Tables • sbcdata

Authors: Sebastian Gibb [aut, cre], Paul Ahrens [aut, dtc], Daniel Steinbach [aut, dtc], Maria Schmidt [aut, dtc], Thorsten Kaiser [aut, dtc], Mark Wernsdorfer [dtc], Matthias Nauck [dtc], Stefan Bollmann [dtc], Thomas Hildebrandt [dtc]
Last modified: 2024-03-07 08:43:33.649335
Compiled: Thu Mar 7 08:46:12 2024

sbcdata <- sbc_exclude_entries(sbcdata)
sbcdata <- sbcdata[(!Excluded),]

.lbl <- function(x, unit) {
    if (nchar(unit))
        paste0(x, " [", unit, "]")
     else
        x
}

for (i in seq_len(nrow(labcodes))) {
    attr(sbcdata[[labcodes$Code[i]]], "label") <-
        .lbl(labcodes$Code[i], labcodes$Unit[i])
}

Baseline Leipzig

library("gtsummary")
theme_gtsummary_journal(journal = "nejm")

## Setting theme `New England Journal of Medicine`

theme_gtsummary_compact()

## Setting theme `Compact`

ukl <- subset(sbcdata, Center == "Leipzig")

tblGeneral <- ukl[!duplicated(ukl$Id),] |>
    select(Age, Sex, Diagnosis) |>
    tbl_summary(by = Diagnosis, missing_text = "(Missing)") |>
    add_p()

tblLabs <- ukl[, c("Diagnosis", labcodes$Code), with = FALSE] |>
    tbl_summary(by = Diagnosis, missing_text = "(Missing)") |>
    add_p()

tbl_stack(
    list(add_n(tblGeneral), add_n(tblLabs)),
    group_header = c("General", "Laboratory Diagnostics")
)

## ℹ Column headers among stacked tables differ. Headers from the first table are
## used. Use `quiet = TRUE` to suppress this message.

Characteristic	N	Control, N = 705,710¹	Sepsis, N = 2,885¹
General
Age	708,595	57 (39 – 71)	67 (58 – 77)
Sex	708,595
M		337,562 (48)	1,847 (64)
W		368,148 (52)	1,038 (36)
Laboratory Diagnostics
CRP [mg/l]	955,616	8 (2 – 32)	57 (18 – 139)
(Missing)		420,089	5,653
HGB [mmol/l]	1,381,358	7.80 (6.50 – 8.70)	5.40 (4.80 – 6.40)
MCV [fl]	1,381,358	87.9 (84.6 – 91.5)	86.8 (82.9 – 91.6)
PCT [ng/ml]	35,687	0.12 (0.07 – 0.32)	1.07 (0.34 – 4.76)
(Missing)		1,330,724	14,947
PLT [Gpt/l]	1,381,358	236 (181 – 297)	70 (26 – 191)
RBC [Tpt/l]	1,381,358	4.20 (3.56 – 4.68)	2.93 (2.59 – 3.50)
WBC [Gpt/l]	1,381,358	7.4 (5.6 – 9.7)	4.9 (0.9 – 10.9)
¹ Median (IQR); n (%)
² Wilcoxon rank sum test; Pearson’s Chi-squared test

Greifswald vs Leipzig

tblGeneral <- sbcdata[
    !duplicated(sbcdata[,c("Id", "Center"), with = FALSE]),
] |>
    select(Age, Sex, Diagnosis, Center) |>
    tbl_summary(by = Center, missing_text = "(Missing)") |>
    add_p()

tblLabs <- sbcdata[, c("Center", labcodes$Code), with = FALSE] |>
    tbl_summary(by = Center, missing_text = "(Missing)") |>
    add_p()

tbl_stack(
    list(add_n(tblGeneral), add_n(tblLabs)),
    group_header = c("General", "Laboratory Diagnostics")
)

## ℹ Column headers among stacked tables differ. Headers from the first table are
## used. Use `quiet = TRUE` to suppress this message.

Characteristic	N	Greifswald, N = 157,922¹	Leipzig, N = 708,595¹	p-value²
General
Age	866,517	63 (50 – 76)	57 (39 – 71)
Sex	866,517
M		79,039 (50)	339,409 (48)
W		78,883 (50)	369,186 (52)
Diagnosis	866,517			0.010
Control		157,206 (100)	705,710 (100)
Sepsis		716 (0.5)	2,885 (0.4)
Laboratory Diagnostics
CRP [mg/l]	1,160,718	26 (10 – 72)	8 (2 – 33)
(Missing)		232,975	425,742
HGB [mmol/l]	1,819,435	7.50 (6.20 – 8.50)	7.70 (6.50 – 8.60)
MCV [fl]	1,819,435	90.3 (86.8 – 94.1)	87.9 (84.5 – 91.5)
PCT [ng/ml]	45,234	0.21 (0.09 – 0.63)	0.13 (0.07 – 0.37)
(Missing)		428,530	1,345,671
PLT [Gpt/l]	1,819,435	225 (173 – 285)	236 (179 – 296)
RBC [Tpt/l]	1,819,435	4.10 (3.40 – 4.60)	4.19 (3.54 – 4.67)
WBC [Gpt/l]	1,819,435	8.1 (6.2 – 10.7)	7.4 (5.5 – 9.7)
¹ Median (IQR); n (%)
² Wilcoxon rank sum test; Pearson’s Chi-squared test

Leipzig PCT

pct <- ukl[sbcdata:::.is_cbc(ukl, labcodes$Code[-1], complete = TRUE), ]
tblGeneral <- pct[!duplicated(pct$Id),] |>
    select(Age, Sex, Diagnosis) |>
    tbl_summary(by = Diagnosis, missing_text = "(Missing)") |>
    add_p()

tblLabs <- pct[, c("Diagnosis", labcodes$Code), with = FALSE] |>
    tbl_summary(by = Diagnosis, missing_text = "(Missing)") |>
    add_p()

tbl_stack(
    list(add_n(tblGeneral), add_n(tblLabs)),
    group_header = c("General", "Laboratory Diagnostics")
)

## ℹ Column headers among stacked tables differ. Headers from the first table are
## used. Use `quiet = TRUE` to suppress this message.

Characteristic	N	Control, N = 24,773¹	Sepsis, N = 1,112¹	p-value²
General
Age	25,885	62 (52 – 71)	66 (56 – 76)
Sex	25,885			0.003
M		14,882 (60)	717 (64)
W		9,891 (40)	395 (36)
Laboratory Diagnostics
CRP [mg/l]	34,354	34 (6 – 114)	131 (51 – 244)
(Missing)		1,291	42
HGB [mmol/l]	35,687	7.20 (6.00 – 8.20)	6.00 (5.00 – 7.50)
MCV [fl]	35,687	87 (83 – 91)	87 (83 – 92)	0.068
PCT [ng/ml]	35,687	0.12 (0.07 – 0.32)	1.07 (0.34 – 4.76)
PLT [Gpt/l]	35,687	221 (153 – 310)	165 (52 – 272)
RBC [Tpt/l]	35,687	3.96 (3.33 – 4.54)	3.28 (2.74 – 4.10)
WBC [Gpt/l]	35,687	7.6 (5.3 – 11.2)	10.4 (4.0 – 17.1)
¹ Median (IQR); n (%)
² Wilcoxon rank sum test; Pearson’s Chi-squared test