Fixes bug in as_epiparam()

.lintr

@@ -5,6 +5,12 @@ linters: linters_with_tags(
     implicit_integer_linter = NULL,
     extraction_operator_linter = NULL,
     todo_comment_linter = NULL,
-    function_argument_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.
+    # Install etdev package from https://github.com/epiverse-trace/etdev
+    backport_linter(if (length(x <- etdev::extract_min_r_version())) x else getRversion())
+  )
+exclusions: list(
+    "tests/testthat.R" = list(unused_import_linter = Inf)
   )
-

R/epidist_utils.R

@@ -546,6 +546,12 @@ clean_epidist_params <- function(prob_dist_params, ...) {
 #' @keywords internal
 clean_epidist_params.gamma <- function(prob_dist_params) {
 
+  # if unparameterised return named vector of NAs
+  if (isTRUE(is.na(prob_dist_params))) {
+    prob_dist_params <- c(shape = NA_real_, scale = NA_real_)
+    return(prob_dist_params)
+  }
+
   # if shape and rate are provided convert to shape and scale
   if (all(c("shape", "rate") %in% names(prob_dist_params))) {
     prob_dist_params[["rate"]] <- 1 / prob_dist_params[["rate"]]
@@ -580,6 +586,12 @@ clean_epidist_params.gamma <- function(prob_dist_params) {
 #' @keywords internal
 clean_epidist_params.lnorm <- function(prob_dist_params) {
 
+  # if unparameterised return named vector of NAs
+  if (isTRUE(is.na(prob_dist_params))) {
+    prob_dist_params <- c(meanlog = NA_real_, sdlog = NA_real_)
+    return(prob_dist_params)
+  }
+
   # if mu and sigma are provided convert to meanlog and sdlog
   if (all(c("mu", "sigma") %in% names(prob_dist_params))) {
 
@@ -616,6 +628,12 @@ clean_epidist_params.lnorm <- function(prob_dist_params) {
 #' @keywords internal
 clean_epidist_params.weibull <- function(prob_dist_params) {
 
+  # if unparameterised return named vector of NAs
+  if (isTRUE(is.na(prob_dist_params))) {
+    prob_dist_params <- c(shape = NA_real_, scale = NA_real_)
+    return(prob_dist_params)
+  }
+
   if (all(c("shape", "scale") %in% names(prob_dist_params))) {
     # remove class attribute from prob_dist_params
     prob_dist_params <- unclass(prob_dist_params)
@@ -638,6 +656,12 @@ clean_epidist_params.weibull <- function(prob_dist_params) {
 #' @keywords internal
 clean_epidist_params.nbinom <- function(prob_dist_params) {
 
+  # if unparameterised return named vector of NAs
+  if (isTRUE(is.na(prob_dist_params))) {
+    prob_dist_params <- c(mean = NA_real_, dispersion = NA_real_)
+    return(prob_dist_params)
+  }
+
   if (all(c("n", "p") %in% names(prob_dist_params))) {
 
     # convert prob to mean
@@ -682,6 +706,12 @@ clean_epidist_params.nbinom <- function(prob_dist_params) {
 #' @keywords internal
 clean_epidist_params.geom <- function(prob_dist_params) {
 
+  # if unparameterised return named NA
+  if (isTRUE(is.na(prob_dist_params))) {
+    prob_dist_params <- c(prob = NA_real_)
+    return(prob_dist_params)
+  }
+
   # if mean is provided convert to prob
   if ("mean" %in% names(prob_dist_params)) {
     prob_dist_params[["mean"]] <- 1 / prob_dist_params[["mean"]]
@@ -732,6 +762,12 @@ clean_epidist_params.geom <- function(prob_dist_params) {
 #' @keywords internal
 clean_epidist_params.pois <- function(prob_dist_params) {
 
+  # if unparameterised return named NA
+  if (isTRUE(is.na(prob_dist_params))) {
+    prob_dist_params <- c(mean = NA_real_)
+    return(prob_dist_params)
+  }
+
   if (names(prob_dist_params) %in% c("mean", "l")) {
     names(prob_dist_params) <- "mean"
 

tests/testthat/test-epidist_utils.R

@@ -92,6 +92,33 @@ test_that("clean_epidist_params works for default method", {
   )
 })
 
+test_that("clean_epidist_params works for unparameterised (NA), (#161)", {
+  params <- NA
+  class(params) <- "gamma"
+  res <- clean_epidist_params(prob_dist_params = params)
+  expect_identical(res, c(shape = NA_real_, scale = NA_real_))
+
+  class(params) <- "lnorm"
+  res <- clean_epidist_params(prob_dist_params = params)
+  expect_identical(res, c(meanlog = NA_real_, sdlog = NA_real_))
+
+  class(params) <- "weibull"
+  res <- clean_epidist_params(prob_dist_params = params)
+  expect_identical(res, c(shape = NA_real_, scale = NA_real_))
+
+  class(params) <- "nbinom"
+  res <- clean_epidist_params(prob_dist_params = params)
+  expect_identical(res, c(mean = NA_real_, dispersion = NA_real_))
+
+  class(params) <- "geom"
+  res <- clean_epidist_params(prob_dist_params = params)
+  expect_identical(res, c(prob = NA_real_))
+
+  class(params) <- "pois"
+  res <- clean_epidist_params(prob_dist_params = params)
+  expect_identical(res, c(mean = NA_real_))
+})
+
 test_that("create_epidist_region works as expected", {
   region <- create_epidist_region(
     continent = "Europe",