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Overview

metalite-table1.Rmd

Motivation

A table for descriptive statistics is widely used in medical research and typically be the first table (i.e. table1) for a manuscript.

There are R packages and examples to create the table1:

For use case in clinical trials, Chapter 4 of the R for clinical study reports and submission contains more details.

The metalite.table1 provide an interactive table1 to enhance the communication between statisticians and clinicians.

# Prepare analysis ready data
df <- r2rtf_adsl
df$AGE[1:3] <- NA # Create missing value for illustration purpose.
df$ARM <- factor(
  df$ARM,
  c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose"),
  c("Placebo", "Low Dose", "High Dose")
)

df[1:6, c("USUBJID", "ARM", "AGE", "SEX", "RACE", "BMIBLGR1")]
#>       USUBJID       ARM AGE SEX  RACE BMIBLGR1
#> 1 01-701-1015   Placebo  NA   F WHITE   25-<30
#> 2 01-701-1023   Placebo  NA   M WHITE     >=30
#> 3 01-701-1028 High Dose  NA   M WHITE     >=30
#> 4 01-701-1033  Low Dose  74   M WHITE   25-<30
#> 5 01-701-1034 High Dose  77   F WHITE   25-<30
#> 6 01-701-1047   Placebo  85   F WHITE     >=30
# Create interactive table1
metalite_table1(~ AGE + SEX + RACE + BMIBLGR1 | ARM, # formula for analysis variables and group
  data = df, # source data
  id = "USUBJID"
) # unique subject id

The interactive features are illustrated in the GIF below.

In comparison with the table1 R package, we are able to answer ad-hoc questions from clinicians with interactive features such as

  • Who are those subjects with missing value.
  • Who are those outliers.
  • What’s the distribution of a variable by treatment group.

Those are common questions for ongoing clinical trials.

# create table1
table1(~ AGE + SEX + RACE + BMIBLGR1 | ARM, data = df)
Placebo
(N=86)		 Low Dose
(N=84)		 High Dose
(N=84)		 Overall
(N=254)
Age
Mean (SD) 75.5 (8.50) 75.7 (8.29) 74.4 (7.93) 75.2 (8.23)
Median [Min, Max] 76.5 [52.0, 89.0] 77.5 [51.0, 88.0] 76.0 [56.0, 88.0] 77.0 [51.0, 89.0]
Missing 2 (2.3%) 0 (0%) 1 (1.2%) 3 (1.2%)
Sex
F 53 (61.6%) 50 (59.5%) 40 (47.6%) 143 (56.3%)
M 33 (38.4%) 34 (40.5%) 44 (52.4%) 111 (43.7%)
Race
BLACK OR AFRICAN AMERICAN 8 (9.3%) 6 (7.1%) 9 (10.7%) 23 (9.1%)
WHITE 78 (90.7%) 78 (92.9%) 74 (88.1%) 230 (90.6%)
AMERICAN INDIAN OR ALASKA NATIVE 0 (0%) 0 (0%) 1 (1.2%) 1 (0.4%)
Pooled Baseline BMI Group 1
59 (68.6%) 47 (56.0%) 44 (52.4%) 150 (59.1%)
>=30 6 (7.0%) 10 (11.9%) 12 (14.3%) 28 (11.0%)
25- 21 (24.4%) 27 (32.1%) 28 (33.3%) 76 (29.9%)