SS_read: Read all Stock Synthesis input files for a model

In r4ss/r4ss: R Code for Stock Synthesis

Read all Stock Synthesis input files for a model

Description

Read all the input files for a Stock Synthesis model into R as a list object. These files will be in a single directory on your machine, i.e., dir. Functionality comes from the ⁠r4ss::SS_read*()⁠ functions. This function simplifies the number of lines of code you need to write by using all of the read functions to read in the starter, control, data, and forecast files and if requested, the weight-at-age file. The starter file is helpful because it provides names for the control and data files.

Usage

SS_read(dir = getwd(), ss_new = FALSE, verbose = FALSE)

Arguments

dir	A file path to the directory of interest or a raw github URL (see example). The default is the current working directory, dir = getwd().
ss_new	A logical that controls if the .ss_new files or the original input files are read in. The default is to read the original files.
verbose	A logical value specifying if output should be printed to the screen.

Value

An invisible list is returned. The first element (dir) is the directory that was provided in the argument dir. The second element (path) is the result of normalizePath(dir), which gives the full path. The remaining four to six elements are list objects from reading in the following input files:

• data

• control

• starter

• forecast

• wtatage (will be NULL if not required by the model)

• par (will be NULL if not required by model or if control and par do not match)

Author(s)

Ian G. Taylor, Kelli F. Johnson

See Also

SS_write() can be used to write the input files using the list created by this function.

Other read/write functions: SS_readctl(), SS_readdat(), SS_readforecast(), SS_readstarter(), SS_write(), SS_writectl(), SS_writedat(), SS_writeforecast(), SS_writestarter()

Examples

# Read in the 'simple' example model stored in {r4ss}
inputs <- SS_read(
  dir = system.file("extdata", "simple_small", package = "r4ss")
)
# Read in an example from GitHub stored in ss3-user-examples,
# wrapped in `dontrun` because it requires an Internet connection
## Not run: 
webexample <- SS_read(dir = file.path(
  "https://raw.githubusercontent.com",
  "nmfs-ost",
  "ss3-user-examples",
  "main",
  "model_files",
  "simple_long_wtatage"
))

## End(Not run)

r4ss/r4ss documentation built on April 30, 2024, 4:42 a.m.