$last_obs <- last_obs
   # summarise estimated cmf of the truncation distribution
   out$cmf <- extract_stan_param(fit, "cmf", CrIs = CrIs)
-  out$cmf <- data.table::as.data.table(out$cmf)[, index := .N:1]
+  out$cmf <- data.table::as.data.table(out$cmf)[, index := seq_len(.N)]
   data.table::setcolorder(out$cmf, "index")
   out$data <- data
   out$fit <- fit

R/opts.R

@@ -132,8 +132,8 @@ delay_opts <- function(..., fixed = FALSE) {
 
   names(data) <- paste0("delay_", names(data))
   # Estimate the mean delay -----------------------------------------------
-  data$seeding_time <- sum(
-    purrr::map2_dbl(data$mean_mean, data$sd_mean, ~ exp(.x + .y^2 / 2))
+  data$seeding_time <- sum(purrr::map2_dbl(
+    data$delay_mean_mean, data$delay_sd_mean, ~ exp(.x + .y^2 / 2))
   )
   if (data$seeding_time < 1) {
     data$seeding_time <- 1
@@ -162,10 +162,9 @@ delay_opts <- function(..., fixed = FALSE) {
 #' Returns a truncation distribution formatted for usage by
 #'  downstream functions. See `estimate_truncation()` for an approach to
 #'  estimate this distribution.
-#' @param ... Any parameters to be passed to [delay_dist]. If the `max` parameter
-#' is not set but other distributional parameters given then the `max` will be
-#' set to 15 to ensure backwards compatibility. Also if no `dist` parameter is given
-#' then a gamma distribution will be used for backwards compatibility.
+#' @param dist Parameters of a discretised (upper-)truncated lognormal
+#' truncation distribution as a list with parameters that are all passed to
+#' [delay_dist].
 #' @seealso convert_to_logmean convert_to_logsd bootstrapped_dist_fit delay_dist
 #' @return A list summarising the input truncation distribution.
 #' @export
@@ -174,14 +173,11 @@ delay_opts <- function(..., fixed = FALSE) {
 #' trunc_opts()
 #'
 #' # truncation dist
-#' trunc_opts(mean = 3, sd = 2)
-trunc_opts <- function(...) {
-  dot_options <- list(...) ## options for delay_dist
-  present <- (length(dot_options) > 0)
-  data <- do.call(delay_dist, dot_options)
+#' trunc_opts(dist = list(mean = 3, sd = 2))
+trunc_opts <- function(dist = list()) {
+  data <- do.call(delay_dist, dist)
   names(data) <- paste0("trunc_", names(data))
-  data$truncation <- as.integer(present)
-
+  data$truncation <- as.integer(length(data$trunc_max) > 0)
   return(data)
 }
 

tests/testthat/test-delays.R

@@ -57,8 +57,10 @@ test_that("truncation parameters can be specified in different ways", {
     c("trunc_mean_mean", "trunc_mean_sd", "trunc_sd_mean", "trunc_sd_sd",
       "trunc_max")
   expect_equal(
-    test_stan_data(truncation = trunc_opts(mean = 3, sd = 1, max = 5),
-                   params = trunc_params),
+    test_stan_data(
+      truncation = trunc_opts(dist =  list(mean = 3, sd = 1, max = 5)),
+      params = trunc_params
+    ),
     c(3, 0, 1, 0, 5)
   )
 })

tests/testthat/test-simulate_infections.R

@@ -52,7 +52,7 @@ test_that("simulate infections fails as expected", {
 })
 
 test_that("simulate_infections works to simulate a passed in estimate_infections object with an adjusted Rt in data frame", {
-  R <- c(rep(NA_real_, 31), rep(0.5, 17))
+  R <- c(rep(NA_real_, 32), rep(0.5, 17))
   R_dt <- data.frame(date = summary(out, type = "parameters", param = "R")$date, value = R)
   sims_dt <- simulate_infections(out, R_dt)
   expect_equal(names(sims_dt), c("samples", "summarised", "observations"))