Remove downloads from {covidregionaldata} in R files

.lintr

@@ -6,6 +6,7 @@ linters: linters_with_tags(
     extraction_operator_linter = NULL,
     todo_comment_linter = NULL,
     function_argument_linter = NULL,
+    indentation_linter = NULL, # unstable as of lintr 3.1.0
     # Use minimum R declared in DESCRIPTION or fall back to current R version
     backport_linter(if (length(x <- etdev::extract_min_r_version())) x else getRversion())
   )

R/estimate_reporting.R

@@ -25,20 +25,24 @@
 #' @export
 #'
 #' @examples
-#' library(cfr)
-#' library(epiparameter)
-#' library(covidregionaldata)
+#' # get data pre-loaded with {incidence2}
+#' df_covid_uk <- incidence2::covidregionaldataUK
 #'
-#' df_covid_uk <- get_national_data(
-#'   countries = "united kingdom", source = "who", verbose = FALSE
+#' # aggregate the covid data for the UK as a whole
+#' df_covid_uk <- aggregate(
+#'   data = df_covid_uk,
+#'   x = cbind(cases_new, deaths_new) ~ date,
+#'   FUN = function(x) sum(x, na.rm = TRUE)
 #' )
+#'
 #' # rename columns
 #' colnames(df_covid_uk)[colnames(df_covid_uk) == "cases_new"] <- "cases"
 #' colnames(df_covid_uk)[colnames(df_covid_uk) == "deaths_new"] <- "deaths"
 #'
 #' df_covid_uk_subset <- subset(df_covid_uk, date <= "2020-05-31")
 #'
-#' onset_to_death_covid <- epidist_db(
+#' # load epidist object from {epiparameter}
+#' onset_to_death_covid <- epiparameter::epidist_db(
 #'   disease = "COVID-19",
 #'   epi_dist = "onset_to_death",
 #'   author = "Linton_etal"
@@ -139,12 +143,11 @@ estimate_reporting <- function(data,
   # here, the estimate called "severity_me" translates to "reporting_me"
   # and the estimate "severity_hi" translates to "reporting_lo"
   # TODO: check if this is correct
-  df_out <- data.frame(
-    reporting_me = df_out$severity_me,
-    reporting_lo = df_out$severity_hi,
-    reporting_hi = df_out$severity_lo
+  df_out <- as.data.frame(df_out,
+    row.names = NULL,
+    col.names = c("reporting_me", "reporting_hi", "reporting_lo")
   )
 
-  # return data
-  df_out
+  # return data with columns in correct order
+  df_out[, c("reporting_me", "reporting_lo", "reporting_hi")]
 }

R/estimate_time_varying.R

@@ -33,32 +33,48 @@
 #' @export
 #'
 #' @examples
-#' # load package data
-#' data("ebola1976")
+#' # get data pre-loaded with {incidence2}
+#' df_covid_uk <- incidence2::covidregionaldataUK
 #'
-#' # get an onset to death distribution from the {epiparameter} package
-#' onset_to_death_ebola <- epiparameter::epidist_db(
-#'   disease = "Ebola Virus Disease",
+#' # aggregate the covid data for the UK as a whole
+#' df_covid_uk <- aggregate(
+#'   data = df_covid_uk,
+#'   x = cbind(cases_new, deaths_new) ~ date,
+#'   FUN = function(x) sum(x, na.rm = TRUE)
+#' )
+#'
+#' # rename columns
+#' colnames(df_covid_uk)[colnames(df_covid_uk) == "cases_new"] <- "cases"
+#' colnames(df_covid_uk)[colnames(df_covid_uk) == "deaths_new"] <- "deaths"
+#'
+#' df_covid_uk_subset <- subset(df_covid_uk, date <= "2020-05-31")
+#'
+#' # load epidist object from {epiparameter}
+#' onset_to_death_covid <- epiparameter::epidist_db(
+#'   disease = "COVID-19",
 #'   epi_dist = "onset_to_death",
-#'   author = "Barry_etal"
+#'   author = "Linton_etal"
 #' )
 #'
 #' # estimate time varying severity without correcting for delays
-#' estimate_time_varying(
-#'   data = ebola1976,
+#' cfr_time_varying <- estimate_time_varying(
+#'   data = df_covid_uk_subset,
 #'   smooth_inputs = TRUE,
 #'   burn_in_value = 7L,
 #'   correct_for_delays = FALSE
 #' )
+#' # View
+#' tail(cfr_time_varying)
 #'
 #' # estimate time varying severity while correcting for delays
-#' estimate_time_varying(
-#'   data = ebola1976,
-#'   epi_dist = onset_to_death_ebola,
+#' cfr_time_varying <- estimate_time_varying(
+#'   data = df_covid_uk_subset,
+#'   epi_dist = onset_to_death_covid,
 #'   smooth_inputs = TRUE,
 #'   burn_in_value = 7L,
 #'   correct_for_delays = TRUE
 #' )
+#' tail(cfr_time_varying)
 #'
 estimate_time_varying <- function(data,
                                   epi_dist = NULL,

R/prepare_data.R

@@ -67,7 +67,7 @@ prepare_data <- function(data, ...) {
 #' )
 #'
 #' # View head of prepared data
-#' head(
+#' tail(
 #'   prepare_data(
 #'     covid_uk_incidence,
 #'     cases_variable = "cases_new",

tests/testthat/_snaps/estimate_reporting.md

@@ -43,6 +43,6 @@
     Code
       reporting_estimate
     Output
-         reporting_me reporting_lo reporting_hi
-      73        0.014        0.014         0.56
+        reporting_me reporting_lo reporting_hi
+      1        0.014        0.014         0.56