Package 'stanedit'

Add a block to a stan model

Description

Add a block to a stan model. If that block exists, it will be removed first.

Usage

add_block(x, name, lines)

Arguments

x	a stanedit object
name	name of the block
lines	character vector, lines in the block

Value

a stanedit object containing the new block

Examples

model_file_name <- system.file(package = "stanedit", "regression.stan")
reg <- stanedit(filename = model_file_name)
reg <- add_block(
  reg,
  "transformed parameters",
  c("real gamma;", "gamma = alpha * beta;")
)

---

Check if two models are equal

Description

Ignores differences in the model name.

Usage

## S3 method for class 'stanedit'
e1 == e2, ...

Arguments

e1	a stanedit
e2	a stanedit
...	ignored

Value

TRUE or FALSE, depending on whether the models are equal or not

Examples

model_file_name <- system.file(package = "rbi", "PZ.bi")
PZ <- stanedit(filename = model_file_name)
PZ == PZ # TRUE

---

Subset and replace model lines

Description

Extracts a subset of lines from the model and assigns new character strings.

Usage

## S3 replacement method for class 'stanedit'
x[i, ...] <- value

Arguments

x	A stanedit
i	A vector of line numbers
...	ignored
value	A vector of the same length as i, containing the replacement strings

Value

the updated stanedit object

Examples

model_file_name <- system.file(package = "rbi", "PZ.bi")
PZ <- stanedit(filename = model_file_name)
PZ[3:4] <- c("const e = 0.4", "const m_l = 0.05")

---

Subset model lines

Description

Extracts a subset of lines from the model.

Usage

## S3 method for class 'stanedit'
x[i, ...]

Arguments

x	A stanedit
i	A vector of line numbers
...	ignored

Value

a character string of the extracted model lines(s)

Examples

model_file_name <- system.file(package = "rbi", "PZ.bi")
PZ <- stanedit(filename = model_file_name)
PZ[3:4]

---

Get the contents of a block in a stan model

Description

Returns the contents of a block in a stan model as a character vector of lines.

Usage

get_block(x, name, shell = FALSE)

Arguments

x	a stanedit object
name	name of the block
shell	if TRUE (default:FALSE), will return the shell (i.e., the definition of the block) as well as content; this is useful, e.g., to see options passed to a transition or ode block

Value

a character vector of the lines in the block, or an empty character vector if the block is not found

Examples

model_file_name <- system.file(package = "stanedit", "regression.stan")
reg <- stanedit(filename = model_file_name)
get_block(reg, "parameters")

---

Get the declaration of a variable in a stan model

Description

Returns the contents of a block in a stan model as a character vector of lines.

Usage

get_declaration(x, name)

Arguments

x	a stanedit object
name	name of the variable

Value

a character vector of length 1 with the line where the variable is declared, or an empty character vector if no declaration is found

Examples

model_file_name <- system.file(package = "stanedit", "regression.stan")
reg <- stanedit(filename = model_file_name)
get_declaration(reg, "alpha")

---

Extract the variables declared in a stan model

Description

Extract the variables declared in a stan model

Usage

get_vars(x, block)

Arguments

x	a stanedit object
block	character (optional), the block or blocks in which to search; by default the whole model will be searched

Value

a character vector of variable names

Examples

model_file_name <- system.file(package = "stanedit", "regression.stan")
reg <- stanedit(filename = model_file_name)
get_vars(reg, "parameters")

---

Insert lines in a stan model

Description

Inserts one or more lines into a libbi model. If one of before or after is given, the line(s) will be inserted before or after a given line number or block name, respectively. If one of at_beginning of or at_end_of is given, the lines will be inserted at the beginning/end of the block, respectively.

Usage

insert_lines(x, lines, before, after, at_beginning_of, at_end_of)

Arguments

x	a stanedit object
lines	vector or line(s)
before	line number before which to insert line(s)
after	line number after which to insert line(s)
at_beginning_of	block at the beginning of which to insert lines(s)
at_end_of	block at the end of which to insert lines(s)

Value

the updated stanedit object

See Also

stanedit

Examples

model_file_name <- system.file(package = "stanedit", "regression.stan")
reg <- stanedit(filename = model_file_name)
insert_lines(reg, lines = "alpha ~ std_normal();", after = 12)

---

Move stan code elsewere

Description

Move stan code elsewere

Usage

move(x, lines, ...)

Arguments

x	a stanedit object
lines	vector of line numbers to move
...	arguments passed to insert_lines

Value

a character vector of variable names

Examples

model_file_name <- system.file(package = "stanedit", "regression.stan")
reg <- stanedit(filename = model_file_name)
move(reg, find_declaration(reg, "alpha"), at_end_of = "data")

---

Remove line(s) and/or block(s) in a libbi model

Description

Removes one or more lines in a libbi model.

Usage

remove_lines(x, what)

Arguments

x	a stanedit object
what	either a vector of line number(s) to remove, or a vector of blocks to remove (e.g., "parameters")

Value

the updated stanedit object

See Also

stanedit

Examples

model_file_name <- system.file(package = "stanedit", "regression.stan")
reg <- stanedit(filename = model_file_name)
reg <- remove_lines(reg, "model")

---

stanedit

Description

stanedit prepares stan model code for programmatically editing.

Usage

stanedit(object, filename)

Arguments

object	either a stanmodel object as generated by rstan::stan_model() or a CmdStanModel object as generated by cmdstanr::cmdstan_model(), or a character vector representing model code.
filename	name of a file containing model code, if object is not given.

Value

A {stanedit} object containing clean model code. This will have some formatting applied to it for further processing so line numbers may not correspond to the original model, and comments will be removed.

Examples

model_file_name <- system.file(package = "stanedit", "regression.stan")
reg <- stanedit(filename = model_file_name)
reg

---

Check if two models are unequal

Description

Ignores differences in the model name.

Usage

## S3 method for class 'stanedit'
e1 != e2, ...

Arguments

e1	a stanedit
e2	a stanedit
...	ignored

Value

TRUE or FALSE, depending on whether the models are equal or not

Examples

model_file_name <- system.file(package = "rbi", "PZ.bi")
PZ <- stanedit(filename = model_file_name)
PZ != PZ # FALSE

---

Writes a bi model to a file.

Description

Writes a bi model to a file given by filename. The extension '.bi' will be added if necessary.

Usage

write_model(x, filename)

Arguments

x	a stanedit object
filename	name of the file to be written

Value

the return value of the writeLines call.

See Also

stanedit

Examples

model_file_name <- system.file(package = "stanedit", "regression.stan")
reg <- stanedit(filename = model_file_name)
new_file_name <- tempfile("reg", fileext = ".stan")
write_model(reg, new_file_name)

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