blimp.update: Blimp Input Updating

In misty: Miscellaneous Functions 'T. Yanagida'

Blimp Input Updating

Description

This function updates specific input command sections of a misty.object of type blimp to create an updated Blimp input file, run the updated input file by using the blimp.run() function, and print the updated Blimp output file by using the blimp.print() function.

Usage

blimp.update(x, update, file = "Blimp_Input_Update.imp", comment = FALSE,
             replace.inp = TRUE, blimp.run = TRUE, posterior = FALSE,
             folder = "Posterior_",
             format = c("csv", "csv2", "xlsx", "rds", "RData"),
             clear = TRUE, replace.out = c("always", "never", "modified"),
             Blimp = detect.blimp(),
             result = c("all", "default", "algo.options",  "data.info",
                        "model.info", "warn.mess", "out.model", "gen.param"),
             exclude = NULL, color = c("none", "blue", "violet"),
             style = c("bold", "regular"), not.result = TRUE,
             write = NULL, append = TRUE, check = TRUE, output = TRUE)

Arguments

x	misty.object object of type blimp.
update	a character vector containing the updated input command sections.
file	a character string indicating the name of the updated Blimp input file with or without the file extension .imp, e.g., "Blimp_Input_Update.imp" or "Blimp_Input_Update.imp".
comment	logical: if FALSE (default), comments (i.e., text after the # symbol) are removed from the input text specified in the argument x.
replace.inp	logical: if TRUE (default), an existing input file will be replaced.
blimp.run	logical: if TRUE, the input file specified in the argument file containing the input text specified in the argument x is run using the blimp.run() function.
posterior	logical: if TRUE, the posterior distribution including burn-in and post-burn-in phase for all parameters are saved in long format in a file called posterior.* in the folder specified in the argument folder and .imp file name in the format specified in the argument format.
folder	a character string indicating the prefix of the folder for saving the posterior distributions. The default setting is folder = "Posterior_".
format	a character vector indicating the file format(s) for saving the posterior distributions, i.e., "csv" (default) for write.csv(), "csv2" for write.csv2(), "xlsx" for write.xlsx(), "rds" for saveRDS(), and "RData" for write().
clear	logical: if TRUE (default), the console is cleared after estimating each model.
replace.out	a character string for specifying three settings: "always" (default), which runs all models, regardless of whether an output file for the model exists, "never", which does not run any model that has an existing output file, and "modified", which only runs a model if the modified date for the input file is more recent than the output file modified date.
Blimp	a character string for specifying the name or path of the Blimp executable to be used for running models. This covers situations where Blimp is not in the system's path, or where one wants to test different versions of the Blimp program. Note that there is no need to specify this argument for most users since it has intelligent defaults.
result	a character vector specifying Blimp result sections included in the output (see 'Details' in the blimp.print function).
exclude	a character vector specifying Blimp input command or result sections excluded from the output (see 'Details' in the blimp.print function).
color	a character vector with two elements indicating the colors used for headers (e.g., "ALGORITHMIC OPTIONS SPECIFIED:"), and for the header Outcome Variable: and Missing predictor: including variables names.
style	a character vector with two elements indicating the style used for headers (e.g., "ALGORITHMIC OPTIONS SPECIFIED:"), and for the header Outcome Variable: and Missing predictor: including variables names, i.e., regular, for regular text, bold for bold text, italic, for italic text, and underline for underline text.
not.result	logical: if TRUE (default), character vector indicating the result sections not requested are shown on the console.
write	a character string naming a file for writing the output into a text file with file extension ".txt" (e.g., "Output.txt").
append	logical: if TRUE (default), output will be appended to an existing text file with extension .txt specified in write, if FALSE existing text file will be overwritten.
check	logical: if TRUE (default), argument specification is checked.
output	logical: if TRUE (default), output is shown on the console by using the function blimp.print().
data	a matrix or data frame from which the variables names for the section VARIABLES are extracted when using the ... specification in the VARIABLES section.

Details

Bimp Input Sections

The function is used to update following Blimp input sections:

• DATA

• VARIABLES

• CLUSTERID

• ORDINAL

• NOMINAL

• COUNT

• WEIGHT

• MISSING

• LATENT

• RANDOMEFFECT

• TRANSFORM

• BYGROUP

• FIXED

• CENTER

• MODEL

• SIMPLE

• PARAMETERS

• TEST

• FCS

• SIMUALTE

• SEED

• BURN

• ITERATIONS

• CHAINS

• NIMPS

• THIN

• OPTIONS

• OUTPUT

• SAVE

The ---; Specification

The ---; specification is used to remove entire sections (e.g., CENTER: ---;) from the Blimp input. Note that ---; including the semicolon ; needs to be specified, i.e., --- without the semicolon ; will result in an error message.

Value

Returns an object of class misty.object, which is a list with following entries:

call	function call
type	type of analysis
x	misty.object object of type blimp
update	a character vector containing the updated Blimp input command sections
args	specification of function arguments
write	updated write command sections
result	list with result sections (result)

Author(s)

Takuya Yanagida

References

Keller, B. T., & Enders, C. K. (2023). Blimp user’s guide (Version 3). Retrieved from www.appliedmissingdata.com/blimp

See Also

blimp.run, blimp.print, blimp.plot, blimp.bayes

Examples

## Not run: 

#----------------------------------------------------------------------------
# Example 1a: Update BURN and ITERATIONS section

# Specify Blimp input
input <- '
DATA: data1.csv;
ORDINAL: d;
MISSING: 999;
FIXED: d;
CENTER: x1 x2;
MODEL: y ~ x1 x2 d;
SEED: 90291;
BURN: 1000;
ITERATIONS: 10000;
'

# Run Blimp input
mod0 <- blimp(input, file = "Ex4.3.imp", clear = FALSE)

# Update sections
update1 <- '
BURN: 5000;
ITERATIONS: 20000;
'

# Run updated Blimp input
mod1 <- blimp.update(mod0, update1, file = "Ex4.3_update1.imp")

#----------------------------------------------------------------------------
# Example 1b: Remove CENTER section

# Remove section
update2 <- '
CENTER: ---;
'

# Run updated Blimp input
mod2 <- blimp.update(mod1, update2, file = "Ex4.3_update2.imp")

## End(Not run)

misty documentation built on Oct. 24, 2024, 5:10 p.m.