Package 'teal.code'

Description

Combine two qenv objects by simple concatenate their environments and the code.

Usage

concat(x, y)

Arguments

Details

We recommend to use the join method to have a stricter control in case x and y contain duplicated bindings and code. RHS argument content has priority over the LHS one.

Value

qenv object.

Examples

q <- qenv()
q1 <- eval_code(q, expression(iris1 <- iris, mtcars1 <- mtcars))
q2 <- q1
q1 <- eval_code(q1, "iris2 <- iris")
q2 <- eval_code(q2, "mtcars2 <- mtcars")
qq <- concat(q1, q2)
get_code(qq)

Description

This function opens a PDF graphics device using grDevices::pdf to suppress the plot display in the IDE. The purpose of this function is to avoid opening graphic devices directly in the IDE.

Usage

dev_suppress(x)

Arguments

Details

The function uses base::on.exit to ensure that the PDF graphics device is closed (using grDevices::dev.off) when the function exits, regardless of whether it exits normally or due to an error. This is necessary to clean up the graphics device properly and avoid any potential issues.

Value

No return value, called for side effects.

Examples

dev_suppress(plot(1:10))

Description

The access of environment included in qenv@env allows to e.g. list object names included in qenv@env slot.

Usage

get_env(object)

Arguments

Value

An environment stored in qenv@env slot.

Examples

q <- qenv()
q1 <- within(q, {
  a <- 5
  b <- data.frame(x = 1:10)
})
get_env(q1)
ls(get_env(q1))

Description

Retrieve variables from the qenv environment.

Usage

get_var(object, var)

## S4 method for signature 'qenv'
x[[i]]

Arguments

Value

The value of required variable (var) within qenv object.

Examples

q <- qenv()
q1 <- eval_code(q, code = quote(a <- 1))
q2 <- eval_code(q1, code = "b <- a")
get_var(q2, "b")
q2[["b"]]

Description

Retrieve all warnings raised during code evaluation in a qenv.

Usage

get_warnings(object)

Arguments

Value

character containing warning information or NULL if no warnings.

Examples

data_q <- qenv()
data_q <- eval_code(data_q, "iris_data <- iris")
warning_qenv <- eval_code(
  data_q,
  bquote(p <- hist(iris_data[, .("Sepal.Length")], ff = ""))
)
cat(get_warnings(warning_qenv))

Description

Checks and merges two qenv objects into one qenv object.

Usage

join(x, y)

Arguments

Details

Any common code at the start of the qenvs is only placed once at the start of the joined qenv. This allows consistent behavior when joining qenvs which share a common ancestor. See below for an example.

There are some situations where join() cannot be properly performed, such as these three scenarios:

1. Both qenv objects contain an object of the same name but are not identical.

   Example:

   x <- eval_code(qenv(), expression(mtcars1 <- mtcars))
   y <- eval_code(qenv(), expression(mtcars1 <- mtcars['wt']))
   
   z <- join(x, y)
   # Error message will occur
   

   In this example, mtcars1 object exists in both x and y objects but the content are not identical. mtcars1 in the ⁠x qenv⁠ object has more columns than mtcars1 in the ⁠y qenv⁠ object (only has one column).

2. join() will look for identical ⁠@id⁠ values in both qenv objects. The index position of these ⁠@id⁠s must be the same to determine the evaluation order. Otherwise, join() will throw an error message.

   Example:

   common_q <- eval_code(qenv(), expression(v <- 1))
   x <- eval_code(
     common_q,
     "x <- v"
   )
   y <- eval_code(
     common_q,
     "y <- v"
   )
   z <- eval_code(
     y,
     "z <- v"
   )
   q <- join(x, y)
   join_q <- join(q, z)
   # Error message will occur
   
   # Check the order of evaluation based on the id slot
   shared_ids <- intersect(q@id, z@id)
   match(shared_ids, q@id) # Output: 1 3
   match(shared_ids, z@id) # Output: 1 2
   

   The error occurs because the index position of identical ⁠@id⁠ between the two objects is not the same.

3. The usage of temporary variable in the code expression could cause join() to fail.

   Example:

   common_q <- qenv()
   x <- eval_code(
     common_q,
     "x <- numeric(0)
      for (i in 1:2) {
        x <- c(x, i)
      }"
   )
   y <- eval_code(
     common_q,
     "y <- numeric(0)
      for (i in 1:3) {
        y <- c(y, i)
      }"
   )
   q <- join(x,y)
   # Error message will occur
   
   # Check the value of temporary variable i in both objects
   x@env$i # Output: 2
   y@env$i # Output: 3
   

   join() fails to provide a proper result because of the temporary variable i exists in both objects but has different value. To fix this, we can set i <- NULL in the code expression for both objects.

   common_q <- qenv()
   x <- eval_code(
     common_q,
     "x <- numeric(0)
      for (i in 1:2) {
        x <- c(x, i)
      }
      # dummy i variable to fix it
      i <- NULL"
   )
   y <- eval_code(
     common_q,
     "y <- numeric(0)
      for (i in 1:3) {
        y <- c(y, i)
      }
      # dummy i variable to fix it
      i <- NULL"
   )
   q <- join(x,y)
   

Value

qenv object.

Examples

q <- qenv()
q1 <- eval_code(q, expression(iris1 <- iris, mtcars1 <- mtcars))
q2 <- q1
q1 <- eval_code(q1, "iris2 <- iris")
q2 <- eval_code(q2, "mtcars2 <- mtcars")
qq <- join(q1, q2)
get_code(qq)

common_q <- eval_code(q, quote(x <- 1))
y_q <- eval_code(common_q, quote(y <- x * 2))
z_q <- eval_code(common_q, quote(z <- x * 3))
join_q <- join(y_q, z_q)
# get_code only has "x <- 1" occurring once
get_code(join_q)

Description

Create a qenv object and evaluate code in it to track code history.

Usage

qenv()

new_qenv(env = new.env(parent = parent.env(.GlobalEnv)), code = character())

eval_code(object, code)

get_code(object, deparse = TRUE, names = NULL, ...)

## S3 method for class 'qenv'
within(data, expr, ...)

Arguments

Details

qenv() instantiates a qenv with an empty environment. Any changes must be made by evaluating code in it with eval_code or within, thereby ensuring reproducibility.

new_qenv() ( and not recommended) can instantiate a qenv object with data in the environment and code registered.

eval_code evaluates given code in the qenv environment and appends it to the code slot. Thus, if the qenv had been instantiated empty, contents of the environment are always a result of the stored code.

get_code retrieves the code stored in the qenv. ... passes arguments to methods.

within is a convenience function for evaluating inline code inside the environment of a qenv. It is a method for the base generic that wraps eval_code to provide a simplified way of passing code. within accepts only inline expressions (both simple and compound) and allows for injecting values into expr through the ... argument: as name:value pairs are passed to ..., name in expr will be replaced with value.

Value

qenv and new_qenv return a qenv object.

eval_code returns a qenv object with expr evaluated or qenv.error if evaluation fails.

get_code returns the traced code (from ⁠@code⁠ slot) in the form specified by deparse.

within returns a qenv object with expr evaluated or qenv.error if evaluation fails.

Extracting dataset-specific code

When names is specified, the code returned will be limited to the lines needed to create the requested objects. The code stored in the ⁠@code⁠ slot is analyzed statically to determine which lines the objects of interest depend upon. The analysis works well when objects are created with standard infix assignment operators (see ?assignOps) but it can fail in some situations.

Consider the following examples:

Case 1: Usual assignments.

q1 <- qenv() |>
  within({
    foo <- function(x) {
      x + 1
    }
    x <- 0
    y <- foo(x)
  })
get_code(q1, names = "y")

x has no dependencies, so get_code(data, names = "x") will return only the second call.
y depends on x and foo, so get_code(data, names = "y") will contain all three calls.

Case 2: Some objects are created by a function's side effects.

q2 <- qenv() |>
  within({
    foo <- function() {
      x <<- x + 1
    }
    x <- 0
    foo()
    y <- x
  })
get_code(q2, names = "y")

Here, y depends on x but x is modified by foo as a side effect (not by reassignment) and so get_code(data, names = "y") will not return the foo() call.
To overcome this limitation, code dependencies can be specified manually. Lines where side effects occur can be flagged by adding "⁠# @linksto <object name>⁠" at the end.
Note that within evaluates code passed to expr as is and comments are ignored. In order to include comments in code one must use the eval_code function instead.

q3 <- qenv() |>
  eval_code("
    foo <- function() {
      x <<- x + 1
    }
    x <- 0
    foo() # @linksto x
    y <- x
  ")
get_code(q3, names = "y")

Now the foo() call will be properly included in the code required to recreate y.

Note that two functions that create objects as side effects, assign and data, are handled automatically.

Here are known cases where manual tagging is necessary:

• non-standard assignment operators, e.g. ⁠%<>%⁠

• objects used as conditions in if statements: ⁠if (<condition>)⁠

• objects used to iterate over in for loops: ⁠for(i in <sequence>)⁠

• creating and evaluating language objects, e.g. ⁠eval(<call>)⁠

Using language objects with within

Passing language objects to expr is generally not intended but can be achieved with do.call. Only single expressions will work and substitution is not available. See examples.

See Also

base::within(), get_var(), get_env(), get_warnings(), join(), concat()

Examples

# create empty qenv
qenv()

# create qenv with data and code (deprecated)
new_qenv(env = list2env(list(a = 1)), code = quote(a <- 1))
new_qenv(env = list2env(list(a = 1)), code = parse(text = "a <- 1", keep.source = TRUE))
new_qenv(env = list2env(list(a = 1)), code = "a <- 1")

# evaluate code in qenv
q <- qenv()
q <- eval_code(q, "a <- 1")
q <- eval_code(q, quote(library(checkmate)))
q <- eval_code(q, expression(assert_number(a)))

# retrieve code
q <- within(qenv(), {
  a <- 1
  b <- 2
})
get_code(q)
get_code(q, deparse = FALSE)
get_code(q, names = "a")

q <- qenv()
q <- eval_code(q, code = c("a <- 1", "b <- 2"))
get_code(q, names = "a")

# evaluate code using within
q <- qenv()
q <- within(q, {
  i <- iris
})
q <- within(q, {
  m <- mtcars
  f <- faithful
})
q
get_code(q)

# inject values into code
q <- qenv()
q <- within(q, i <- iris)
within(q, print(dim(subset(i, Species == "virginica"))))
within(q, print(dim(subset(i, Species == species)))) # fails
within(q, print(dim(subset(i, Species == species))), species = "versicolor")
species_external <- "versicolor"
within(q, print(dim(subset(i, Species == species))), species = species_external)

# pass language objects
expr <- expression(i <- iris, m <- mtcars)
within(q, expr) # fails
do.call(within, list(q, expr))

exprlist <- list(expression(i <- iris), expression(m <- mtcars))
within(q, exprlist) # fails
do.call(within, list(q, do.call(c, exprlist)))

Description

Prints the qenv object.

Usage

## S4 method for signature 'qenv'
show(object)

Arguments

Value

object, invisibly.

Examples

q <- qenv()
q1 <- eval_code(q, expression(a <- 5, b <- data.frame(x = 1:10)))
q1