Programming Concepts and Conventions

Introduction

This vignette aims to discuss some of the common programming concepts and conventions that have been adopted within the admiral family of packages. It is intended to be a user-facing version of the Programming Strategy vignette, but users can also read the latter after becoming more familiar with the package to expand further on any topics of interest. For some of common admiral FAQ, visit the corresponding FAQ page provided in the same drop down menu as this vignette.

Input and Output

It is expected that the input dataset is not grouped. Otherwise an error is issued.

The output dataset is ungrouped. The observations are not ordered in a dedicated way. In particular, the order of the observations of the input dataset may not be preserved.

`{admiral}` Functions and Options

As a general principle, the behavior of the admiral functions is only determined by their input, not by any global object, i.e. all inputs like datasets, variable names, options, etc. must be provided to the function by arguments. Correspondingly, in general functions do not have any side-effects like creating or modifying global objects, printing, writing files, etc.

An exception to the above principle is found in our approach to package options (see get_admiral_option() and set_admiral_options()), which allow for user-defined defaults on commonly used function arguments. For instance, the option subject_keys is currently pre-defined as exprs(STUDYID, USUBJID), but can be modified using set_admiral_options(subject_keys = exprs(...)) at the top of a script.

For a full discussion on admiral Inputs, Outputs and Options, see this section on our developer-facing Programming Strategy.

Handling of Missing Values

When using the haven package to read SAS datasets into R, SAS-style character missing values, i.e. "", are not converted into proper R NA values. Rather they are kept as is. This is problematic for any downstream data processing as R handles "" just as any other string. Thus, before any data manipulation is being performed SAS blanks should be converted to R NAs using admiral’s convert_blanks_to_na() function, e.g.

dm <- haven::read_sas("dm.sas7bdat") %>% 
  convert_blanks_to_na()

Note that any logical operator being applied to an NA value always returns NA rather than TRUE or FALSE.

visits <- c("Baseline", NA, "Screening", "Week 1 Day 7")
visits != "Baseline"
#> [1] FALSE    NA  TRUE  TRUE

The only exception is is.na() which returns TRUE if the input is NA.

is.na(visits)
#> [1] FALSE  TRUE FALSE FALSE

Thus, to filter all visits which are not "Baseline" the following condition would need to be used.

visits != "Baseline" | is.na(visits)
#> [1] FALSE  TRUE  TRUE  TRUE

Also note that most aggregation functions, like mean() or max(), also return NA if any element of the input vector is missing.

mean(c(1, NA, 2))
#> [1] NA

To avoid this behavior one has to explicitly set na.rm = TRUE.

mean(c(1, NA, 2), na.rm = TRUE)
#> [1] 1.5

This is very important to keep in mind when using admiral’s aggregation functions such as derive_summary_records().

For handling of NAs in sorting variables see Sort Order.

Expressions in Scripts

Quoting and Unquoting: Introducing `expr()`, `exprs()`, `!!` and `!!!`

`expr()` and `exprs()`

expr() is a function from the rlang package, which is used to create an expression. The expression is not evaluated - rather, it is passed on to the derivation function which evaluates it in its own environment. exprs() is the plural version of expr(), so it accepts multiple comma-separated items and returns a list of expressions.

library(rlang)

adae <- data.frame(USUBJID = "XXX-1", AEDECOD = "HEADACHE")

# Return the adae object
adae
#>   USUBJID  AEDECOD
#> 1   XXX-1 HEADACHE


# Return an expression
expr(adae)
#> adae

When used within the contest of an admiral derivation function, expr() and exprs() allow the function to evaluate the expressions in the context of the input dataset. As an example, expr() and exprs() allow users to pass variable names of datasets to the function without wrapping them in quotation marks.

The expressions framework is powerful because users are able to intuitively “inject code” into admiral functions (through the function parameters) using very similar syntax as if they were writing open code, with the exception possibly being an outer exprs() wrapper. For instance, in the derive_vars_merged() call below, the user is merging adsl with ex and is able to filter ex prior to the merge using an expression passed to the filter_add parameter. Because filter_add accepts expressions, the user has full power to filter their dataset as they please. In the same vein, the user is able to create any new variables they wish after the merge using the new_vars argument, to which they pass a list of expressions containing “standard” R code.

derive_vars_merged(
  adsl,
  dataset_add = ex,
  filter_add = !is.na(EXENDTM),
  by_vars = exprs(STUDYID, USUBJID),
  new_vars = exprs(
    TRTEDTM = EXENDTM,
    TRTETMF = EXENTMF,
    COMPTRT = if_else(!is.na(EXENDTM), "Y", "N")
  ),
  order = exprs(EXENDTM),
  mode = "last"
)

Bang-Bang (`!!`) and Bang-Bang-Bang (`!!!`)

Sometimes you may want to construct an expression using other, pre-existing expressions. However, it’s not immediately clear how to achieve this because expressions inherently pause evaluation of your code before it’s executed:

a <- expr(2)
b <- expr(3)

expr(a + b)
#> a + b

# NOT 2 + 3

This is where !! (bang-bang) comes in: provided again by the rlang package, it allows you to inject the contents of an expression into another expression, meaning that by using !! you can modify the code inside an expression before R evaluates it. By using !! you are unquoting an expression, i.e. evaluating it before you pass it onwards.

expr(!!a + !!b)
#> 2 + 3

You can see an example of where !! comes in handy within admiral code in Common Pitfall 1, where the contents of an expression is unquoted so that it can be passed to derive_vars_merged().

!!! (bang-bang-bang) is the plural version of !! and can be used to unquote a list of expressions:

exprs(!!!list(a, b))
#> [[1]]
#> [1] 2
#> 
#> [[2]]
#> [1] 3

Within admiral, this operator can be useful if we need to unquote a list of variables (stored as expressions) to use them inside of an admiral or even dplyr call. One example is the admiral subject keys:

get_admiral_option("subject_keys")
#> [[1]]
#> STUDYID
#> 
#> [[2]]
#> USUBJID

If we want to use the subject keys stored within this admiral option to subset a dataset, we need to use !!! to unquote this list. Let’s construct a dummy example to illustrate the point:

adcm <- data.frame(STUDYID = "XXX", USUBJID = "XXX-1", CMTRT = "ASPIRIN")
adcm
#>   STUDYID USUBJID   CMTRT
#> 1     XXX   XXX-1 ASPIRIN


# This doesn't work as we are not unquoting the subject keys
adcm %>% select(get_admiral_option("subject_keys"))
#> Error in `select()`:
#> ! Can't select columns with `get_admiral_option("subject_keys")`.
#> ✖ `get_admiral_option("subject_keys")` must be numeric or character, not a list.


# This works because we are unquoting the subject keys
adcm %>% select(!!!get_admiral_option("subject_keys"))
#>   STUDYID USUBJID
#> 1     XXX   XXX-1

You can see another example of !!! in action in this line of the admiral ADEX template script, where it is used to dynamically control the by variables passed to an admiral function.

Summary

In summary, although the expressions framework may seem slightly clunky and mysterious to begin with, it allows for such power and flexibility that it forms a key part of the admiral package. For a comprehensive treatment of expressions, see Chapter 18 and Chapter 19 of the Advanced R textbook. Chapter 19 specifically covers in much more detail the concept of unquoting.

Common pitfalls

Expressions are very powerful, but this can also lead to misunderstandings about their functionality. Let’s set up some dummy data to explore common issues that new (or experienced!) programmers may encounter when dealing with expressions.

library(dplyr, warn.conflicts = FALSE)
library(admiral)

vs <- tribble(
  ~USUBJID, ~VSTESTCD, ~VISIT, ~VSSTRESN, ~VSSTRESU, ~VSDTC,
  "01-1301", "WEIGHT", "SCREENING", 82.1, "kg", "2013-08-29",
  "01-1301", "WEIGHT", "WEEK 2", 81.19, "kg", "2013-09-15",
  "01-1301", "WEIGHT", "WEEK 4", 82.56, "kg", "2013-09-24",
  "01-1302", "BMI", "SCREENING", 20.1, "kg/m2", "2013-08-29",
  "01-1302", "BMI", "WEEK 2", 20.2, "kg/m2", "2013-09-15",
  "01-1302", "BMI", "WEEK 4", 19.9, "kg/m2", "2013-09-24"
)

dm <- tribble(
  ~USUBJID, ~AGE,
  "01-1301", 18
)

1. Mistakenly passing something that isn’t an expression to an argument

When writing more complex admiral code it can be easy to mistakenly pass the wrong input to an argument that expects an expression. For example, the code below fails because my_expression is not an expression - it is the name of an object in the global environment containing an expression.

my_expression <- expr(VSTESTCD == "WEIGHT" & VISIT == "SCREENING")

derive_vars_merged(
  dm,
  dataset_add = select(vs, USUBJID, VSTESTCD, VISIT),
  by_vars = exprs(USUBJID),
  filter_add = my_expression
)
#> Error in `derive_vars_merged()`:
#> ! Argument `filter_add` must be a filter condition, but is a symbol

To fix this code, we need to unquote my_expression so that the expression that it is holding is passed correctly to derive_vars_merged():

derive_vars_merged(
  dm,
  dataset_add = select(vs, USUBJID, VSTESTCD, VISIT),
  by_vars = exprs(USUBJID),
  filter_add = !!my_expression
)
#> # A tibble: 1 × 4
#>   USUBJID   AGE VSTESTCD VISIT    
#>   <chr>   <dbl> <chr>    <chr>    
#> 1 01-1301    18 WEIGHT   SCREENING

2. Forgetting that expressions must be evaluable in the dataset

In a similar vein to above, even if an actual expression is passed as an argument, you must make sure that it can be evaluated within the dataset of interest. This may seem trivial, but it is a common pitfall because expressions delay evaluation of code and so can delay the identification of issues. For instance, consider this example:

filter_vs_and_merge <- function(my_expression) {
  derive_vars_merged(
    dm,
    dataset_add = select(vs, USUBJID, VSTESTCD, VISIT),
    by_vars = exprs(USUBJID),
    filter_add = !!my_expression
  )
}

# This works
filter_vs_and_merge(expr(VSTESTCD == "WEIGHT" & VISIT == "SCREENING"))
#> # A tibble: 1 × 4
#>   USUBJID   AGE VSTESTCD VISIT    
#>   <chr>   <dbl> <chr>    <chr>    
#> 1 01-1301    18 WEIGHT   SCREENING


# This fails
filter_vs_and_merge(expr(VSTESTCD == "WEIGHT" & VISIT == "SCREENING" & VSTPT == "PREDOSE"))
#> Error in `filter()`:
#> ℹ In argument: `VSTESTCD == "WEIGHT" & VISIT == "SCREENING" & VSTPT ==
#>   "PREDOSE"`.
#> Caused by error:
#> ! object 'VSTPT' not found

The second call fails because hidden within the expression is a mention of VSTPT, which was dropped from vs in filter_vs_and_merge().