_ in type for data and change to data_big

.covrignore

@@ -3,3 +3,5 @@
 # Exclude a specific file
 R/zzz.R
 R/check_fims.R
+R/use-gtest-template.R
+R/use-testthat-template.R

NAMESPACE

@@ -76,6 +76,7 @@ export(m_landings)
 export(m_lengthcomp)
 export(m_weight_at_age)
 export(multinomial)
+export(plot)
 export(set_fixed)
 export(set_log_throw_on_error)
 export(set_random)

R/create_default_configurations.R

@@ -60,8 +60,8 @@ utils::globalVariables(c(
 #'
 #' @examples
 #' # Load the example dataset and create a FIMS data frame
-#' data("data1")
-#' fims_frame <- FIMSFrame(data1)
+#' data("data_big")
+#' fims_frame <- FIMSFrame(data_big)
 #'
 #' # Create the default model configuration tibble
 #' default_configurations <- create_default_configurations(data = fims_frame)
@@ -106,8 +106,8 @@ create_default_configurations <- function(data, model_family = c("catch_at_age")
     dplyr::mutate(module_type = snake_to_pascal(type)) |>
     # Set module_type to NA for weight-at-age and age-to-length-conversion
     dplyr::mutate(module_type = dplyr::case_when(
-      type == "weight-at-age" ~ NA_character_,
-      type == "age-to-length-conversion" ~ NA_character_,
+      type == "weight_at_age" ~ NA_character_,
+      type == "age_to_length_conversion" ~ NA_character_,
       TRUE ~ module_type
     )) |>
     # Remove any combinations where the type did not match a known module.

R/create_default_parameters.R

@@ -68,8 +68,8 @@ utils::globalVariables(c(
 #' @examples
 #' \dontrun{
 #' # Load the example dataset and create a FIMS data frame
-#' data("data1")
-#' fims_frame <- FIMSFrame(data1)
+#' data("data_big")
+#' fims_frame <- FIMSFrame(data_big)
 #'
 #' # Create default configurations
 #' default_configurations <- create_default_configurations(fims_frame)

R/data1.R → R/data_.R

@@ -1,21 +1,21 @@
 #' FIMS input data frame
 #'
-#' A dataset containing information necessary to run an age-structured stock
+#' A data frame containing the information needed to run an age-structured stock
 #' assessment model in FIMS. This data was generated using
 #' the `ASSAMC` package written for the [model comparison project](
 #' www.github.com/NOAA-FIMS/Age_Structured_Stock_Assessment_Model_Comparison).
-#' The source code to make this dataset is in `data-raw/data1.R` which is on
-#' Github, but won't be local because it's in the .Rbuildignore file.
+#' The source code to make this dataset is in `data-raw/data_big.R` which is on
+#' GitHub but will not be in your local installation because it is in the
+#' .Rbuildignore file.
 #'
 #' @format
-#' A data frame with `r NROW(data1)` observations of `r NCOL(data1)`
+#' A data frame with `r NROW(data_big)` observations of `r NCOL(data_big)`
 #' variables:
 #' \describe{
-#'   \item{type}{The type of data the row contains. Allowed types
-#'   include `age`, `length`, `index`, `landings`, `age-to-length-conversion`,
-#'     and `weight-at-age` data.}
+#'   \item{type}{The type of input the row contains. Allowed types include
+#'   `r glue::glue_collapse(fims_input_types, sep = ", ", last = ", and ")`.}
 #'   \item{name}{A character string providing the name of the information source
-#'     that the data was collected from, e.g., `"Trawl fishery"`.}
+#'     that the input was collected from, e.g., `"Trawl fishery"`.}
 #'   \item{age}{An integer age. Entry can be `NA` if information pertains to
 #'     multiple ages, e.g., total landings rather than landings of age-4 fish.}
 #'   \item{length}{A numeric length. Entry can be `NA` if information doesn't
@@ -24,7 +24,7 @@
 #'   \item{value}{The measurement of interest.}
 #'   \item{unit}{A character string specifying the units of `value`. Allowed
 #'     units for each data type are as follows. `mt` is used for `index`,
-#'     `landings`, and `weight-at-age` data. `number` or `proportion` are each
+#'     `landings`, and `weight_at_age` data. `number` or `proportion` are each
 #'     viable units for the composition data, where the former is the preferred
 #'     unit of measurement.}
 #'   \item{uncertainty}{A real value providing a measurement of uncertainty
@@ -35,4 +35,4 @@
 #' }
 #' }
 #' @source \url{www.github.com/NOAA-FIMS/Age_Structured_Stock_Assessment_Model_Comparison}
-"data1"
+"data_big"

R/fims_input_types.R

@@ -0,0 +1,9 @@
+#' Vector of acceptable FIMS input types
+#'
+#' A vector of strings that define which input types are allowed in the column
+#' labeled `type` in the data slot of a FIMSFrame object. Strings are composed
+#' of words separated by underscores, e.g., `"weight_at_age"`.
+#'
+#' @format
+#' A vector of strings.
+"fims_input_types"

R/fimsfit.R

@@ -5,11 +5,14 @@ utils::globalVariables(c(
   "estimate", "estimate.x", "estimate.y",
   "initial", "initial.x", "initial.y",
   "derived_quantity_id",
-  "distribution", "module_type", "n", "type_id", "values",
+  "distribution", "gradient",
+  "log_like_cv",
+  "module_type", "n", "type_id", "values",
   "module_name.x", "module_name.y",
   "module_id.x", "module_id.y",
   "module_id_init",
-  "module_type.x", "module_type.y"
+  "module_type.x", "module_type.y",
+  "unique_id"
 ))
 
 # Developers: ----