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FIMS input data frame

Source: R/data_big.R
data_big.Rd

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. 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.

Usage

data_big

Format

A data frame with 2808 observations of 8 variables:

type

The type of input the row contains. Allowed types include age_comp, age_to_length_conversion, ageing_error, index, catch, length_bin, length_comp, and weight_at_age.

fleet

A character string providing the name of the information source that the input was collected from, e.g., "Trawl fishery" or "age_zero_survey". Entries can be NA for information that is not fleet/vessel specific.

age

An integer age. Entry can be NA if information pertains to multiple ages, e.g., total catch rather than catch of age-4 fish. In this dataset, ages start at one, therefore recruitment happens at age one not age zero.

length

A numeric length. Entry can be NA if information doesn't pertain to length. For length_comp, length_bin, and age_to_length_conversion rows, this is the lower edge of the length bin. A bin holds lengths from its lower edge up to the next lower edge. When growth is estimated in FIMS, the first bin also holds all smaller fish and the last bin holds all larger fish. With fixed age_to_length_conversion rows, those rows set what each bin holds. In this dataset, the bins are 50 mm wide, so length = 250 is the bin from 250 to 300 mm, and the conversion puts all fish under 50 mm in the first bin and all fish of 1100 mm or more in the last.

timing

The timing, i.e., year the data was collected.

observed

The observed measurement of interest.

unit

A character string specifying the units of observed. Allowed units for each data type are as follows. mt or number are used for index and catch data, with 1 unit per fleet for each type. mt is used for weight_at_age data. number or proportion are each viable units for the composition data, where the former is the preferred unit of measurement. proportion is also used for ageing_error data, the probability that a fish of a given true age is read as the age in age.

uncertainty

A character string with a right-handed formula specifying the distributional assumptions for the entry in observed. See FIMSFrame() for more information about this column. For ageing_error rows, the string is the true age, e.g., "5".

Source

https://github.com/NOAA-FIMS/Age_Structured_Stock_Assessment_Model_Comparison

See also