qenv

Introduction to `qenv`

A qenv is an R object which contains code and an environment and can be used to create reproducible outputs.

Initialization

The qenv() function serves as the gateway to create an initial qenv object:

library(teal.code)

# create a new qenv object
empty_qenv <- qenv()
print(empty_qenv)

## <environment: 0x6313ba3ae010> [L]
## Parent: <environment: package:teal.code>

`qenv` basic usage

The eval_code() function executes code within a qenv environment, yielding a new qenv object as the output.

library(magrittr)

# evaluate code in qenv
my_qenv <- eval_code(empty_qenv, "x <- 2")
print(my_qenv)

## <environment: 0x6313bd23cf08> [L]
## Parent: <environment: package:magrittr>
## Bindings:
## • x: <dbl> [L]

get_env(my_qenv)

## <environment: 0x6313bd23cf08>

q1 <- eval_code(my_qenv, "y <- x * 2") %>% eval_code("z <- y * 2")

# my_qenv still contains only x
print(my_qenv)

## <environment: 0x6313bd23cf08> [L]
## Parent: <environment: package:magrittr>
## Bindings:
## • x: <dbl> [L]

ls(get_env(my_qenv))

## [1] "x"

# q1 contains x, y and z
print(q1)

## <environment: 0x6313be287e70> [L]
## Parent: <environment: package:magrittr>
## Bindings:
## • x: <dbl> [L]
## • y: <dbl> [L]
## • z: <dbl> [L]

ls(get_env(q1))

## [1] "x" "y" "z"

The same result can be achieved with the within method for the qenv class.

q2 <- within(my_qenv, y <- x * 2) %>% within(z <- y * 2)
print(q2)

## <environment: 0x6313bec382c0> [L]
## Parent: <environment: package:magrittr>
## Bindings:
## • x: <dbl> [L]
## • y: <dbl> [L]
## • z: <dbl> [L]

To extract objects from a qenv, use [[; this is particularly useful for displaying them in a shiny app. You can retrieve the code used to generate the qenv using the get_code() function.

print(q2[["y"]])

## [1] 4

cat(get_code(q2))

## x <- 2
## y <- x * 2
## z <- y * 2

Substitutions

In some cases, one may want to substitute some elements of the code before evaluation. Consider a case when a subset of iris is defined by an input value.

q <- qenv()
q <- eval_code(q, quote(i <- subset(iris, Species == "setosa")))
q <- eval_code(q, substitute(
  ii <- subset(iris, Species == species),
  env = list(species = "versicolor")
))
input_value <- "virginica"
q <- eval_code(q, substitute(
  iii <- subset(iris, Species == species),
  env = list(species = input_value)
))

summary(q[["i"]]$Species)

##     setosa versicolor  virginica 
##         50          0          0

summary(q[["ii"]]$Species)

##     setosa versicolor  virginica 
##          0         50          0

summary(q[["iii"]]$Species)

##     setosa versicolor  virginica 
##          0          0         50

A more convenient way to pass code with substitution is to use the within method.

qq <- qenv()
qq <- within(qq, i <- subset(iris, Species == "setosa"))
qq <- within(qq, ii <- subset(iris, Species == species), species = "versicolor")
input_value <- "virginica"
qq <- within(qq, iii <- subset(iris, Species == species), species = input_value)

summary(qq[["i"]]$Species)

##     setosa versicolor  virginica 
##         50          0          0

summary(qq[["ii"]]$Species)

##     setosa versicolor  virginica 
##          0         50          0

summary(qq[["iii"]]$Species)

##     setosa versicolor  virginica 
##          0          0         50

See ?qenv for more details.

Combining `qenv` objects

Given a pair of qenv objects, you may be able to “join” them, creating a new qenv object encompassing the union of both environments, along with the requisite code for reproduction:

common_q <- eval_code(qenv(), quote(x <- 1))

x_q <- eval_code(common_q, quote(y <- 5))
y_q <- eval_code(common_q, quote(z <- 5))

join_q <- join(x_q, y_q)

print(join_q)

## <environment: 0x6313be25f560>
## Parent: <environment: package:magrittr>
## Bindings:
## • x: <dbl>
## • y: <dbl>
## • z: <dbl>

ls(get_env(join_q))

## [1] "x" "y" "z"

The feasibility of joining qenv objects hinges on the contents of the environments and the code’s order. Refer to the function documentation for further details.

Warnings and messages in `qenv` objects

In cases where warnings or messages arise while evaluating code within a qenv environment, these are captured and stored within the qenv object. Access these messages and warnings using the @ operator.

q_message <- eval_code(qenv(), quote(message("this is a message")))
q_message@messages

## [1] "> this is a message\n"

q_warning <- eval_code(qenv(), quote(warning("and this is a warning")))
q_warning@warnings

## [1] "> and this is a warning\n"

If a particular line of code doesn’t trigger any warnings or messages, the corresponding message/warning value will be an empty string.

q_message@warnings

## [1] ""

q_warning@messages

## [1] ""

Additionally, a helper function, get_warnings(), is available to generate a formatted string comprising the warnings and the code responsible for generating them. It returns NULL when no warnings are present.

Utilizing `qenv` inside `shiny` applications

These functions can be seamlessly integrated into shiny applications to produce reproducible outputs. In the example below, the rcode section showcases the code employed for generating the output.

When employing a qenv to evaluate code, should an error occur, an object of type qenv.error is generated. This object can be utilized wherever a qenv object is used, alleviating the need for code alterations to handle these errors. Select the error_option in the example below to witness qenv error handling in action.

library(shiny)
library(magrittr)
# create an initial qenv with the data in
data_q <- qenv() %>% eval_code("iris_data <- iris")

ui <- fluidPage(
  radioButtons(
    "option", "Choose a column to plot:",
    c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width", "error_option")
  ),
  verbatimTextOutput("rcode"),
  plotOutput("plot")
)

server <- function(input, output, session) {
  # create a qenv containing the reproducible output
  output_q <- reactive({
    req(input$option)
    eval_code(
      data_q,
      bquote(p <- hist(iris_data[, .(input$option)]))
    )
  })

  # display output
  output$plot <- renderPlot(output_q()[["p"]])
  # display code
  output$rcode <- renderText(get_code(output_q()))
}

if (interactive()) {
  shinyApp(ui, server)
}

`qenv` and `teal` applications

The versatile qenv object can seamlessly integrate into teal modules. Explore the teal vignette Creating Custom Modules for detailed guidance.

NEST coreDev

Introduction to qenv

Initialization

qenv basic usage

Substitutions

Combining qenv objects

Warnings and messages in qenv objects