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Occurrence Counts

Source: R/count_occurrences.R
count_occurrences.Rd

[Stable]

Usage 

s_count_occurrences(
  df,
  denom = c("N_col", "n"),
  .N_col,
  .df_row,
  drop = TRUE,
  .var = "MHDECOD",
  id = "USUBJID"
)

a_count_occurrences(
  df,
  denom = c("N_col", "n"),
  .N_col,
  .df_row,
  drop = TRUE,
  .var = "MHDECOD",
  id = "USUBJID"
)

count_occurrences(
  lyt,
  vars,
  var_labels = vars,
  show_labels = "hidden",
  ...,
  table_names = vars,
  .stats = "count_fraction",
  .formats = NULL,
  .labels = NULL,
  .indent_mods = NULL
)

Arguments

df

(data.frame)
data set containing all analysis variables.

denom

(string)
choice of denominator for patient proportions. Can be:

  • N_col: total number of patients in this column across rows

  • n: number of patients with any occurrences

.N_col

(count)
row-wise N (row group count) for the group of observations being analyzed (i.e. with no column-based subsetting) that is passed by rtables.

.df_row

(data.frame)
data frame across all of the columns for the given row split.

drop

(flag)
should non appearing occurrence levels be dropped from the resulting table. Note that in that case the remaining occurrence levels in the table are sorted alphabetically.

.var

(string)
single variable name that is passed by rtables when requested by a statistics function.

id

(string)
subject variable name.

lyt

(layout)
input layout where analyses will be added to.

vars

(character)
variable names for the primary analysis variable to be iterated over.

var_labels

character for label.

show_labels

label visibility: one of "default", "visible" and "hidden".

...

additional arguments for the lower level functions.

table_names

(character)
this can be customized in case that the same vars are analyzed multiple times, to avoid warnings from rtables.

.stats

(character)
statistics to select for the table.

.formats

(named character or list)
formats for the statistics.

.labels

(named character)
labels for the statistics (without indent).

.indent_mods

(named integer)
indent modifiers for the labels.

Value

A list with:

count

list of counts with one element per occurrence.

count_fraction

list of counts and fractions with one element per occurrence.

fraction

list of numerators and denominators with one element per occurrence.

Details

Functions for analyzing frequencies and fractions of occurrences for patients with occurrence data. Primary analysis variables are the dictionary terms. All occurrences are counted for total counts. Multiple occurrences within patient at the lowest term level displayed in the table are counted only once. Note that by default occurrences which don't appear in a given row split are dropped from the table and the occurrences in the table are sorted alphabetically per row split. Therefore the corresponding layout needs to use split_fun = drop_split_levels in the split_rows_by calls. Use drop = FALSE if you would like to show all occurrences.

Functions

  • s_count_occurrences(): Statistics function which counts number of patients that report an occurrence.

  • a_count_occurrences(): Formatted Analysis function which can be further customized by calling rtables::make_afun() on it. It is used as afun in rtables::analyze().

  • count_occurrences(): Analyze Function that counts occurrences as part of rtables layouts.

Examples 

df <- data.frame(
  USUBJID = as.character(c(1, 1, 2, 4, 4, 4)),
  MHDECOD = c("MH1", "MH2", "MH1", "MH1", "MH1", "MH3")
)

N_per_col <- 4L

# Count unique occurrences per subject.
s_count_occurrences(
  df,
  .N_col = N_per_col,
  .df_row = df,
  .var = "MHDECOD",
  id = "USUBJID"
)
#> $count
#> $count$MH1
#> [1] 3
#> 
#> $count$MH2
#> [1] 1
#> 
#> $count$MH3
#> [1] 1
#> 
#> 
#> $count_fraction
#> $count_fraction$MH1
#> [1] 3.00 0.75
#> 
#> $count_fraction$MH2
#> [1] 1.00 0.25
#> 
#> $count_fraction$MH3
#> [1] 1.00 0.25
#> 
#> 
#> $fraction
#> $fraction$MH1
#>   num denom 
#>     3     4 
#> 
#> $fraction$MH2
#>   num denom 
#>     1     4 
#> 
#> $fraction$MH3
#>   num denom 
#>     1     4 
#> 
#> 

#  We need to ungroup `count_fraction` first so that the `rtables` formatting
# function `format_count_fraction()` can be applied correctly.
afun <- make_afun(a_count_occurrences, .ungroup_stats = c("count", "count_fraction", "fraction"))
afun(
  df,
  .N_col = N_per_col,
  .df_row = df,
  .var = "MHDECOD",
  id = "USUBJID"
)
#> RowsVerticalSection (in_rows) object print method:
#> ----------------------------
#>   row_name formatted_cell indent_mod row_label
#> 1      MH1              3          0       MH1
#> 2      MH2              1          0       MH2
#> 3      MH3              1          0       MH3
#> 4      MH1      3 (75.0%)          0       MH1
#> 5      MH2      1 (25.0%)          0       MH2
#> 6      MH3      1 (25.0%)          0       MH3
#> 7      MH1    3/4 (75.0%)          0       MH1
#> 8      MH2    1/4 (25.0%)          0       MH2
#> 9      MH3    1/4 (25.0%)          0       MH3

library(dplyr)
df <- data.frame(
  USUBJID = as.character(c(
    1, 1, 2, 4, 4, 4,
    6, 6, 6, 7, 7, 8
  )),
  MHDECOD = c(
    "MH1", "MH2", "MH1", "MH1", "MH1", "MH3",
    "MH2", "MH2", "MH3", "MH1", "MH2", "MH4"
  ),
  ARM = rep(c("A", "B"), each = 6)
)
df_adsl <- df %>%
  select(USUBJID, ARM) %>%
  unique()

# Create table layout
lyt <- basic_table() %>%
  split_cols_by("ARM") %>%
  add_colcounts() %>%
  count_occurrences(vars = "MHDECOD", .stats = c("count_fraction"))

# Apply table layout to data and produce `rtable` object
lyt %>%
  build_table(df, alt_counts_df = df_adsl) %>%
  prune_table()
#>           A           B    
#>         (N=3)       (N=3)  
#> ———————————————————————————
#> MH1   3 (100%)    1 (33.3%)
#> MH2   1 (33.3%)   2 (66.7%)
#> MH3   1 (33.3%)   1 (33.3%)
#> MH4       0       1 (33.3%)