gadget_update.gadgetstock: Update comonents of a gadgetstock object

In Hafro/rgadget: Tools to Create and Maintain Gadget Models

Update comonents of a gadgetstock object

Description

Replace components of a gadgetstock with either new values or or content derived from an MFDB query.

Usage

## S3 method for class 'gadgetstock'
gadget_update(gf, component, ...)

Arguments

gf	The gadgetfile object to update
component	The component to update, or 'stock' to update the initial values
...	Either 0, data = (mfdb_query), or keys to update. See details. If ... is 0, then the component is replaced with "doesgrow 0", for instance. If ... is data = mfdb_query, then the component is generated based on the data. How depends in which component: stock The query should contain age & length columns, inserts min/max for both refweight The query should contain age & length columns, inserted into refweight file initialconditions The query should contain area, age, length, number, mean columns doesrenew The query should contain year, step, area, age, length, number, mean columns Finally, any other value of ... will update the relevant keys/values in that component. naturalmortality is slightly different. It takes a single vector with one value per-age-group. It will be pre-populated with 0.2 for each age group. doesgrow / growth can be populated with default values with gadget_update(gs, 'growth', 1) gadget_update('refweight', data = data.frame(length = ..., weight = ...)) will also update minlength/maxlength/dl gadget_update('refweight', data = data.frame(length = ..., alpha = ..., beta = ...)) will generate lengths via alpha * length^beta doesmature / maturation will populate the maturityfile data file with all given parameters apart from maturityfunction, e.g. gadget_update('maturation',maturityfunction = 'constant', maturestocksandratios = c( ... ), coefficients = c( ... )) doesrenew / recruitment can be populated from MFDB queries, e.g. gadget_update('doesrenew', number = data)

Examples

## Not run: 
library(magrittr)  # import %>% function
path <- './model'
gadgetstock('codimm', path, missingOkay = TRUE) %>%  # Create a skeleton if missing
   gadget_update('stock', minage = 2, maxage = 4) %>%
   gadget_update('stock', stockname = 'codmat') %>%  # Will change the name of the file we write
   gadget_update('doesmigrate', yearstepfile = gadgetfile('data/yearstepfile', components = list(
                                  data.frame(year = 1998, step = 1:4, 
                                             matrix = 'codmat-migration')))) %>%
   gadget_update('doesrenew', 0) %>%
   write.gadget.file(path)
   
## End(Not run)

Hafro/rgadget documentation built on July 21, 2022, 8:38 a.m.