Class constructors for FIMSFrame and associated child classes

All constructor functions take a single input and build an object specific to the needs of each model type within FIMS. FIMSFrame is the parent class. Future, associated child classes will have the additional slots needed for different types of models.

Usage

FIMSFrame(data)

Arguments

data

A data.frame that contains the necessary columns to construct a FIMSFrame-class object. Currently, those columns are type, name, age, length, datestart, dateend, value, unit, and uncertainty. See the data1 object in FIMS, e.g., data(data1, package = "FIMS").

Value

An object of the S4 class FIMSFrame class, or one of its child classes, is validated and then returned. All objects will at a minimum have a slot called data to store the input data frame. Additional slots are dependent on the child class. Use methods::showClass() to see all available slots.

Details

data

The input data are both sorted and expanded before returning them in the data slot.

Sorting

It is important that the order of the rows in the data are correct but it is not expected that the user will do this. Instead, the returned data are sorted using dplyr::arrange() before placing them in the data slot. Data are first sorted by data type, placing all weight-at-age data next to other weight-at-age data and all landings data next to landings data. Thus, age-composition data will come first because their type is "age" and "a" is first in the alphabet. All other types will follow according to their order in the alphabet. Next, within each type, data are organized by fleet. So, age-composition information for fleet1 will come before survey1. Next, all data within type and fleet are arranged by datestart, e.g., by year. That is the end of the sorting for time series data like landings and indices. The biological data are further sorted by bin. Thus, age-composition information will be arranged as follows:

type	name	datestart	age	value
age	fleet1	2022-01-01	1	0.3
age	fleet1	2022-01-01	2	0.7
age	fleet1	2023-01-01	1	0.5

Length composition-data are sorted the same way but by length bin instead of by age bin. It becomes more complicated for the age-to-length-conversion data, which are sorted by type, name, datestart, age, and then length. So, a full set of length, e.g., length 10, length 20, length 30, etc., is placed together for a given age. After that age, another entire set of length information will be provided for that next age. Once the year is complete for a given fleet then the next year will begin.