cleanup from attempted run (#55)

* Read param as a var in CLI message

* Truncate PMFs longer than the data

To the length of the data and throw a warning rather than an error.
This change allows us to run on old right-truncation estimates.

* Bump NEWS

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Call a length a length

* No margin for error

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

NEWS.md

@@ -24,3 +24,5 @@
 * Specify number of samples draws with `iter_sampling`
 * Fix NOTE from missing variable name used with NSE
 * Read from new parameters schema
+* Fix bugs in parameter reading from local test run
+* Fix bugs in parameter reading from local test run

R/fit_model.R

@@ -160,15 +160,24 @@ format_right_truncation <- function(pmf, data) {
     # silently removed if length of the PMF was longer than the data,
     # effectively eliminating the right-truncation correction
 
-    cli::cli_abort(
+    trunc_len <- nrow(data)
+    cli::cli_warn(
       c(
+        "Removing right-truncation PMF elements after {.val {trunc_len}}",
         "Right truncation PMF longer than the data",
         "PMF length: {.val {length(pmf)}}",
         "Data length: {.val {nrow(data)}}",
-        "PMF can only be up to length as the data"
+        "PMF can only be up to the length of the data"
       ),
       class = "right_trunc_too_long"
     )
+    suppressWarnings({
+      EpiNow2::trunc_opts(
+        dist = EpiNow2::dist_spec(
+          pmf = pmf[seq_len(trunc_len)]
+        )
+      )
+    })
   } else {
     suppressWarnings({
       EpiNow2::trunc_opts(

R/parameters.R

@@ -131,7 +131,7 @@ read_interval_pmf <- function(path,
   rlang::arg_match(disease)
 
   as_of_date <- stringify_date(as_of_date)
-  cli::cli_alert_info("Reading {.arg right_truncation} from {.path {path}}")
+  cli::cli_alert_info("Reading {.arg {parameter}} from {.path {path}}")
   if (!file.exists(path)) {
     cli::cli_abort("File {.path {path}} does not exist",
       class = "file_not_found"

tests/testthat/_snaps/fit_model.md

@@ -0,0 +1,8 @@
+# Right truncation longer than data throws error
+
+    Removing right-truncation PMF elements after 2
+    Right truncation PMF longer than the data
+    PMF length: 3
+    Data length: 2
+    PMF can only be up to the length of the data
+

tests/testthat/test-fit_model.R

@@ -178,12 +178,11 @@ test_that("Right truncation longer than data throws error", {
   data <- data.frame(x = c(1, 2))
   right_truncation_pmf <- c(0.1, 0.2, 0.7)
 
-  expect_error(
+  expect_snapshot_warning(
     format_right_truncation(
       right_truncation_pmf,
       data
-    ),
-    class = "right_trunc_too_long"
+    )
   )
 })