fix(0.3.0.0): Fixes cli and -999 (#726)

* Pluralism in cli was incorrect where a single integer needs to be passed
  before the {?*} to inform if it should be plural or not, instead of
  passing a vector like what was being done.
* Composition modules are initialized using the composition times the
  uncertainty, which was failing for -999 values because -999 * uncertainty
  does not equal -999 and was leading to the likelihood being evaluated.

Thanks to the scamp example for bringing these errors to our attention.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: FIMS
 Title: The Fisheries Integrated Modeling System
-Version: 0.3.0.0
+Version: 0.3.0.1
 Authors@R: c(
     person(c("Kelli", "F."), "Johnson", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-5149-451X")),

R/distribution_formulas.R

@@ -54,7 +54,8 @@ check_distribution_validity <- function(args) {
     bad <- names(check_present[unlist(check_present)])
     abort_bullets <- c(
       abort_bullets,
-      "x" = "{.var {bad}} {?is/are} missing from {.var args}."
+      "x" = "{.var {bad}} {cli::qty(length(bad))} {?is/are} missing from
+             {.var args}."
     )
     # Abort early because not all of the necessary items were in args
     cli::cli_abort(abort_bullets)
@@ -107,14 +108,15 @@ check_distribution_validity <- function(args) {
     abort_bullets <- c(
       abort_bullets,
       "x" = "{.var {elements_of_sd}} need to be present in sd.",
-      "i" = "Only {.code {names(sd)}} {?is/are} present."
+      "i" = "Only {.code {names(sd)}} {cli::qty(length(sd))} {?is/are} present."
     )
   } else {
-    if (!all(sd[["value"]] > 0)) {
+    if (!all(sd[["value"]] > 0, na.rm = TRUE)) {
       abort_bullets <- c(
         abort_bullets,
         "x" = "Values passed to {.var sd} are out of bounds.",
-        "i" = "Values passed to {.var sd} {?is/are} {.code {sd[['value']]}}.",
+        "i" = "Values passed to {.var sd} {cli::qty(length(sd[['value']]))}
+               {?is/are} {.code {sd[['value']]}}.",
         "i" = "All standard deviation (sd) values need to be positive."
       )
     }

R/initialize_modules.R

@@ -514,12 +514,16 @@ initialize_age_comp <- function(data, fleet_name) {
   # TODO: review the AgeComp interface, do we want to add
   # `age_comp_data` as an argument?
 
-  module$age_comp_data <- age_comp_data * dplyr::filter(
-    .data = as.data.frame(data@data),
-    name == fleet_name,
-    type == "age"
-  ) |>
-    dplyr::pull(uncertainty)
+  module$age_comp_data <- age_comp_data *
+    get_data(data) |>
+      dplyr::filter(
+        name == fleet_name,
+        type == "age"
+      ) |>
+      dplyr::mutate(
+        valid_n = ifelse(value == -999, 1, uncertainty)
+      ) |>
+      dplyr::pull(valid_n)
 
   return(module)
 }
@@ -558,12 +562,16 @@ initialize_length_comp <- function(data, fleet_name) {
   # TODO: review the LengthComp interface, do we want to add
   # `age_comp_data` as an argument?
 
-  module$length_comp_data <- length_comp_data * dplyr::filter(
-    .data = as.data.frame(data@data),
-    name == fleet_name,
-    type == "length"
-  ) |>
-    dplyr::pull(uncertainty)
+  module$length_comp_data <- length_comp_data *
+    get_data(data) |>
+      dplyr::filter(
+        name == fleet_name,
+        type == "length"
+      ) |>
+      dplyr::mutate(
+        valid_n = ifelse(value == -999, 1, uncertainty)
+      ) |>
+      dplyr::pull(valid_n)
 
   return(module)
 }

tests/testthat/_snaps/fimsfit.md

@@ -3,7 +3,7 @@
     Code
       print(result)
     Message
-      i FIMS model version: 0.3.0.0
+      i FIMS model version: 0.3.0.1
       i Total run time was 10 seconds
       i Number of parameters: total=1, fixed_effects=1, and random_effects=0
       i Maximum gradient= NA