Improve database: add first author name et al to Reference column

R/utils.R

@@ -36,3 +36,35 @@ calc_disc_dist_quantile <- function(prob, days, quantile) {
   names(quantiles) <- as.character(quantile)
   quantiles
 }
+
+#' Format short citation from `<bibentry>` object
+#'
+#' @description
+#' Output is equivalent to the `\citet{}` function in the \pkg{natbib} LaTeX
+#' package.
+#'
+#' @param x A `<bibentry>` object, see [bibentry()].
+#'
+#' @return A `character` string with the short citation.
+#' @keywords internal
+.citet <- function(x) {
+  stopifnot(inherits(x, "bibentry"))
+  num_author <- length(x$author)
+  # check if first author is an organisation
+  is_org_author <- is.null(x$author[1]$family)
+  # this covers single author entries
+  if (is_org_author) {
+    # organisation name stored in $given
+    cit <- x$author[1]$given
+  } else {
+    cit <- x$author[1]$family
+  }
+  # append second author or et al for multi-author entries
+  if (num_author == 2) {
+    cit <- paste(cit, "&", x$author[2]$family)
+  } else if (num_author > 2) {
+    cit <- paste(cit, "et al.")
+  }
+  cit <- paste0(cit, " (", x$year, ")")
+  cit
+}

tests/testthat/test-utils.R

@@ -56,3 +56,50 @@ test_that("calc_disc_dist_quantile fails as expected", {
     )
   )
 })
+
+test_that(".citet works as expected for multi-author", {
+  suppressMessages(
+    epidist <- epidist_db(
+      author = "Lessler",
+      disease = "RSV",
+      single_epidist = TRUE
+    )
+  )
+  expect_identical(.citet(epidist$citation), "Lessler et al. (2009)")
+})
+
+test_that(".citet works as expected for single author", {
+  suppressMessages(
+    epidist <- epidist_db(
+      author = "Pavlin",
+      disease = "Marburg",
+      single_epidist = TRUE
+    )
+  )
+  expect_identical(.citet(epidist$citation), "Pavlin (2014)")
+})
+
+test_that(".citet works as expected for two authors", {
+  suppressMessages(
+    epidist <- epidist_db(
+      author = "Nishiura",
+      disease = "Influenza",
+      single_epidist = TRUE
+    )
+  )
+  expect_identical(.citet(epidist$citation), "Nishiura & Inaba (2011)")
+})
+
+test_that(".citet works as expected for organisation author", {
+  suppressMessages(
+    epidist <- epidist_db(
+      author = "WHO",
+      disease = "Ebola",
+      single_epidist = TRUE
+    )
+  )
+  expect_identical(
+    .citet(epidist$citation),
+    "WHO Ebola Response Team et al. (2015)"
+  )
+})

vignettes/database.Rmd

@@ -20,7 +20,9 @@ tbl <- lapply(db, function(x) {
     disease = x$disease,
     pathogen = x$pathogen,
     epi_dist = x$epi_dist,
-    url = paste0(
+    citation_info = paste0(
+      epiparameter:::.citet(x$citation), # nolint undesirable_operator_linter
+      ", DOI: ",
       "<a href=\"https://doi.org/", x$citation$doi, "\">",
       x$citation$doi, "</a>"
     )