Adds fits to length on R side

Still need to check for when lengths are present and deal
with those errors

NAMESPACE

@@ -11,6 +11,7 @@ export(EWAAgrowth)
 export(FIMSFrame)
 export(Fleet)
 export(Index)
+export(LengthComp)
 export(LogisticMaturity)
 export(LogisticSelectivity)
 export(Parameter)
@@ -38,9 +39,11 @@ export(log_error)
 export(log_info)
 export(log_warning)
 export(lognormal)
+export(m_age_to_length_conversion)
 export(m_agecomp)
 export(m_index)
 export(m_landings)
+export(m_lengthcomp)
 export(m_weight_at_age)
 export(multinomial)
 export(run_gtest)
@@ -54,6 +57,7 @@ exportMethods(Summary)
 exportMethods(m_agecomp)
 exportMethods(m_index)
 exportMethods(m_landings)
+exportMethods(m_lengthcomp)
 import(methods)
 import(stats)
 importFrom(Rcpp,sourceCpp)

R/distribution_formulas.R

@@ -167,7 +167,8 @@ get_expected_name <- function(family, data_type) {
     data_type == "index" &&
       grepl("lognormal|gaussian", family_string) &&
       link_string == "identity" ~ "expected_index",
-    grepl("comp", data_type) ~ "proportion_catch_numbers_at_age"
+    grepl("agecomp", data_type) ~ "proportion_catch_numbers_at_age",
+    grepl("lengthcomp", data_type) ~ "proportion_catch_numbers_at_length",
   )
   # Check combination of entries was okay and led to valid name
   if (is.na(expected_name)) {

R/fimsframe.R

@@ -18,6 +18,8 @@ setClass(
     n_years = "integer",
     ages = "numeric",
     n_ages = "integer",
+    lengths = "numeric",
+    n_lengths = "integer",
     weight_at_age = "data.frame",
     start_year = "integer",
     end_year = "integer"
@@ -96,6 +98,22 @@ setMethod(
   function(x) FIMSFrame(x)@n_ages
 )
 
+setGeneric("get_lengths", function(x) standardGeneric("get_lengths"))
+setMethod("get_lengths", "FIMSFrame", function(x) x@lengths)
+setMethod(
+  "get_lengths",
+  "data.frame",
+  function(x) FIMSFrame(x)@lengths
+)
+
+setGeneric("n_lengths", function(x) standardGeneric("n_lengths"))
+setMethod("n_lengths", "FIMSFrame", function(x) x@n_lengths)
+setMethod(
+  "n_lengths",
+  "data.frame",
+  function(x) FIMSFrame(x)@n_lengths
+)
+
 setGeneric("weight_at_age", function(x) standardGeneric("weight_at_age"))
 setMethod("weight_at_age", "FIMSFrame", function(x) x@weight_at_age)
 setMethod(
@@ -203,6 +221,72 @@ setMethod(
   }
 )
 
+#' Get the length-composition data to be used in the model
+#'
+#' @param x The object containing the length-composition data.
+#' @param fleet_name The name of the fleet for the length-composition data.
+#' @export
+setGeneric(
+  "m_lengthcomp",
+  function(x, fleet_name) standardGeneric("m_lengthcomp")
+)
+# Should we add name as an argument here?
+
+#' Get the length-composition data data to be used in the model
+#'
+#' @param x  The FIMSFrame containing length-composition data.
+#' @param fleet_name  The name of the fleet for the length-composition data.
+#' @export
+setMethod(
+  "m_lengthcomp",
+  "FIMSFrame",
+  function(x, fleet_name) {
+    dplyr::filter(
+      .data = x@data,
+      .data[["type"]] == "length",
+      .data[["name"]] == fleet_name
+    ) |>
+      dplyr::pull(.data[["value"]])
+  }
+)
+
+#' Get the age-to-length-conversion data to be used in the model
+#'
+#' @param x The object containing the age-to-length-conversion data (i.e.,
+#'   proportion of age "a" that are length "l").
+#' @param fleet_name A string specifying the name of the fleet that you want
+#'   data for.
+#' @export
+setGeneric(
+  "m_age_to_length_conversion",
+  function(x, fleet_name) standardGeneric("m_age_to_length_conversion")
+)
+
+#' Get the age-to-length-conversion matrix to be used in the model
+#'
+#' @param x The object containing the age-to-length-conversion data (i.e.,
+#'   proportion of age "a" that are length "l").
+#' @param fleet_name A string specifying the name of the fleet that you want
+#'   data for.
+setMethod(
+  "m_age_to_length_conversion",
+  "FIMSFrame",
+  function(x, fleet_name) {
+    if ("length" %in% colnames(x@data)) {
+      dplyr::filter(
+        .data = as.data.frame(x@data),
+        .data[["type"]] == "age-to-length-conversion",
+        .data[["name"]] == fleet_name
+      ) |>
+        dplyr::group_by(.data[["age"]], .data[["length"]]) |>
+        dplyr::summarize(
+          mean_value = mean(as.numeric(.data[["value"]]), na.rm = TRUE)
+        ) |>
+        dplyr::pull(as.numeric(.data[["mean_value"]]))
+    }
+  }
+)
+
 # Note: don't include setters, because for right now, we don't want users to be
 # setting ages, fleets, etc. However, we could allow it in the future, if there
 # is away to update the object based on changing the fleets?
@@ -394,8 +478,20 @@ FIMSFrame <- function(data) {
   # Make empty NA data frames in the format needed to pass to FIMS
   # Get the range of ages displayed in the data to use to specify population
   # simulation range
-  ages <- min(data[["age"]], na.rm = TRUE):max(data[["age"]], na.rm = TRUE)
+  if ("age" %in% colnames(data)) {
+    ages <- min(data[["age"]], na.rm = TRUE):max(data[["age"]], na.rm = TRUE)
+  } else {
+    ages <- numeric()
+  }
   n_ages <- length(ages)
+  if ("length" %in% colnames(data)) {
+    lengths <- min(data[["length"]], na.rm = TRUE):
+      max(data[["length"]], na.rm = TRUE)
+  } else {
+    lengths <- numeric()
+  }
+  n_lengths <- length(lengths)
+
   weight_at_age <- dplyr::filter(
     data,
     .data[["type"]] == "weight-at-age"
@@ -410,6 +506,8 @@ FIMSFrame <- function(data) {
     end_year = end_year,
     ages = ages,
     n_ages = n_ages,
+    lengths = lengths,
+    n_lengths = n_lengths,
     weight_at_age = weight_at_age
   )
   return(out)

R/initialize_modules.R

@@ -86,6 +86,15 @@ initialize_module <- function(parameters, data, module_name) {
         "log_Fmort"
       ))
     }
+
+    if (!"age-to-length-conversion" %in% fleet_types) {
+      module_fields <- setdiff(module_fields, c(
+        "age_length_conversion_matrix",
+        # Right now we can also remove nlengths because the default is 0
+        "nlengths",
+        "proportion_catch_numbers_at_length"
+      ))
+    }
   }
 
 
@@ -110,7 +119,8 @@ initialize_module <- function(parameters, data, module_name) {
   #     index and agecomp distributions. No input values are required.
 
   non_standard_field <- c(
-    "ages", "nages", "proportion_female", "estimate_prop_female",
+    "ages", "nages", "nlengths",
+    "proportion_female", "estimate_prop_female",
     "nyears", "nseasons", "nfleets", "estimate_log_devs", "weights",
     "is_survey", "estimate_q", "random_q"
   )
@@ -121,6 +131,7 @@ initialize_module <- function(parameters, data, module_name) {
         field,
         "ages" = ages(data),
         "nages" = n_ages(data),
+        "nlengths" = n_lengths(data),
         "proportion_female" = numeric(0),
         "estimate_prop_female" = TRUE,
         "nyears" = n_years(data),