Laboratory Results - Chemistry

Summary Statistics by Visit

Setup

See Prerequisites for installation instructions.

library(arframe)
library(pharmaverseadam)
library(dplyr, warn.conflicts = FALSE)
library(tidyr)
library(cards)

# Chemistry panel — 6 key parameters
param_subset <- c("ALT", "AST", "BILI", "CREAT", "GLUC", "SODIUM")

adlb_saf <- pharmaverseadam::adlb |>
  blank_to_na() |>
  filter(
    SAFFL   == "Y",
    TRT01A  != "Screen Failure",
    PARCAT1 == "CHEMISTRY",
    PARAMCD %in% param_subset,
    ANL01FL == "Y" | AVISIT == "Baseline"
  )

adsl_saf <- pharmaverseadam::adsl |>
  blank_to_na() |>
  filter(SAFFL == "Y", TRT01A != "Screen Failure")

arm_levels <- c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose")
arm_n      <- adsl_saf |> count(TRT01A) |> pull(n, name = TRT01A)

visit_order <- c(
  "Baseline", "Week 2", "Week 4", "Week 6", "Week 8",
  "Week 12", "Week 16", "Week 20", "Week 24", "Week 26"
)

adlb_saf <- adlb_saf |>
  mutate(
    AVISIT = factor(AVISIT, levels = visit_order),
    TRT01A = factor(TRT01A, levels = arm_levels)
  ) |>
  filter(!is.na(AVISIT))

Data Preparation

# ── Vertical layout: stats as rows, arms as columns ──
# Per PARAM × AVISIT × TRT01A: N, Mean, SD, Median, Min, Max
lab_stats <- adlb_saf |>
  group_by(PARAM, PARAMCD, AVISIT, TRT01A) |>
  summarise(
    n      = as.character(sum(!is.na(AVAL))),
    Mean   = sprintf("%.1f", mean(AVAL, na.rm = TRUE)),
    SD     = sprintf("%.2f", sd(AVAL, na.rm = TRUE)),
    Median = sprintf("%.1f", median(AVAL, na.rm = TRUE)),
    Min    = sprintf("%.0f", min(AVAL, na.rm = TRUE)),
    Max    = sprintf("%.0f", max(AVAL, na.rm = TRUE)),
    .groups = "drop"
  ) |>
  pivot_longer(
    cols      = c(n, Mean, SD, Median, Min, Max),
    names_to  = "stat_label",
    values_to = "value"
  ) |>
  pivot_wider(names_from = TRT01A, values_from = value) |>
  arrange(PARAM, AVISIT, match(stat_label, c("n", "Mean", "SD", "Median", "Min", "Max"))) |>
  mutate(across(where(is.factor), as.character))

# Ensure all arm columns present
for (arm in arm_levels) {
  if (!arm %in% names(lab_stats)) lab_stats[[arm]] <- ""
}

lab_wide <- lab_stats |>
  select(PARAM, PARAMCD, AVISIT, stat_label, all_of(arm_levels))

This tab showcases fr_wide_ard() with per-variable decimal precision — different lab parameters get different formatting based on their scale and clinical convention:

lab_data <- adlb_saf |>
  mutate(across(where(is.factor), as.character))

lab_ard <- ard_stack(
  data  = lab_data,
  .by   = c("TRT01A", "PARAM", "PARAMCD", "AVISIT"),
  ard_continuous(
    variables = "AVAL",
    statistic = ~ continuous_summary_fns(c("N", "mean", "sd", "median", "min", "max"))
  ),
  .overall = FALSE
) |>
  filter(variable == "AVAL")

# Per-variable decimals: different precision per lab parameter
lab_cards <- fr_wide_ard(
  lab_ard,
  statistic = list(
    continuous = c(
      "n"      = "{N}",
      "Mean"   = "{mean}",
      "SD"     = "{sd}",
      "Median" = "{median}",
      "Min"    = "{min}",
      "Max"    = "{max}"
    )
  ),
  decimals = list(
    ALT    = c(mean = 1, sd = 2, median = 1, min = 0, max = 0),
    AST    = c(mean = 1, sd = 2, median = 1, min = 0, max = 0),
    BILI   = c(mean = 2, sd = 3, median = 2, min = 1, max = 1),
    CREAT  = c(mean = 1, sd = 2, median = 1, min = 0, max = 0),
    GLUC   = c(mean = 1, sd = 2, median = 1, min = 0, max = 0),
    SODIUM = c(mean = 1, sd = 2, median = 1, min = 0, max = 0)
  ),
  column = "TRT01A",
  label  = c(AVAL = "Value")
) |>
  mutate(across(where(is.factor), as.character))

arframe Pipeline

The rendered table below uses the dplyr data prep (lab_wide). The cards tab produces an equivalent lab_cards — swap it in to use the cards path instead.

Stats as rows with treatment arms as columns, grouped by visit, one page per parameter:

lab_wide |>
  fr_table() |>
  fr_titles(
    "Table 14.3.4",
    "Laboratory Results Summary - Chemistry Panel",
    "Safety Population"
  ) |>
  fr_cols(
    PARAMCD    = fr_col(visible = FALSE),
    PARAM      = fr_col(visible = FALSE),
    AVISIT     = fr_col(visible = FALSE),
    stat_label = fr_col("", width = 1.5),
    !!!setNames(
      lapply(arm_levels, function(a) fr_col(a, align = "decimal")),
      arm_levels
    ),
    .n = arm_n
  ) |>
  fr_header(bold = TRUE, align = "center") |>
  fr_rows(
    group_by    = list(cols = "AVISIT", label = "stat_label"),
    blank_after = "AVISIT",
    page_by     = "PARAM",
    group_style = list(bold = TRUE)
  ) |>
  fr_footnotes(
    "N is the number of subjects in the Safety Population per treatment group.",
    "Statistics: n = number of non-missing observations, SD = Standard Deviation.",
    "Chemistry panel: ALT, AST, Bilirubin, Creatinine, Glucose, Sodium."
  )

Rendered Table

Table 14.3.4

Laboratory Results Summary - Chemistry Panel

Safety Population

Alanine Aminotransferase (U/L)

	Placebo (N=86)	Xanomeline Low Dose (N=96)	Xanomeline High Dose (N=72)
Baseline
n	86	94	72
Mean	17.6	18.1	19.2
SD	9.22	8.74	10.25
Median	15.0	16.5	16.5
Min	7	5	6
Max	69	70	64

Week 2
n	82	73	70
Mean	18.0	21.1	21.2
SD	12.59	10.74	8.87
Median	15.0	20.0	19.0
Min	6	5	8
Max	104	88	49

Week 4
n	75	65	67
Mean	17.2	17.4	21.5
SD	7.93	7.83	9.78
Median	15.0	16.0	20.0
Min	6	5	8
Max	45	62	61

Week 6
n	71	58	55
Mean	17.0	17.0	21.0
SD	10.04	8.25	10.08
Median	15.0	16.0	18.0
Min	4	5	10
Max	76	57	60

Week 8
n	70	54	52
Mean	16.9	18.0	23.4
SD	9.39	8.04	18.01
Median	15.0	17.0	18.0
Min	7	4	10
Max	63	54	129

Week 12
n	66	40	42
Mean	18.1	18.7	21.0
SD	9.16	13.24	10.69
Median	16.0	15.0	19.0
Min	6	9	9
Max	64	88	70

Week 16
n	67	32	33
Mean	17.1	17.0	20.0
SD	7.44	8.28	7.89
Median	15.0	15.5	19.0
Min	5	6	7
Max	48	43	38

Week 20
n	61	26	29
Mean	16.3	16.9	19.9
SD	6.71	6.21	6.81
Median	14.0	15.0	20.0
Min	7	11	9
Max	48	37	35

Week 24
n	57	24	28
Mean	17.9	18.6	21.3
SD	15.61	9.42	8.80
Median	14.0	17.0	18.5
Min	5	7	9
Max	124	48	43

Week 26
n	50	22	24
Mean	15.8	16.3	18.3
SD	6.03	6.36	6.01
Median	15.0	15.0	19.0
Min	3	7	8
Max	31	33	28

N is the number of subjects in the Safety Population per treatment group.

Statistics: n = number of non-missing observations, SD = Standard Deviation.

Chemistry panel: ALT, AST, Bilirubin, Creatinine, Glucose, Sodium.

/opt/quarto/share/rmd/rmd.R 01APR2026 09:54:00

Table 14.3.4

Laboratory Results Summary - Chemistry Panel

Safety Population

Aspartate Aminotransferase (U/L)

	Placebo (N=86)	Xanomeline Low Dose (N=96)	Xanomeline High Dose (N=72)
Baseline
n	86	94	72
Mean	23.2	23.3	23.2
SD	7.50	7.99	6.71
Median	22.0	21.0	21.0
Min	12	13	13
Max	54	60	52

Week 2
n	82	73	70
Mean	23.7	25.0	23.5
SD	12.40	8.31	4.93
Median	22.0	24.0	23.0
Min	12	10	15
Max	118	62	37

Week 4
n	75	65	67
Mean	22.4	22.2	24.0
SD	8.08	6.64	5.98
Median	21.0	20.0	24.0
Min	12	12	12
Max	66	46	43

Week 6
n	71	58	55
Mean	22.1	22.3	24.7
SD	6.44	6.19	8.29
Median	21.0	22.0	23.0
Min	14	9	15
Max	58	48	73

Week 8
n	70	54	52
Mean	22.5	22.8	26.1
SD	7.11	6.14	13.72
Median	21.0	22.0	24.5
Min	9	14	13
Max	54	44	114

Week 12
n	66	40	42
Mean	22.9	25.0	23.6
SD	7.64	17.43	6.52
Median	22.0	21.5	23.0
Min	11	14	12
Max	62	125	50

Week 16
n	67	32	33
Mean	22.9	22.8	23.5
SD	6.45	11.57	5.61
Median	22.0	20.0	22.0
Min	13	12	15
Max	49	76	40

Week 20
n	61	26	29
Mean	22.1	20.3	24.3
SD	6.03	4.87	7.00
Median	21.0	19.0	22.0
Min	12	12	16
Max	48	33	45

Week 24
n	57	24	28
Mean	25.2	22.7	24.9
SD	21.02	11.18	7.37
Median	22.0	20.0	22.5
Min	11	11	17
Max	168	68	48

Week 26
n	50	22	24
Mean	21.5	20.0	21.1
SD	7.29	4.53	5.54
Median	20.5	19.0	19.5
Min	10	14	15
Max	58	32	38

N is the number of subjects in the Safety Population per treatment group.

Statistics: n = number of non-missing observations, SD = Standard Deviation.

Chemistry panel: ALT, AST, Bilirubin, Creatinine, Glucose, Sodium.

/opt/quarto/share/rmd/rmd.R 01APR2026 09:54:00

Table 14.3.4

Laboratory Results Summary - Chemistry Panel

Safety Population

Bilirubin (umol/L)

	Placebo (N=86)	Xanomeline Low Dose (N=96)	Xanomeline High Dose (N=72)
Baseline
n	86	94	72
Mean	9.7	9.5	11.2
SD	3.96	3.91	5.63
Median	8.5	8.5	10.3
Min	5	5	3
Max	26	27	39

Week 2
n	82	72	70
Mean	10.8	9.6	10.5
SD	12.33	4.29	4.04
Median	8.5	8.5	10.3
Min	3	5	5
Max	116	26	26

Week 4
n	75	64	67
Mean	9.7	9.0	11.1
SD	4.12	3.67	5.77
Median	8.5	8.5	10.3
Min	5	3	5
Max	22	22	34

Week 6
n	71	58	55
Mean	9.7	9.3	10.9
SD	3.80	3.91	4.98
Median	8.5	8.5	10.3
Min	3	3	5
Max	22	24	29

Week 8
n	70	54	52
Mean	9.4	9.5	10.9
SD	3.94	4.79	5.40
Median	8.5	8.5	9.4
Min	3	3	5
Max	26	26	29

Week 12
n	66	40	42
Mean	9.5	8.9	11.2
SD	3.59	4.44	6.06
Median	8.5	8.5	8.5
Min	5	3	3
Max	22	24	36

Week 16
n	67	32	33
Mean	10.0	8.6	11.5
SD	3.65	4.06	4.88
Median	8.5	6.8	10.3
Min	5	5	5
Max	22	24	26

Week 20
n	61	26	29
Mean	9.8	8.9	12.0
SD	5.10	4.17	8.95
Median	8.5	7.7	8.5
Min	3	5	5
Max	27	21	53

Week 24
n	55	24	28
Mean	9.4	10.1	12.2
SD	3.39	4.54	6.72
Median	8.5	8.5	10.3
Min	5	5	5
Max	24	22	31

Week 26
n	50	22	24
Mean	10.3	10.5	12.0
SD	4.85	6.56	7.10
Median	8.5	8.5	10.3
Min	5	5	3
Max	31	32	29

N is the number of subjects in the Safety Population per treatment group.

Statistics: n = number of non-missing observations, SD = Standard Deviation.

Chemistry panel: ALT, AST, Bilirubin, Creatinine, Glucose, Sodium.

/opt/quarto/share/rmd/rmd.R 01APR2026 09:54:00

Table 14.3.4

Laboratory Results Summary - Chemistry Panel

Safety Population

Creatinine (umol/L)

	Placebo (N=86)	Xanomeline Low Dose (N=96)	Xanomeline High Dose (N=72)
Baseline
n	86	94	72
Mean	97.7	103.8	103.3
SD	17.78	19.40	20.06
Median	97.2	101.7	97.2
Min	62	71	62
Max	159	168	159

Week 2
n	83	73	70
Mean	99.1	105.6	106.2
SD	17.61	21.40	21.84
Median	97.2	106.1	106.1
Min	71	71	62
Max	141	177	168

Week 4
n	78	65	67
Mean	98.8	104.7	105.8
SD	18.67	20.45	21.38
Median	97.2	97.2	106.1
Min	71	71	71
Max	177	168	177

Week 6
n	73	60	56
Mean	101.6	104.0	106.4
SD	18.70	20.29	22.17
Median	97.2	97.2	106.1
Min	71	71	71
Max	150	168	177

Week 8
n	71	54	52
Mean	99.1	102.0	105.1
SD	16.29	19.10	21.63
Median	97.2	106.1	106.1
Min	71	62	71
Max	141	159	177

Week 12
n	66	41	42
Mean	101.4	103.9	105.4
SD	16.64	18.73	18.97
Median	106.1	97.2	106.1
Min	71	71	62
Max	133	168	141

Week 16
n	67	32	33
Mean	100.4	97.5	102.1
SD	16.55	17.17	17.69
Median	97.2	97.2	97.2
Min	71	71	71
Max	133	133	133

Week 20
n	62	27	29
Mean	99.9	97.2	102.7
SD	17.79	18.35	19.97
Median	101.7	97.2	106.1
Min	62	71	71
Max	133	133	141

Week 24
n	57	25	28
Mean	99.3	99.4	99.4
SD	15.85	16.79	20.08
Median	97.2	97.2	101.7
Min	71	80	62
Max	141	141	133

Week 26
n	50	22	24
Mean	101.3	98.8	100.2
SD	19.09	19.79	18.74
Median	97.2	97.2	106.1
Min	71	71	71
Max	150	141	133

N is the number of subjects in the Safety Population per treatment group.

Statistics: n = number of non-missing observations, SD = Standard Deviation.

Chemistry panel: ALT, AST, Bilirubin, Creatinine, Glucose, Sodium.

/opt/quarto/share/rmd/rmd.R 01APR2026 09:54:00

Table 14.3.4

Laboratory Results Summary - Chemistry Panel

Safety Population

Glucose (mmol/L)

	Placebo (N=86)	Xanomeline Low Dose (N=96)	Xanomeline High Dose (N=72)
Baseline
n	86	94	72
Mean	5.6	5.4	5.4
SD	2.14	0.99	1.36
Median	5.2	5.2	5.1
Min	4	3	3
Max	22	9	11

Week 2
n	82	73	70
Mean	5.6	5.6	6.2
SD	1.88	1.82	3.06
Median	5.2	5.3	5.4
Min	3	4	3
Max	18	17	23

Week 4
n	75	63	67
Mean	5.6	5.5	5.8
SD	1.92	1.46	1.71
Median	5.2	5.3	5.3
Min	3	3	4
Max	18	13	14

Week 6
n	71	58	55
Mean	5.7	5.4	5.9
SD	2.25	1.38	2.87
Median	5.2	5.2	5.2
Min	3	4	4
Max	20	14	24

Week 8
n	70	54	52
Mean	5.5	5.6	5.7
SD	1.36	1.82	1.88
Median	5.2	5.2	5.4
Min	3	4	4
Max	12	15	16

Week 12
n	66	40	41
Mean	6.1	6.1	5.8
SD	1.98	3.52	2.05
Median	5.6	5.4	5.2
Min	4	3	4
Max	15	26	15

Week 16
n	67	32	33
Mean	5.5	5.4	5.4
SD	1.42	0.86	1.16
Median	5.2	5.3	5.2
Min	4	4	3
Max	12	9	8

Week 20
n	61	26	29
Mean	5.8	5.6	5.8
SD	1.54	1.68	1.66
Median	5.6	5.3	5.3
Min	4	4	4
Max	15	12	11

Week 24
n	57	24	28
Mean	5.7	5.8	6.0
SD	1.83	1.28	1.91
Median	5.3	5.3	5.4
Min	3	4	4
Max	13	10	14

Week 26
n	50	22	24
Mean	5.7	5.6	5.6
SD	1.90	1.84	1.07
Median	5.3	5.3	5.4
Min	3	3	4
Max	15	11	8

N is the number of subjects in the Safety Population per treatment group.

Statistics: n = number of non-missing observations, SD = Standard Deviation.

Chemistry panel: ALT, AST, Bilirubin, Creatinine, Glucose, Sodium.

/opt/quarto/share/rmd/rmd.R 01APR2026 09:54:00

Table 14.3.4

Laboratory Results Summary - Chemistry Panel

Safety Population

Sodium (mmol/L)

	Placebo (N=86)	Xanomeline Low Dose (N=96)	Xanomeline High Dose (N=72)
Baseline
n	86	94	71
Mean	140.3	140.0	140.0
SD	2.74	2.66	3.13
Median	140.0	140.0	140.0
Min	132	132	130
Max	147	145	148

Week 2
n	83	73	69
Mean	140.3	139.7	139.1
SD	2.59	2.57	2.77
Median	140.0	139.0	139.0
Min	129	135	131
Max	149	147	147

Week 4
n	78	65	67
Mean	139.9	140.2	139.7
SD	2.76	2.48	2.73
Median	140.0	140.0	140.0
Min	132	133	134
Max	146	145	147

Week 6
n	73	60	56
Mean	140.3	140.6	140.1
SD	2.61	2.74	2.49
Median	140.0	141.0	140.5
Min	129	133	135
Max	145	146	145

Week 8
n	71	54	52
Mean	140.6	140.2	140.3
SD	2.47	2.42	3.24
Median	140.0	141.0	140.5
Min	135	134	132
Max	148	146	154

Week 12
n	66	41	41
Mean	140.4	140.7	140.3
SD	2.41	2.65	2.40
Median	141.0	140.0	140.0
Min	134	135	134
Max	145	146	145

Week 16
n	67	32	33
Mean	141.1	140.9	141.8
SD	2.34	2.58	2.89
Median	141.0	140.5	142.0
Min	134	135	138
Max	145	145	148

Week 20
n	61	27	29
Mean	141.2	141.4	142.0
SD	2.16	2.58	3.93
Median	141.0	141.0	142.0
Min	136	137	133
Max	145	146	151

Week 24
n	57	25	28
Mean	141.7	141.4	141.4
SD	2.23	2.18	2.96
Median	142.0	142.0	141.5
Min	135	136	134
Max	146	145	149

Week 26
n	50	22	24
Mean	142.5	142.0	142.2
SD	2.22	2.17	3.19
Median	142.0	142.0	142.5
Min	138	137	134
Max	148	145	149

N is the number of subjects in the Safety Population per treatment group.

Statistics: n = number of non-missing observations, SD = Standard Deviation.

Chemistry panel: ALT, AST, Bilirubin, Creatinine, Glucose, Sodium.

/opt/quarto/share/rmd/rmd.R 01APR2026 09:54:00