View source: R/count_occurrences_by_grade.R
count_occurrences_by_grade | R Documentation |
Functions for analyzing frequencies and fractions of occurrences by grade for patients with occurrence data. Multiple occurrences within one individual are counted once at the greatest intensity/highest grade level.
count_occurrences_by_grade(
lyt,
var,
id = "USUBJID",
grade_groups = list(),
remove_single = TRUE,
only_grade_groups = FALSE,
var_labels = var,
show_labels = "default",
riskdiff = FALSE,
na_str = default_na_str(),
nested = TRUE,
...,
table_names = var,
.stats = NULL,
.formats = NULL,
.indent_mods = NULL,
.labels = NULL
)
summarize_occurrences_by_grade(
lyt,
var,
id = "USUBJID",
grade_groups = list(),
remove_single = TRUE,
only_grade_groups = FALSE,
na_str = default_na_str(),
...,
.stats = NULL,
.formats = NULL,
.indent_mods = NULL,
.labels = NULL
)
s_count_occurrences_by_grade(
df,
.var,
.N_col,
id = "USUBJID",
grade_groups = list(),
remove_single = TRUE,
only_grade_groups = FALSE,
labelstr = ""
)
a_count_occurrences_by_grade(
df,
.var,
.N_col,
id = "USUBJID",
grade_groups = list(),
remove_single = TRUE,
only_grade_groups = FALSE,
labelstr = ""
)
lyt |
( |
id |
( |
grade_groups |
(named |
remove_single |
( |
only_grade_groups |
( |
var_labels |
( |
show_labels |
( |
riskdiff |
( |
na_str |
( |
nested |
( |
... |
additional arguments for the lower level functions. |
table_names |
( |
.stats |
( |
.formats |
(named |
.indent_mods |
(named |
.labels |
(named |
df |
( |
.var , var |
( |
.N_col |
( |
labelstr |
( |
count_occurrences_by_grade()
returns a layout object suitable for passing to further layouting functions,
or to rtables::build_table()
. Adding this function to an rtable
layout will add formatted rows containing
the statistics from s_count_occurrences_by_grade()
to the table layout.
summarize_occurrences_by_grade()
returns a layout object suitable for passing to further layouting functions,
or to rtables::build_table()
. Adding this function to an rtable
layout will add formatted content rows
containing the statistics from s_count_occurrences_by_grade()
to the table layout.
s_count_occurrences_by_grade()
returns a list of counts and fractions with one element per grade level or
grade level grouping.
a_count_occurrences_by_grade()
returns the corresponding list with formatted rtables::CellValue()
.
count_occurrences_by_grade()
: Layout-creating function which can take statistics function
arguments and additional format arguments. This function is a wrapper for rtables::analyze()
.
summarize_occurrences_by_grade()
: Layout-creating function which can take content function arguments
and additional format arguments. This function is a wrapper for rtables::summarize_row_groups()
.
s_count_occurrences_by_grade()
: Statistics function which counts the
number of patients by highest grade.
a_count_occurrences_by_grade()
: Formatted analysis function which is used as afun
in count_occurrences_by_grade()
.
Relevant helper function h_append_grade_groups()
.
library(dplyr)
df <- data.frame(
USUBJID = as.character(c(1:6, 1)),
ARM = factor(c("A", "A", "A", "B", "B", "B", "A"), levels = c("A", "B")),
AETOXGR = factor(c(1, 2, 3, 4, 1, 2, 3), levels = c(1:5)),
AESEV = factor(
x = c("MILD", "MODERATE", "SEVERE", "MILD", "MILD", "MODERATE", "SEVERE"),
levels = c("MILD", "MODERATE", "SEVERE")
),
stringsAsFactors = FALSE
)
df_adsl <- df %>%
select(USUBJID, ARM) %>%
unique()
# Layout creating function with custom format.
basic_table() %>%
split_cols_by("ARM") %>%
add_colcounts() %>%
count_occurrences_by_grade(
var = "AESEV",
.formats = c("count_fraction" = "xx.xx (xx.xx%)")
) %>%
build_table(df, alt_counts_df = df_adsl)
# Define additional grade groupings.
grade_groups <- list(
"-Any-" = c("1", "2", "3", "4", "5"),
"Grade 1-2" = c("1", "2"),
"Grade 3-5" = c("3", "4", "5")
)
basic_table() %>%
split_cols_by("ARM") %>%
add_colcounts() %>%
count_occurrences_by_grade(
var = "AETOXGR",
grade_groups = grade_groups,
only_grade_groups = TRUE
) %>%
build_table(df, alt_counts_df = df_adsl)
# Layout creating function with custom format.
basic_table() %>%
add_colcounts() %>%
split_rows_by("ARM", child_labels = "visible", nested = TRUE) %>%
summarize_occurrences_by_grade(
var = "AESEV",
.formats = c("count_fraction" = "xx.xx (xx.xx%)")
) %>%
build_table(df, alt_counts_df = df_adsl)
basic_table() %>%
add_colcounts() %>%
split_rows_by("ARM", child_labels = "visible", nested = TRUE) %>%
summarize_occurrences_by_grade(
var = "AETOXGR",
grade_groups = grade_groups
) %>%
build_table(df, alt_counts_df = df_adsl)
s_count_occurrences_by_grade(
df,
.N_col = 10L,
.var = "AETOXGR",
id = "USUBJID",
grade_groups = list("ANY" = levels(df$AETOXGR))
)
# We need to ungroup `count_fraction` first so that the `rtables` formatting
# function `format_count_fraction()` can be applied correctly.
afun <- make_afun(a_count_occurrences_by_grade, .ungroup_stats = "count_fraction")
afun(
df,
.N_col = 10L,
.var = "AETOXGR",
id = "USUBJID",
grade_groups = list("ANY" = levels(df$AETOXGR))
)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.