jidea-157 Support ISO codes as country parameter to daedalus

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: daedalus
 Title: Model health, social, and economic costs of a pandemic using
     _DAEDALUS_
-Version: 0.0.18
+Version: 0.0.19
 Authors@R: c(
     person("Pratik", "Gupte", , "p.gupte24@imperial.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5294-7819")),

R/class_country.R

@@ -33,8 +33,9 @@ new_daedalus_country <- function(name, parameters) {
 #' parameter access and editing, as well as processing raw country
 #' characteristics for the DAEDALUS model.
 #'
-#' @param name A string giving the country or territory name; must be from among
-#' [daedalus::country_names].
+#' @param country A string giving the country or territory name, or ISO2 or
+#' ISO3 code; must be from among [daedalus::country_codes_iso2c] or
+#' [daedalus::country_codes_iso3c] or [daedalus::country_names].
 #'
 #' @param parameters An optional named list of country parameters that are
 #' allowed to be modified. Currently, users may only pass their own contact
@@ -72,14 +73,14 @@ new_daedalus_country <- function(name, parameters) {
 #' # using assignment operators
 #' x$contact_matrix <- matrix(99, 4, 4)
 #' x
-daedalus_country <- function(name,
+daedalus_country <- function(country,
                              parameters = list(
                                contact_matrix = NULL,
                                contacts_workplace = NULL,
                                contacts_consumer_worker = NULL
                              )) {
   # input checking
-  name <- rlang::arg_match(name, daedalus::country_names)
+  name <- country_name_from_arg(country)
   # check list but allow missing and NULL
   checkmate::assert_list(
     parameters, c("numeric", "matrix", "NULL")

R/country_helpers.R

@@ -0,0 +1,32 @@
+#' Get country name from arg
+#' @description Function to get a supported country name given an arg which
+#' may be a country name or may be an ISO2 or ISO3 code. In all cases,
+#' the function checks if the country identifier is supported.
+#'
+#' @param country A string which could be a country name, or an ISO2 or ISO3
+#' code.
+#'
+#' @return A supported country name
+#' @keywords internal
+country_name_from_arg <- function(country) {
+  lookup_country_name_from_code <- function(code, code_list) {
+    # check code is known, and lookup country name from idx
+    code <- rlang::arg_match(code, code_list)
+    idx <- match(code, code_list)
+    daedalus::country_names[[idx]]
+  }
+
+  if (any(grep("^[A-Z]{2}$", country))) { # regex check for ISO2
+    country <- lookup_country_name_from_code(
+      country, daedalus::country_codes_iso2c
+    )
+  } else if (any(grep("^[A-Z]{3}$", country))) { # regex check for ISO3
+    country <- lookup_country_name_from_code(
+      country, daedalus::country_codes_iso3c
+    )
+  } else {
+    # check country name is known
+    country <- rlang::arg_match(country, daedalus::country_names)
+  }
+  country
+}

R/daedalus.R

@@ -4,7 +4,8 @@
 #'
 #' @param country A country or territory object of class `<daedalus_country>`,
 #' **or** a country or territory name from those included in the package;
-#' see [daedalus::country_names].
+#' see [daedalus::country_names], **or** a country ISO2 or ISO3 code; see
+#' [daedalus::country_codes_iso2c] and [daedalus::country_codes_iso3c] .
 #' Country-specific data such as the community and workplace contacts, the
 #' demography, and the distribution of the workforce into economic sectors is
 #' automatically accessed from package data for the relevant country name if it
@@ -122,7 +123,6 @@ daedalus <- function(country,
   # NOTE: names are case sensitive
   checkmate::assert_multi_class(country, c("daedalus_country", "character"))
   if (is.character(country)) {
-    country <- rlang::arg_match(country, daedalus::country_names)
     country <- daedalus_country(country)
   }
   checkmate::assert_multi_class(infection, c("daedalus_infection", "character"))

inst/WORDLIST

@@ -14,6 +14,7 @@ Pianella
 SARS
 SEIR
 Sumali
+arg
 asymp
 doi
 econ
@@ -24,6 +25,5 @@ rootfinding
 started’
 symp
 th
-timeframe
 timeseries
 timesteps

tests/testthat/test-class_daedalus_country.R

@@ -20,13 +20,27 @@ test_that("class <daedalus_country>: basic expectations", {
   )
 })
 
-test_that("class <daedalus_country>`: works for all countries", {
+test_that("class <daedalus_country>`: works for all country names", {
   expect_no_condition({
     countries <- lapply(daedalus::country_names, daedalus_country) # nolint
   })
   checkmate::expect_list(countries, "daedalus_country")
 })
 
+test_that("class <daedalus_country>`: works for all country ISO2 codes", {
+  expect_no_condition({
+    countries <- lapply(daedalus::country_codes_iso2c, daedalus_country) # nolint
+  })
+  checkmate::expect_list(countries, "daedalus_country")
+})
+
+test_that("class <daedalus_country>`: works for all country ISO3 codes", {
+  expect_no_condition({
+    countries <- lapply(daedalus::country_codes_iso3c, daedalus_country) # nolint
+  })
+  checkmate::expect_list(countries, "daedalus_country")
+})
+
 test_that("class <daedalus_country>: access and assignment", {
   name <- "Canada"
   country_x <- daedalus_country(name)
@@ -121,7 +135,19 @@ test_that("class <daedalus_country>`: errors", {
   # invalid name
   expect_error(
     daedalus_country("dummy"),
-    regexp = "`name` must be one of"
+    regexp = "`country` must be one of"
+  )
+
+  # invalid ISO2
+  expect_error(
+    daedalus_country("ZZ"),
+    regexp = "`code` must be one of"
+  )
+
+  # invalid ISO3
+  expect_error(
+    daedalus_country("ZZZ"),
+    regexp = "`code` must be one of"
   )
 
   # invalid `parameter` type

tests/testthat/test-daedalus.R

@@ -69,6 +69,22 @@ test_that("daedalus: basic expectations", {
   )
 })
 
+test_that("Can run with ISO2 country parameter", {
+  expect_no_condition({
+    output <- daedalus("CA", "influenza_1918")
+  })
+  data <- get_data(output)
+  expect_length(data, N_OUTPUT_COLS)
+})
+
+test_that("Can run with ISO3 country parameter", {
+  expect_no_condition({
+    output <- daedalus("CAN", "influenza_1918")
+  })
+  data <- get_data(output)
+  expect_length(data, N_OUTPUT_COLS)
+})
+
 # test that daedalus runs for all epidemic infection parameter sets
 test_that("daedalus: Runs for all country x infection x response", {
   country_infection_combos <- data.table::CJ(

tests/testthat/test_country_helpers.R

@@ -0,0 +1,32 @@
+test_that("country_name_from_arg looks up name from iso2", {
+  expect_identical(country_name_from_arg("CA"), "Canada")
+})
+
+test_that("country_name_from_arg looks up name from iso3", {
+  expect_identical(country_name_from_arg("CAN"), "Canada")
+})
+
+test_that("country_name_from_arg passes through supported country name", {
+  expect_identical(country_name_from_arg("Canada"), "Canada")
+})
+
+test_that("country_name_from_arg errors on unsupported iso2", {
+  expect_error(
+    country_name_from_arg("ZZ"),
+    regexp = "must be one of"
+  )
+})
+
+test_that("country_name_from_arg errors on unsupported iso3", {
+  expect_error(
+    country_name_from_arg("ZZZ"),
+    regexp = "must be one of"
+  )
+})
+
+test_that("country_name_from_arg errors on unsupported country name", {
+  expect_error(
+    country_name_from_arg("Narnia"),
+    regexp = "must be one of"
+  )
+})