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The function summaryByVisit() produces a table with
descriptive statistics for continues variables at different time points
(visits). It is largely based on the function
gtsummary::tbl_summary() and
gtsummary::tbl_strata_nested_stack. The changes as compared
to these functions are:
To demonstrate the various functionalities of the function, we will create a small dataset. We have three hypotetical lab-values: LDH, ANC and Lymphocytes. Each lab-value has been measured at 10 time points (visits), which can further be divided into three visit groups (baseline, treatment and follow-up). In addition, we have a grouping variable called ‘arm’.
data<-NULL
visit <- c(paste0(rep("Visit ", 10), rbind(c(1:10))),
paste0(rep("Visit ", 10), rbind(c(1:10))),
paste0(rep("Visit ", 10), rbind(c(1:10))))
data <- as.data.frame(cbind( visit, rnorm(30)))
data<-as.data.frame(rbind(data, data, data, data, data))
data$visitgroup<- ifelse(data$visit %in% c("Visit 1", "Visit 2"), "Baseline", ifelse(data$visit %in% c("Visit 3", "Visit 4"), "Treatment", "Follow-up"))
data$visitgroup<-factor(data$visitgroup, levels = c("Baseline", "Treatment", "Follow-up"))
data$LDH<-rnorm(150)
data$Lymphocytes<-rnorm(150)
data$ANC<-rnorm(150)
data$LDH[3]<-NA
data$arm<- c(rep("Arm A", 70), rep("Arm B", 80))Now, we use summarySCI::summaryLevels to create a
summary table for median and range of each lab-value by visit.
Visit | N | N = 151 |
|---|---|---|
LDH | ||
Visit 1 | 15 | 0.3 (-1.4, 1.3) |
Visit 2 | 15 | 0.5 (-1.5, 1.9) |
Visit 3 | 14 | 0.0 (-2.2, 1.4) |
Visit 4 | 15 | 0.0 (-2.2, 1.1) |
Visit 5 | 15 | -0.1 (-2.0, 1.1) |
Visit 6 | 15 | -0.1 (-1.4, 2.4) |
Visit 7 | 15 | -0.2 (-1.7, 1.3) |
Visit 8 | 15 | 0.4 (-1.7, 1.7) |
Visit 9 | 15 | 0.0 (-1.8, 1.6) |
Visit 10 | 15 | -0.1 (-1.3, 1.1) |
Lymphocytes | ||
Visit 1 | 15 | 0.1 (-1.3, 1.5) |
Visit 2 | 15 | -0.1 (-1.5, 2.0) |
Visit 3 | 15 | 0.0 (-1.7, 2.3) |
Visit 4 | 15 | 0.3 (-1.4, 1.2) |
Visit 5 | 15 | 0.5 (-1.5, 2.1) |
Visit 6 | 15 | -0.2 (-2.9, 1.7) |
Visit 7 | 15 | 0.0 (-1.6, 1.9) |
Visit 8 | 15 | 0.2 (-1.2, 1.3) |
Visit 9 | 15 | 0.8 (-1.5, 1.7) |
Visit 10 | 15 | 0.8 (-1.5, 2.5) |
ANC | ||
Visit 1 | 15 | -0.8 (-1.5, 2.4) |
Visit 2 | 15 | -0.1 (-2.0, 1.5) |
Visit 3 | 15 | -0.2 (-2.0, 1.5) |
Visit 4 | 15 | 0.2 (-1.6, 0.9) |
Visit 5 | 15 | -0.1 (-1.7, 2.0) |
Visit 6 | 15 | 0.3 (-1.4, 1.2) |
Visit 7 | 15 | -0.2 (-1.9, 1.4) |
Visit 8 | 15 | 0.4 (-2.2, 1.3) |
Visit 9 | 15 | 0.0 (-3.4, 1.5) |
Visit 10 | 15 | 0.2 (-1.6, 1.7) |
1Median (Min, Max) | ||
We can the visit group to group visits accordingly. Visitgroup needs to be an ordered factor.
summaryByVisit(data,
vars = c("LDH", "Lymphocytes", "ANC"),
visitgroup = "visitgroup",
visit = "visit")Visit | N = 151 |
|---|---|
LDH | |
Baseline | |
Visit 1 | 0.3 (-1.4, 1.3) |
Visit 2 | 0.5 (-1.5, 1.9) |
Treatment | |
Visit 3 | 0.0 (-2.2, 1.4) |
Visit 4 | 0.0 (-2.2, 1.1) |
Follow-up | |
Visit 5 | -0.1 (-2.0, 1.1) |
Visit 6 | -0.1 (-1.4, 2.4) |
Visit 7 | -0.2 (-1.7, 1.3) |
Visit 8 | 0.4 (-1.7, 1.7) |
Visit 9 | 0.0 (-1.8, 1.6) |
Visit 10 | -0.1 (-1.3, 1.1) |
Lymphocytes | |
Baseline | |
Visit 1 | 0.1 (-1.3, 1.5) |
Visit 2 | -0.1 (-1.5, 2.0) |
Treatment | |
Visit 3 | 0.0 (-1.7, 2.3) |
Visit 4 | 0.3 (-1.4, 1.2) |
Follow-up | |
Visit 5 | 0.5 (-1.5, 2.1) |
Visit 6 | -0.2 (-2.9, 1.7) |
Visit 7 | 0.0 (-1.6, 1.9) |
Visit 8 | 0.2 (-1.2, 1.3) |
Visit 9 | 0.8 (-1.5, 1.7) |
Visit 10 | 0.8 (-1.5, 2.5) |
ANC | |
Baseline | |
Visit 1 | -0.8 (-1.5, 2.4) |
Visit 2 | -0.1 (-2.0, 1.5) |
Treatment | |
Visit 3 | -0.2 (-2.0, 1.5) |
Visit 4 | 0.2 (-1.6, 0.9) |
Follow-up | |
Visit 5 | -0.1 (-1.7, 2.0) |
Visit 6 | 0.3 (-1.4, 1.2) |
Visit 7 | -0.2 (-1.9, 1.4) |
Visit 8 | 0.4 (-2.2, 1.3) |
Visit 9 | 0.0 (-3.4, 1.5) |
Visit 10 | 0.2 (-1.6, 1.7) |
1Median (Min, Max) | |
We can stratify the table by groups via the group
argument. The overall column can still be shown if desired, using the
overall = TRUE argument. A maximum of 3 groups are
supported.
summaryByVisit(data,
vars = c("LDH", "Lymphocytes", "ANC"),
group = "arm",
visitgroup = "visitgroup",
visit = "visit")Visit | Arm A | Arm B |
|---|---|---|
LDH | ||
Baseline | ||
Visit 1 | 0.3 (-1.3, 1.3) | 0.1 (-1.4, 1.2) |
Visit 2 | 0.5 (-0.2, 1.8) | 0.6 (-1.5, 1.9) |
Treatment | ||
Visit 3 | 0.3 (-2.2, 1.4) | 0.0 (-1.0, 0.3) |
Visit 4 | -0.2 (-2.2, 0.5) | 0.1 (-1.1, 1.1) |
Follow-up | ||
Visit 5 | -0.5 (-2.0, 1.1) | 0.0 (-1.4, 0.7) |
Visit 6 | -0.1 (-0.3, 1.1) | -0.9 (-1.4, 2.4) |
Visit 7 | 0.0 (-1.0, 1.3) | -0.3 (-1.7, 0.8) |
Visit 8 | 0.4 (-1.7, 1.7) | -0.2 (-1.7, 1.4) |
Visit 9 | 0.0 (-1.2, 0.8) | 0.1 (-1.8, 1.6) |
Visit 10 | 0.1 (-1.3, 1.1) | -0.2 (-0.8, 1.0) |
Lymphocytes | ||
Baseline | ||
Visit 1 | -0.2 (-1.3, 1.5) | 0.2 (-1.2, 0.7) |
Visit 2 | -0.1 (-1.4, 2.0) | 0.3 (-1.5, 2.0) |
Treatment | ||
Visit 3 | -0.2 (-1.7, 1.7) | 0.4 (-0.4, 2.3) |
Visit 4 | 0.3 (-0.8, 0.9) | 0.1 (-1.4, 1.2) |
Follow-up | ||
Visit 5 | -0.4 (-1.5, 0.8) | 0.6 (-0.2, 2.1) |
Visit 6 | -1.1 (-2.9, 0.6) | 0.2 (-2.2, 1.7) |
Visit 7 | 0.5 (-1.4, 1.1) | -0.6 (-1.6, 1.9) |
Visit 8 | 0.4 (-0.5, 0.8) | 0.0 (-1.2, 1.3) |
Visit 9 | 0.8 (-1.5, 1.0) | 0.5 (-0.9, 1.7) |
Visit 10 | 0.3 (-0.6, 2.5) | 0.8 (-1.5, 1.3) |
ANC | ||
Baseline | ||
Visit 1 | -0.1 (-1.4, 2.0) | -0.8 (-1.5, 2.4) |
Visit 2 | -0.3 (-2.0, 1.5) | 0.0 (-1.8, 1.2) |
Treatment | ||
Visit 3 | -0.6 (-2.0, 0.2) | 0.0 (-1.4, 1.5) |
Visit 4 | 0.2 (-1.0, 0.7) | 0.3 (-1.6, 0.9) |
Follow-up | ||
Visit 5 | -0.4 (-1.7, 0.1) | 0.1 (-0.8, 2.0) |
Visit 6 | 0.3 (-1.4, 1.2) | 0.2 (-1.4, 1.2) |
Visit 7 | -0.1 (-1.9, 0.6) | -0.2 (-1.5, 1.4) |
Visit 8 | 0.7 (-0.5, 1.3) | 0.1 (-2.2, 1.3) |
Visit 9 | -0.1 (-3.4, 1.5) | 0.1 (-1.1, 1.1) |
Visit 10 | 0.4 (-1.6, 1.3) | 0.0 (-1.2, 1.7) |
1Median (Min, Max) | ||
summaryByVisit(data,
vars = c("LDH", "Lymphocytes", "ANC"),
group = "arm",
overall = TRUE,
visitgroup = "visitgroup",
visit = "visit")Visit | Overall | Arm A | Arm B |
|---|---|---|---|
LDH | |||
Baseline | |||
Visit 1 | 0.3 (-1.4, 1.3) | 0.3 (-1.3, 1.3) | 0.1 (-1.4, 1.2) |
Visit 2 | 0.5 (-1.5, 1.9) | 0.5 (-0.2, 1.8) | 0.6 (-1.5, 1.9) |
Treatment | |||
Visit 3 | 0.0 (-2.2, 1.4) | 0.3 (-2.2, 1.4) | 0.0 (-1.0, 0.3) |
Visit 4 | 0.0 (-2.2, 1.1) | -0.2 (-2.2, 0.5) | 0.1 (-1.1, 1.1) |
Follow-up | |||
Visit 5 | -0.1 (-2.0, 1.1) | -0.5 (-2.0, 1.1) | 0.0 (-1.4, 0.7) |
Visit 6 | -0.1 (-1.4, 2.4) | -0.1 (-0.3, 1.1) | -0.9 (-1.4, 2.4) |
Visit 7 | -0.2 (-1.7, 1.3) | 0.0 (-1.0, 1.3) | -0.3 (-1.7, 0.8) |
Visit 8 | 0.4 (-1.7, 1.7) | 0.4 (-1.7, 1.7) | -0.2 (-1.7, 1.4) |
Visit 9 | 0.0 (-1.8, 1.6) | 0.0 (-1.2, 0.8) | 0.1 (-1.8, 1.6) |
Visit 10 | -0.1 (-1.3, 1.1) | 0.1 (-1.3, 1.1) | -0.2 (-0.8, 1.0) |
Lymphocytes | |||
Baseline | |||
Visit 1 | 0.1 (-1.3, 1.5) | -0.2 (-1.3, 1.5) | 0.2 (-1.2, 0.7) |
Visit 2 | -0.1 (-1.5, 2.0) | -0.1 (-1.4, 2.0) | 0.3 (-1.5, 2.0) |
Treatment | |||
Visit 3 | 0.0 (-1.7, 2.3) | -0.2 (-1.7, 1.7) | 0.4 (-0.4, 2.3) |
Visit 4 | 0.3 (-1.4, 1.2) | 0.3 (-0.8, 0.9) | 0.1 (-1.4, 1.2) |
Follow-up | |||
Visit 5 | 0.5 (-1.5, 2.1) | -0.4 (-1.5, 0.8) | 0.6 (-0.2, 2.1) |
Visit 6 | -0.2 (-2.9, 1.7) | -1.1 (-2.9, 0.6) | 0.2 (-2.2, 1.7) |
Visit 7 | 0.0 (-1.6, 1.9) | 0.5 (-1.4, 1.1) | -0.6 (-1.6, 1.9) |
Visit 8 | 0.2 (-1.2, 1.3) | 0.4 (-0.5, 0.8) | 0.0 (-1.2, 1.3) |
Visit 9 | 0.8 (-1.5, 1.7) | 0.8 (-1.5, 1.0) | 0.5 (-0.9, 1.7) |
Visit 10 | 0.8 (-1.5, 2.5) | 0.3 (-0.6, 2.5) | 0.8 (-1.5, 1.3) |
ANC | |||
Baseline | |||
Visit 1 | -0.8 (-1.5, 2.4) | -0.1 (-1.4, 2.0) | -0.8 (-1.5, 2.4) |
Visit 2 | -0.1 (-2.0, 1.5) | -0.3 (-2.0, 1.5) | 0.0 (-1.8, 1.2) |
Treatment | |||
Visit 3 | -0.2 (-2.0, 1.5) | -0.6 (-2.0, 0.2) | 0.0 (-1.4, 1.5) |
Visit 4 | 0.2 (-1.6, 0.9) | 0.2 (-1.0, 0.7) | 0.3 (-1.6, 0.9) |
Follow-up | |||
Visit 5 | -0.1 (-1.7, 2.0) | -0.4 (-1.7, 0.1) | 0.1 (-0.8, 2.0) |
Visit 6 | 0.3 (-1.4, 1.2) | 0.3 (-1.4, 1.2) | 0.2 (-1.4, 1.2) |
Visit 7 | -0.2 (-1.9, 1.4) | -0.1 (-1.9, 0.6) | -0.2 (-1.5, 1.4) |
Visit 8 | 0.4 (-2.2, 1.3) | 0.7 (-0.5, 1.3) | 0.1 (-2.2, 1.3) |
Visit 9 | 0.0 (-3.4, 1.5) | -0.1 (-3.4, 1.5) | 0.1 (-1.1, 1.1) |
Visit 10 | 0.2 (-1.6, 1.7) | 0.4 (-1.6, 1.3) | 0.0 (-1.2, 1.7) |
1Median (Min, Max) | |||
Sample size can be shown for each column, if the option
add_n is set to TRUE.
summaryByVisit(data,
vars = c("LDH", "Lymphocytes", "ANC"),
group = "arm",
overall = TRUE,
visitgroup = "visitgroup",
visit = "visit",
add_n = TRUE)Visit | N | Overall | N | Arm A | N | Arm B |
|---|---|---|---|---|---|---|
LDH | ||||||
Baseline | ||||||
Visit 1 | 15 | 0.3 (-1.4, 1.3) | 7 | 0.3 (-1.3, 1.3) | 8 | 0.1 (-1.4, 1.2) |
Visit 2 | 15 | 0.5 (-1.5, 1.9) | 7 | 0.5 (-0.2, 1.8) | 8 | 0.6 (-1.5, 1.9) |
Treatment | ||||||
Visit 3 | 14 | 0.0 (-2.2, 1.4) | 6 | 0.3 (-2.2, 1.4) | 8 | 0.0 (-1.0, 0.3) |
Visit 4 | 15 | 0.0 (-2.2, 1.1) | 7 | -0.2 (-2.2, 0.5) | 8 | 0.1 (-1.1, 1.1) |
Follow-up | ||||||
Visit 5 | 15 | -0.1 (-2.0, 1.1) | 7 | -0.5 (-2.0, 1.1) | 8 | 0.0 (-1.4, 0.7) |
Visit 6 | 15 | -0.1 (-1.4, 2.4) | 7 | -0.1 (-0.3, 1.1) | 8 | -0.9 (-1.4, 2.4) |
Visit 7 | 15 | -0.2 (-1.7, 1.3) | 7 | 0.0 (-1.0, 1.3) | 8 | -0.3 (-1.7, 0.8) |
Visit 8 | 15 | 0.4 (-1.7, 1.7) | 7 | 0.4 (-1.7, 1.7) | 8 | -0.2 (-1.7, 1.4) |
Visit 9 | 15 | 0.0 (-1.8, 1.6) | 7 | 0.0 (-1.2, 0.8) | 8 | 0.1 (-1.8, 1.6) |
Visit 10 | 15 | -0.1 (-1.3, 1.1) | 7 | 0.1 (-1.3, 1.1) | 8 | -0.2 (-0.8, 1.0) |
Lymphocytes | ||||||
Baseline | ||||||
Visit 1 | 15 | 0.1 (-1.3, 1.5) | 7 | -0.2 (-1.3, 1.5) | 8 | 0.2 (-1.2, 0.7) |
Visit 2 | 15 | -0.1 (-1.5, 2.0) | 7 | -0.1 (-1.4, 2.0) | 8 | 0.3 (-1.5, 2.0) |
Treatment | ||||||
Visit 3 | 15 | 0.0 (-1.7, 2.3) | 7 | -0.2 (-1.7, 1.7) | 8 | 0.4 (-0.4, 2.3) |
Visit 4 | 15 | 0.3 (-1.4, 1.2) | 7 | 0.3 (-0.8, 0.9) | 8 | 0.1 (-1.4, 1.2) |
Follow-up | ||||||
Visit 5 | 15 | 0.5 (-1.5, 2.1) | 7 | -0.4 (-1.5, 0.8) | 8 | 0.6 (-0.2, 2.1) |
Visit 6 | 15 | -0.2 (-2.9, 1.7) | 7 | -1.1 (-2.9, 0.6) | 8 | 0.2 (-2.2, 1.7) |
Visit 7 | 15 | 0.0 (-1.6, 1.9) | 7 | 0.5 (-1.4, 1.1) | 8 | -0.6 (-1.6, 1.9) |
Visit 8 | 15 | 0.2 (-1.2, 1.3) | 7 | 0.4 (-0.5, 0.8) | 8 | 0.0 (-1.2, 1.3) |
Visit 9 | 15 | 0.8 (-1.5, 1.7) | 7 | 0.8 (-1.5, 1.0) | 8 | 0.5 (-0.9, 1.7) |
Visit 10 | 15 | 0.8 (-1.5, 2.5) | 7 | 0.3 (-0.6, 2.5) | 8 | 0.8 (-1.5, 1.3) |
ANC | ||||||
Baseline | ||||||
Visit 1 | 15 | -0.8 (-1.5, 2.4) | 7 | -0.1 (-1.4, 2.0) | 8 | -0.8 (-1.5, 2.4) |
Visit 2 | 15 | -0.1 (-2.0, 1.5) | 7 | -0.3 (-2.0, 1.5) | 8 | 0.0 (-1.8, 1.2) |
Treatment | ||||||
Visit 3 | 15 | -0.2 (-2.0, 1.5) | 7 | -0.6 (-2.0, 0.2) | 8 | 0.0 (-1.4, 1.5) |
Visit 4 | 15 | 0.2 (-1.6, 0.9) | 7 | 0.2 (-1.0, 0.7) | 8 | 0.3 (-1.6, 0.9) |
Follow-up | ||||||
Visit 5 | 15 | -0.1 (-1.7, 2.0) | 7 | -0.4 (-1.7, 0.1) | 8 | 0.1 (-0.8, 2.0) |
Visit 6 | 15 | 0.3 (-1.4, 1.2) | 7 | 0.3 (-1.4, 1.2) | 8 | 0.2 (-1.4, 1.2) |
Visit 7 | 15 | -0.2 (-1.9, 1.4) | 7 | -0.1 (-1.9, 0.6) | 8 | -0.2 (-1.5, 1.4) |
Visit 8 | 15 | 0.4 (-2.2, 1.3) | 7 | 0.7 (-0.5, 1.3) | 8 | 0.1 (-2.2, 1.3) |
Visit 9 | 15 | 0.0 (-3.4, 1.5) | 7 | -0.1 (-3.4, 1.5) | 8 | 0.1 (-1.1, 1.1) |
Visit 10 | 15 | 0.2 (-1.6, 1.7) | 7 | 0.4 (-1.6, 1.3) | 8 | 0.0 (-1.2, 1.7) |
1Median (Min, Max) | ||||||
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They may not be fully stable and should be used with caution. We make no claims about them.
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