summaryByVisit

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:

Setup and data

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))

Basic table

Now, we use summarySCI::summaryLevels to create a summary table for median and range of each lab-value by visit.

summaryByVisit(data,
         vars = c("LDH", "Lymphocytes", "ANC"),
         visit = "visit", 
         add_n = TRUE)

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)

Add visit group

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)

By group

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 N = 71	Arm B N = 81
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 N = 151	Arm A N = 71	Arm B N = 81
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)

Add N

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)