Issue 17: Fixes to data.table assignment (#18)

* Add omitted assignments

* Correct typo (draw to draws) as suggested by seabbs

* Add Adam Howes as contributor

Former-commit-id: 358d4706f12e5c68058a627f9fa101d8e40eae76 [formerly efd2f7e7a841c31d86106f231ebeab82989de206]
Former-commit-id: 59460a126c53f6fa91f66c3f51ec3b405d4069f0

DESCRIPTION

@@ -10,7 +10,11 @@ Authors@R:
     person(given = "Sam Abbott",
            role = c("aut"),
            email = "contact@samabbott.co.uk",
-           comment = c(ORCID = "0000-0001-8057-8037")))
+           comment = c(ORCID = "0000-0001-8057-8037")),
+    person(given = "Adam Howes",
+           role = c("aut"),
+           email = "adamthowes@gmail.com",
+           comment = c(ORCID = "0000-0003-2386-4031")))
 Description: Understanding and accurately estimating epidemiological delay
     distributions is important for public health policy. These estimates
     directly influence epidemic situational awareness, control strategies, and resource allocation. In this package, we provide methods to address the key challenges in estimating these distributions, including truncation, interval censoring, and dynamical biases. Despite their importance, these issues are frequently overlooked, often resulting in biased conclusions.

R/fitting-and-postprocessing.R

@@ -204,7 +204,7 @@ primary_censoring_bias_correction <- function(draws) {
   draws <- data.table::copy(draws)
   draws[, mean := mean - runif(.N, min = 0, max = 1)]
   draws[, meanlog := log(mean^2 / sqrt(sd^2 + mean^2))]
-  draw[, sdlog := sqrt(log(1 + (sd^2 / mean^2)))]
+  draws[, sdlog := sqrt(log(1 + (sd^2 / mean^2)))]
 
   return(draws[])
 }

R/observe.R

@@ -82,7 +82,7 @@ pad_zero <- function(data, pad = 1e-3) {
 #' @export
 drop_zero <- function(data) {
   data <- data.table::copy(data)
-  data[delay_daily != 0]
+  data <- data[delay_daily != 0]
 
   return(data)
 }

R/plot-helpers.R

@@ -9,7 +9,7 @@ calculate_cohort_mean <- function(data, type = c("cohort", "cumulative"),
     mean = mean(delay_daily), n = .N),
     by = c("ptime_daily", by)]
 
-  out[order(rank(ptime_daily))]
+  out <- out[order(rank(ptime_daily))]
 
   if (type == "cumulative") {
     out[, mean := cumsum(mean * n) / cumsum(n), by = by]

R/preprocess.R

@@ -142,7 +142,7 @@ event_to_incidence <- function(data, by = c()) {
   dd <- data.table::copy(data)
 
   dd[, .(cases = .N), by = c("ptime_daily", by)]
-  dd[order(ptime_daily)]
+  dd <- dd[order(ptime_daily)]
 
   setnames(dd, old = c("ptime_daily"), new = c("time"))