abnormal_by_marked | R Documentation |
Primary analysis variable .var
indicates whether single, replicated or last marked laboratory
abnormality was observed (factor
). Additional analysis variables are id
(character
or factor
)
and direction
(factor
) indicating the direction of the abnormality. Denominator is number of
patients with at least one valid measurement during the analysis.
For Single, not last
and Last or replicated
: Numerator is number of patients
with Single, not last
and Last or replicated
levels, respectively.
For Any
: Numerator is the number of patients with either single or
replicated marked abnormalities.
count_abnormal_by_marked(
lyt,
var,
category = list(single = "SINGLE", last_replicated = c("LAST", "REPLICATED")),
variables = list(id = "USUBJID", param = "PARAM", direction = "abn_dir"),
na_str = default_na_str(),
nested = TRUE,
...,
.stats = NULL,
.formats = NULL,
.labels = NULL,
.indent_mods = NULL
)
s_count_abnormal_by_marked(
df,
.var = "AVALCAT1",
.spl_context,
category = list(single = "SINGLE", last_replicated = c("LAST", "REPLICATED")),
variables = list(id = "USUBJID", param = "PARAM", direction = "abn_dir")
)
a_count_abnormal_by_marked(
df,
.var = "AVALCAT1",
.spl_context,
category = list(single = "SINGLE", last_replicated = c("LAST", "REPLICATED")),
variables = list(id = "USUBJID", param = "PARAM", direction = "abn_dir")
)
lyt |
( |
category |
( |
variables |
(named |
na_str |
( |
nested |
( |
... |
additional arguments for the lower level functions. |
.stats |
( |
.formats |
(named |
.labels |
(named |
.indent_mods |
(named |
df |
( |
.var , var |
( |
.spl_context |
( |
count_abnormal_by_marked()
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_abnormal_by_marked()
to the table layout.
s_count_abnormal_by_marked()
returns statistic count_fraction
with Single, not last
,
Last or replicated
, and Any
results.
a_count_abnormal_by_marked()
returns the corresponding list with formatted rtables::CellValue()
.
count_abnormal_by_marked()
: Layout-creating function which can take statistics function arguments
and additional format arguments. This function is a wrapper for rtables::analyze()
.
s_count_abnormal_by_marked()
: Statistics function for patients with marked lab abnormalities.
a_count_abnormal_by_marked()
: Formatted analysis function which is used as afun
in count_abnormal_by_marked()
.
Single, not last
and Last or replicated
levels are mutually exclusive. If a patient has
abnormalities that meet both the Single, not last
and Last or replicated
criteria, then the
patient will be counted only under the Last or replicated
category.
library(dplyr)
df <- data.frame(
USUBJID = as.character(c(rep(1, 5), rep(2, 5), rep(1, 5), rep(2, 5))),
ARMCD = factor(c(rep("ARM A", 5), rep("ARM B", 5), rep("ARM A", 5), rep("ARM B", 5))),
ANRIND = factor(c(
"NORMAL", "HIGH", "HIGH", "HIGH HIGH", "HIGH",
"HIGH", "HIGH", "HIGH HIGH", "NORMAL", "HIGH HIGH", "NORMAL", "LOW", "LOW", "LOW LOW", "LOW",
"LOW", "LOW", "LOW LOW", "NORMAL", "LOW LOW"
)),
ONTRTFL = rep(c("", "Y", "Y", "Y", "Y", "Y", "Y", "Y", "Y", "Y"), 2),
PARAMCD = factor(c(rep("CRP", 10), rep("ALT", 10))),
AVALCAT1 = factor(rep(c("", "", "", "SINGLE", "REPLICATED", "", "", "LAST", "", "SINGLE"), 2)),
stringsAsFactors = FALSE
)
df <- df %>%
mutate(abn_dir = factor(
case_when(
ANRIND == "LOW LOW" ~ "Low",
ANRIND == "HIGH HIGH" ~ "High",
TRUE ~ ""
),
levels = c("Low", "High")
))
# Select only post-baseline records.
df <- df %>% filter(ONTRTFL == "Y")
df_crp <- df %>%
filter(PARAMCD == "CRP") %>%
droplevels()
full_parent_df <- list(df_crp, "not_needed")
cur_col_subset <- list(rep(TRUE, nrow(df_crp)), "not_needed")
spl_context <- data.frame(
split = c("PARAMCD", "GRADE_DIR"),
full_parent_df = I(full_parent_df),
cur_col_subset = I(cur_col_subset)
)
map <- unique(
df[df$abn_dir %in% c("Low", "High") & df$AVALCAT1 != "", c("PARAMCD", "abn_dir")]
) %>%
lapply(as.character) %>%
as.data.frame() %>%
arrange(PARAMCD, abn_dir)
basic_table() %>%
split_cols_by("ARMCD") %>%
split_rows_by("PARAMCD") %>%
summarize_num_patients(
var = "USUBJID",
.stats = "unique_count"
) %>%
split_rows_by(
"abn_dir",
split_fun = trim_levels_to_map(map)
) %>%
count_abnormal_by_marked(
var = "AVALCAT1",
variables = list(
id = "USUBJID",
param = "PARAMCD",
direction = "abn_dir"
)
) %>%
build_table(df = df)
basic_table() %>%
split_cols_by("ARMCD") %>%
split_rows_by("PARAMCD") %>%
summarize_num_patients(
var = "USUBJID",
.stats = "unique_count"
) %>%
split_rows_by(
"abn_dir",
split_fun = trim_levels_in_group("abn_dir")
) %>%
count_abnormal_by_marked(
var = "AVALCAT1",
variables = list(
id = "USUBJID",
param = "PARAMCD",
direction = "abn_dir"
)
) %>%
build_table(df = df)
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