Helper Function to Prepare Data for Proportion Analyses

Prepares response, group, and optional strata vectors, and constructs a 2 x 2 contingency table for proportion-based analyses. The function extracts the variables from an analysis dataset and, optionally, a reference dataset, combines them into vectors suitable for downstream statistical functions, and returns the resulting contingency table together with the prepared vectors.

Usage

h_prepare_rsp_table(
  df,
  df_ref = NULL,
  var,
  val = TRUE,
  strata_vars = NULL,
  complete_cases = FALSE,
  quiet = FALSE
)

Arguments

df: (data.frame)
A data frame containing the observations for the non-reference group.
df_ref: (data.frame or NULL)
An optional data frame containing the observations for the reference group. Columns specified by var and strata_vars (if not NULL) must have the same classes as the corresponding columns in df. If they are factors, their levels must also be identical between df and df_ref.
var: (character(1))
The column name in df (and, if supplied, df_ref) specifying the response variable. The response is converted to a logical vector by comparing its values with val. df[[var]] (and df_ref[[var]], if supplied) must be an atomic vector as defined by checkmate::check_atomic_vector(), of one of the following types: logical, integer, numeric, or character.
val: (logical(1) or integer(1) or numeric(1) or character(1))
The value in df[[var]] (and, if supplied, in df_ref[[var]]) that defines a positive response. Observations matching this value are returned as TRUE in the rsp vector; all other observations are returned as FALSE. If df[[var]] is a factor, val must be a character value matching one of its levels. Otherwise, val must have the same class as df[[var]].
strata_vars: (character or NULL)
Optional column names in df (and, if supplied, df_ref) specifying the strata variables. The specified columns must all be factors.
complete_cases: (logical(1))
Whether to remove incomplete rows from df (and, if supplied, df_ref) before constructing the response, group, strata, and contingency table. Completeness is assessed only for the columns specified by var and strata_vars (if supplied) using get_complete_cases(). If complete_cases = TRUE, rows containing missing values in any of these columns are removed. If complete_cases = FALSE, the function fails if any of these columns contain missing values, rather than returning results containing NA values.
quiet: (logical(1))
Passed to get_complete_cases(). If complete_cases = TRUE, controls whether a message is displayed for rows removed due to missing values. Has no effect when complete_cases = FALSE.

Value

A named list containing:

rsp: A logical vector indicating whether each observation has the value specified by val in df[[var]] (and, if supplied, df_ref).
grp: A factor identifying the group of each observation. The levels are always "ref" and "Not-ref" (in this order), corresponding to observations from df_ref and df, respectively. If df_ref is NULL, all observations belong to "Not-ref".
strata: A factor defining the analysis strata when strata_vars is supplied, or NULL otherwise. When multiple stratification variables are supplied, their combinations, using interaction(), are used to define the strata.
tbl: A contingency table produced by base::table() from grp, rsp (after converting it to a factor with two levels, "TRUE" and "FALSE"), and, if strata_vars is supplied, strata. When strata_vars is NULL, a 2 x 2 table is returned, with grp defining the rows and rsp defining the columns. The rsp dimension always contains the levels "TRUE" and "FALSE", in that order, even when one or both response outcomes are not observed. When strata_vars is supplied, a 3-dimensional contingency table with dimensions 2 x 2 x k is returned, where k is the number of strata. The dimensions correspond to grp, rsp, and strata, respectively.

Details

The function prepares the response, group, and optional strata variables required for proportion-based analyses and constructs a safe contingency table for downstream statistical functions. See the proportion difference documentation h_prop_diff and h_prop_diff_test for related functions.

If complete_cases = TRUE, incomplete observations are removed separately from df and df_ref (if supplied) before the vectors and contingency table are constructed. Completeness is assessed jointly across the var and strata_vars columns when strata_vars is supplied, and only across var otherwise. This is performed using get_complete_cases(). If complete_cases = FALSE, the function fails if any of these columns contain missing values, rather than returning results containing NA values.

The response variable specified by var, and optionally the strata variables specified by strata_vars, are extracted independently from df and df_ref (if supplied). The response vectors are then combined into a single vector and converted to a logical vector by comparing each value with val, such that observations matching val are TRUE and all other observations are FALSE.

When multiple stratification variables are provided, their combinations are collapsed into a single factor using interaction(). This is done independently for df and df_ref (if supplied), after which the resulting strata vectors are combined into a single factor.

A group factor is constructed to identify the source of each observation. Observations from df are assigned to the "Not-ref" group, while observations from df_ref are assigned to the "ref" group. The factor always has "ref" and "Not-ref" as its levels, in this order. The level order is important because proportion-difference calculations in tern use the first level as the reference group and calculate the difference as "Not-ref" - "ref".

The contingency table is constructed from group, response (after converting it to a factor with two levels, "TRUE" and "FALSE"), and, if strata_vars is supplied, strata.

Examples


set.seed(123)
n <- 28
dta <- data.frame(
  "rsp" = sample(c(TRUE, FALSE), n, TRUE),
  "grp" = sample(c("X", "Placebo"), n, TRUE),
  "f1" = sample(c("a1", "a2"), n, TRUE),
  "f2" = sample(c("x", "y"), n, TRUE),
  stringsAsFactors = TRUE
)
head(dta)
#>     rsp     grp f1 f2
#> 1  TRUE       X a2  y
#> 2  TRUE Placebo a1  y
#> 3  TRUE       X a2  x
#> 4 FALSE Placebo a1  x
#> 5  TRUE       X a1  y
#> 6 FALSE Placebo a2  x

trgs <- h_prepare_rsp_table(
  df = subset(dta, grp == "X"),
  df_ref = subset(dta, grp == "Placebo"),
  var = "rsp",
  strata_vars = c("f1", "f2")
)

rbind(
  subset(dta, grp == "X"),
  subset(dta, grp == "Placebo"),
  make.row.names = FALSE
)
#>      rsp     grp f1 f2
#> 1   TRUE       X a2  y
#> 2   TRUE       X a2  x
#> 3   TRUE       X a1  y
#> 4  FALSE       X a1  y
#> 5   TRUE       X a1  x
#> 6   TRUE       X a2  y
#> 7  FALSE       X a1  y
#> 8  FALSE       X a1  x
#> 9   TRUE       X a1  x
#> 10 FALSE       X a1  x
#> 11  TRUE       X a1  y
#> 12  TRUE       X a1  y
#> 13  TRUE       X a2  y
#> 14 FALSE       X a1  y
#> 15  TRUE       X a2  x
#> 16  TRUE       X a2  x
#> 17  TRUE       X a2  y
#> 18 FALSE       X a1  y
#> 19  TRUE Placebo a1  y
#> 20 FALSE Placebo a1  x
#> 21 FALSE Placebo a2  x
#> 22 FALSE Placebo a2  y
#> 23 FALSE Placebo a1  x
#> 24  TRUE Placebo a1  y
#> 25 FALSE Placebo a2  x
#> 26  TRUE Placebo a2  x
#> 27  TRUE Placebo a2  x
#> 28 FALSE Placebo a2  y

trgs$rsp
#>  [1]  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE  TRUE
#> [13]  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE
#> [25]  TRUE  TRUE  TRUE FALSE
trgs$grp
#>  [1] ref     ref     ref     ref     ref     ref     ref     ref     ref    
#> [10] ref     Not-ref Not-ref Not-ref Not-ref Not-ref Not-ref Not-ref Not-ref
#> [19] Not-ref Not-ref Not-ref Not-ref Not-ref Not-ref Not-ref Not-ref Not-ref
#> [28] Not-ref
#> Levels: ref Not-ref
trgs$strata
#>  [1] a1.y a1.x a2.x a2.y a1.x a1.y a2.x a2.x a2.x a2.y a2.y a2.x a1.y a1.y a1.x
#> [16] a2.y a1.y a1.x a1.x a1.x a1.y a1.y a2.y a1.y a2.x a2.x a2.y a1.y
#> Levels: a1.x a2.x a1.y a2.y
trgs$tbl
#> , , strata = a1.x
#> 
#>          rsp
#> grp       TRUE FALSE
#>   ref        0     2
#>   Not-ref    2     2
#> 
#> , , strata = a2.x
#> 
#>          rsp
#> grp       TRUE FALSE
#>   ref        2     2
#>   Not-ref    3     0
#> 
#> , , strata = a1.y
#> 
#>          rsp
#> grp       TRUE FALSE
#>   ref        2     0
#>   Not-ref    3     4
#> 
#> , , strata = a2.y
#> 
#>          rsp
#> grp       TRUE FALSE
#>   ref        0     2
#>   Not-ref    4     0
#> 

# Example use case.
prop_diff_cmh(trgs$rsp, trgs$grp, trgs$strata)
#> $prop
#>       ref   Not-ref 
#> 0.4064171 0.7379679 
#> 
#> $prop_ci
#> $prop_ci$ref
#> [1] 0.2649224 0.5479118
#> 
#> $prop_ci$`Not-ref`
#> [1] 0.5918892 0.8840466
#> 
#> 
#> $diff
#> [1] 0.3315508
#> 
#> $diff_ci
#> [1] 0.1281798 0.5349218
#> 
#> $se_diff
#> [1] 0.1037626
#> 
#> $weights
#>      a1.x      a2.x      a1.y      a2.y 
#> 0.2245989 0.2887701 0.2620321 0.2245989 
#> 
#> $n1
#> a1.x a2.x a1.y a2.y 
#>    2    4    2    2 
#> 
#> $n2
#> a1.x a2.x a1.y a2.y 
#>    4    3    7    4 
#> 
prop_cmh(trgs$tbl)
#> [1] 0.114052
#> attr(,"z_stat")
#> [1] 1.58024

# The FALSE/TRUE levels are retained even when only one outcome is observed.
dta2 <- dta
dta2$rsp <- TRUE
h_prepare_rsp_table(
  df = subset(dta2, grp == "X"),
  df_ref = subset(dta2, grp == "Placebo"),
  var = "rsp",
)$tbl
#>          rsp
#> grp       TRUE FALSE
#>   ref       10     0
#>   Not-ref   18     0

# Handling missing values.
if (FALSE) { # \dontrun{
dta_missing <- dta
dta_missing[1, "rsp"] <- NA

# By default, the function fails when missing values are present.
h_prepare_rsp_table(
  df = subset(dta_missing, grp == "X"),
  df_ref = subset(dta_missing, grp == "Placebo"),
  var = "rsp",
  strata_vars = c("f1", "f2")
)

# Set complete_cases = TRUE to remove incomplete observations.
h_prepare_rsp_table(
  df = subset(dta_missing, grp == "X"),
  df_ref = subset(dta_missing, grp == "Placebo"),
  var = "rsp",
  strata_vars = c("f1", "f2"),
  complete_cases = TRUE
)
} # }