cttab: Generate an table of descriptive statistics.

In shug0131/cctu: In-house Functions for Report Writing at Cambridge Clinical Trials Unit

Generate an table of descriptive statistics.

Description

This is a wrapper function of stat_tab, allowing for groupped variables, split statistics table by 'row_split' variable.

Usage

cttab(x, ...)

## Default S3 method:
cttab(
  x,
  data,
  group = NULL,
  row_split = NULL,
  total = TRUE,
  select = NULL,
  add_missing = TRUE,
  add_obs = TRUE,
  digits = getOption("cctu_digits", default = 3),
  digits_pct = getOption("cctu_digits_pct", default = 0),
  rounding_fn = signif_pad,
  subjid_string = getOption("cctu_subjid_string", default = "subjid"),
  print_plot = getOption("cctu_print_plot", default = TRUE),
  render_num = getOption("cctu_render_num", default = "Median [Min, Max]"),
  logical_na_impute = c(FALSE, NA, TRUE),
  blinded = getOption("cctu_blinded", default = FALSE),
  ...
)

## S3 method for class 'formula'
cttab(
  x,
  data,
  total = TRUE,
  select = NULL,
  add_missing = TRUE,
  add_obs = TRUE,
  digits = getOption("cctu_digits", default = 3),
  digits_pct = getOption("cctu_digits_pct", default = 0),
  rounding_fn = signif_pad,
  subjid_string = getOption("cctu_subjid_string", default = "subjid"),
  print_plot = getOption("cctu_print_plot", default = TRUE),
  render_num = getOption("cctu_render_num", default = "Median [Min, Max]"),
  logical_na_impute = c(FALSE, NA, TRUE),
  blinded = getOption("cctu_blinded", default = FALSE),
  ...
)

Arguments

x	Variables to be used or a formula for summary table. If x is a formula, then the group variable should be provided at the right had side, use 1 if there's no grouping variable. And row_split should also be provided on the right hand side of the formula and separate it using | with grouping variable. For example, age + sex ~ treat|cycle or age + sex ~ 1|cycle without grouping. See details.
...	Not used.
data	A data.frame from which the variables in vars should be taken.
group	Name of the grouping variable.
row_split	Variable that used for splitting table rows, rows will be splited using this variable. Useful for repeated measures.
total	If a "Total" column will be created (default). Specify FALSE to omit the column.
select	a named vector with as many components as row-variables. Every element of 'select' will be used to select the individuals to be analyzed for every row-variable. Name of the vector corresponds to the row variable, element is the selection.
add_missing	If missing number and missing percentage will be reported in the summary table, default is 'TRUE'. This will also produce data missingness report if set TRUE. See report_missing for details.
add_obs	Add an observation row (default).
digits	An integer specifying the number of significant digits to keep, default is 3.
digits_pct	An integer specifying the number of digits after the decimal place for percentages, default is 0.
rounding_fn	The function to use to do the rounding. Defaults is signif_pad. To round up by digits instead of significant values, set it to round_pad.
subjid_string	A character naming the column used to identify subject, default is "subjid".
print_plot	A logical value, print summary plot of the variables (default).
render_num	A character or vector indicatin which summary will be reported, default is "Median [Min, Max]". You can change this to "Median [IQR]" then the median and IQR will be reported instead of "Median [Min, Max]". Use options(cctu_render_num = "Median [IQR]") to set global options. See details render_numeric.
logical_na_impute	Impute missing values with FALSE (default), NA keep as it is, or TRUE. The nominator for the logical vector is the number of TRUE. For FALSE or TRUE, the denominator will be all values regardless of missingness, but the non-missing number used as denominator for NA. Set it to FALSE if you want to summarise multiple choice variables and NA for Yes/No type logical variables but don't want No in the summary. You can used a named list in x and stack multiple choice in one category.
blinded	A logical scalar, if summary table will be report by group (default) or not. This will ignore group if set to TRUE and grouping summary will not be reported.

Details

1. Parameter settings with global options

Some of the function parameters can be set with options. This will have an global effect on the cctab function. It is an ideal way to set a global settings if you want this to be effctive globally. Currently, you can set digits, digits_pct, subjid_string, print_plot, render_num and blinded by adding "cctu_" prefix in the options. For example, you can suppress the plot from printting by setting options(cctu_print_plot = FALSE).

2. Formula interface

There are two interfaces, the default, which typically takes a variable vector from data.frame for x, and the formula interface. The formula interface is less flexible, but simpler to use and designed to handle the most common use cases. For the formula version, the formula is expected to be a two-sided formula. Left hand side is the variables to be summarised and the right hand side is the group and/or split variable. To include a row splitting variable, use | to separate the row splitting variable after the grouping variable and then the row split variable. For example, age + sex ~ treat|visit. The right hand side of the formula will be treated as a grouping variable by default. A value of 1 should be provided if there is no grouping variable, for example age + sex ~ 1 or age + sex ~ 1|visit by visit.

3. Return

A summary table with some attributes will be reutned, a method has been writen for rbind. So you can use rbind to combine two tables without losing any attributes. An attribute position will be used to produce a nice table. There are three 4 possible values for each rows. Row name printed as the first column in the word table. Some styles will be applied to each row based on the position attributes.

0	indicates the row will be bolded, spanned through all columns and a grey background in the word
1	indicates the row will be bolded
2	the row will be bolded and spanned through all columns
3	indicates the row of the first column will be indented

Value

A matrix with 'cttab' class.

Methods (by class)

• cttab(default): The default interface, where x is a data.frame.

• cttab(formula): The formula interface, where x is a formula.

See Also

signif_pad round_pad stat_tab sumby dump_missing_report get_missing_report render_numeric render_cat

Examples

# Read data
dt <- read.csv(system.file("extdata", "pilotdata.csv", package="cctu"))
dlu <- read.csv(system.file("extdata", "pilotdata_dlu.csv", package="cctu"))
clu <- read.csv(system.file("extdata", "pilotdata_clu.csv", package="cctu"))

dt$subjid <- substr(dt$USUBJID, 8, 11)

# Apply variable attributes
dt <- apply_macro_dict(dt, dlu, clu, clean_names = FALSE)

# Extract form data to be analysed
df <- extract_form(dt, "PatientReg", vars_keep = c("subjid"))

########################################################
#  Simple analysis no group and variable subset
######################################################
# Variable as a vector
X <- cttab(x = c("AGE", "SEX", "BMIBL"),
             data = df,
             select = c("BMIBL" = "RACEN != 1"))

# Variable as a formula, equivalent to above
X1 <- cttab(AGE + SEX + BMIBL ~ 1,
            data = df,
            select = c("BMIBL" = "RACEN != 1"))

#############################################
#  Analysis by group
############################################
# Variable as a vector
X <- cttab(x = c("AGE", "SEX", "BMIBL"),
             group = "ARM",
             data = df,
             select = c("BMIBL" = "RACEN != 1"))

############################################
# Analysis by group and cycles
############################################

df <- extract_form(dt, "Lab", vars_keep = c("subjid", "ARM"))

X <- cttab(x = c("AST", "BILI", "ALT"),
                  group = "ARM",
                  data = df,
                  row_split = "AVISIT",
                  select = c("ALT" = "PERF == 1"))

############################################
# Group variables
############################################

df <- extract_form(dt, "PatientReg", vars_keep = c("subjid"))
base_lab <- extract_form(dt, "Lab", visit = "SCREENING", vars_keep = c("subjid"))

base_lab$ABNORMALT <- base_lab$ALT > 22.5
var_lab(base_lab$ABNORMALT) <- "ALT abnormal"
base_lab$ABNORMAST <- base_lab$AST > 25.5
var_lab(base_lab$ABNORMAST) <- "AST abnormal"

df <- merge(df, base_lab, by = "subjid")

X <- cttab(x = list(c("AGE", "SEX", "BMIBL"),
                      "Blood" = c("ALT", "AST"),
                      "Patients with Abnormal" = c("ABNORMAST", "ABNORMALT")),
          group = "ARM",
          data = df,
          select = c("BMIBL" = "RACEN != 1",
                     "ALT" = "PERF == 1"))

shug0131/cctu documentation built on Nov. 10, 2023, 12:03 p.m.