Issue 40: Add example test data (#41)

* Add example test data generation in data-raw and as .rda

* Make the test data internal

* Delete PNAS data (assume copied here from another package)

* Revert back to non-internal data

* Add data documentation

* Move simulated data generation from data-raw to tests/testthat

* Add PNAS ebola data in raw xlsx format with script for saving it to rda in data

* Remove simulated data from data/

* Clean the ebola column names

* Document ebola data

* Add readxl and janitor to Suggests

* Add newline to end of file

* Add ask to cite and spacing change

* Change name to "ebola_outbreak_sierra_leone" and document roxygen2

* Fix linter issues

* Rename to sierra_leone_ebola_outbreak_data

* Use shorter ebola data name, and change code style

Former-commit-id: d140527
Former-commit-id: 4ec821ababa950c635bdc96ad43a3dc1def7f70a

DESCRIPTION

@@ -32,7 +32,9 @@ Imports:
 Suggests:
     bookdown,
     epinowcast,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    readxl,
+    janitor
 Remotes:
     stan-dev/cmdstanr,
     Rdatatable/data.table,
@@ -42,3 +44,6 @@ Config/Needs/website:
     epinowcast/enwtheme
 Config/testthat/edition: 3
 URL: https://epidist.epinowcast.org/
+Depends: 
+    R (>= 2.10)
+LazyData: true

R/data.R

@@ -0,0 +1,19 @@
+#' Ebola linelist data from Fang et al. (2016)
+#'
+#' Linelist data for the Ebola virus collected in Sierra Leone. If you use this
+#' data in your work, please cite the corresponding paper.
+#'
+#' @format A `tibble` with 8,358 rows and 8 columns:
+#' \describe{
+#'   \item{id}{Unique identification number for the case}
+#'   \item{name}{Name as character, omitted}
+#'   \item{age}{Age as numeric}
+#'   \item{sex}{Sex as character, either "F", "M" or NA}
+#'   \item{date_of_symptom_onset}{The date symptoms began}
+#'   \item{date_of_sample_tested}{The date the sample was tested}
+#'   \item{district}{The district (ADM2)}
+#'   \item{chiefdom}{The chiefdom (ADM3)}
+#' }
+#' @family data
+#' @source <https://www.pnas.org/doi/full/10.1073/pnas.1518587113>
+"sierra_leone_ebola_data"

_pkgdown.yml

@@ -36,3 +36,7 @@ reference:
   desc: Functions and helper functions for plotting
   contents:
   - has_concept("plot")
+- title: Data
+  desc: Data included with the package
+  contents:
+  - has_concept("data")

data-raw/process_raw_data.R

@@ -0,0 +1,5 @@
+sierra_leone_ebola_data <-
+  readxl::read_xlsx("data-raw/pnas.1518587113.sd02.xlsx") |>
+  janitor::clean_names()
+
+usethis::use_data(sierra_leone_ebola_data, overwrite = TRUE)

tests/testthat/setup.R

@@ -0,0 +1,15 @@
+set.seed(101)
+
+meanlog <- 1.8
+sdlog <- 0.5
+obs_time <- 25
+sample_size <- 200
+
+sim_obs <- simulate_gillespie() |>
+  simulate_secondary(
+    meanlog = meanlog,
+    sdlog = sdlog
+  ) |>
+  observe_process() |>
+  filter_obs_by_obs_time(obs_time = obs_time) %>%
+  .[sample(seq_len(.N), sample_size, replace = FALSE)]