5 ‘flextable’ et le package ‘tables’

5.1 tables

Le package ‘tables’ https://dmurdoch.github.io/tables/ fournit une interface basée sur un système de formules pour calculer le contenu des tableaux et pour les formater.

Il a été très inspiré par SAS PROC TABULATE.

L’utilisateur peut créer un objet tableau en spécifiant une formule, avec le côté gauche indiquant les lignes et le côté droit indiquant les colonnes. La formule décrit les fonctions de résumé à appliquer et la manière de les organiser. Les objets peuvent être filtrés ou combinés en utilisant des opérations similaires à celles des matrices. Les tableaux peuvent être rendus sous forme de texte brut, de code LaTeX pour apparaître dans un document PDF, ou de code HTML pour un document web.

5.2 Un exemple de tableau d’évènements indésirables

On va avoir besoin de deux tables “cliniques”.

Code

ex_adae <- formatters::ex_adae
ex_adae

STUDYID	USUBJID	SUBJID	SITEID	AGE	SEX	RACE	COUNTRY	INVID	ARM	ARMCD	ACTARM	ACTARMCD	STRATA1	STRATA2	BMRKR1	BMRKR2	ITTFL	SAFFL	BMEASIFL	BEP01FL	RANDDT	TRTSDTM	TRTEDTM	EOSSTT	EOSDT	EOSDY	DCSREAS	DTHDT	LSTALVDT	study_duration_secs	ASEQ	AESEQ	AETERM	AELLT	AEDECOD	AEHLT	AEHLGT	AEBODSYS	AESOC	AESEV	AESER	AREL	ASTDTM	AENDTM	ASTDY	AENDY	AETOXGR
character	character	character	character	integer	factor	factor	factor	character	factor	factor	factor	factor	factor	factor	numeric	factor	factor	factor	factor	factor	Date	POSIXct	POSIXct	factor	Date	integer	factor	Date	Date	numeric	integer	integer	factor	factor	factor	factor	factor	factor	factor	factor	factor	factor	POSIXct	POSIXct	integer	integer	factor
AB12345	AB12345-BRA-1-id-134	id-134	BRA-1	47	M	WHITE	BRA	BRA-1	A: Drug X	ARM A	A: Drug X	ARM A	B	S2	6.5	LOW	Y	Y	Y	N	2021-06-09	2021-06-10 13:26:53	2023-06-11 01:05:17	COMPLETED	2023-06-11	731		2023-06-11	2023-06-29	63,113,904	1	1	trm B.2.1.2.1	llt B.2.1.2.1	dcd B.2.1.2.1	hlt B.2.1.2	hlgt B.2.1	cl B.2	cl B	MODERATE	N	N	2022-02-16 00:00:00	2022-11-10 00:00:00	251	518	3
AB12345	AB12345-BRA-1-id-134	id-134	BRA-1	47	M	WHITE	BRA	BRA-1	A: Drug X	ARM A	A: Drug X	ARM A	B	S2	6.5	LOW	Y	Y	Y	N	2021-06-09	2021-06-10 13:26:53	2023-06-11 01:05:17	COMPLETED	2023-06-11	731		2023-06-11	2023-06-29	63,113,904	2	2	trm D.1.1.4.2	llt D.1.1.4.2	dcd D.1.1.4.2	hlt D.1.1.4	hlgt D.1.1	cl D.1	cl D	MODERATE	N	N	2022-04-10 00:00:00	2022-12-21 00:00:00	304	559	3
AB12345	AB12345-BRA-1-id-134	id-134	BRA-1	47	M	WHITE	BRA	BRA-1	A: Drug X	ARM A	A: Drug X	ARM A	B	S2	6.5	LOW	Y	Y	Y	N	2021-06-09	2021-06-10 13:26:53	2023-06-11 01:05:17	COMPLETED	2023-06-11	731		2023-06-11	2023-06-29	63,113,904	3	3	trm A.1.1.1.2	llt A.1.1.1.2	dcd A.1.1.1.2	hlt A.1.1.1	hlgt A.1.1	cl A.1	cl A	MODERATE	Y	N	2022-10-20 00:00:00	2023-06-05 00:00:00	497	725	2
AB12345	AB12345-BRA-1-id-134	id-134	BRA-1	47	M	WHITE	BRA	BRA-1	A: Drug X	ARM A	A: Drug X	ARM A	B	S2	6.5	LOW	Y	Y	Y	N	2021-06-09	2021-06-10 13:26:53	2023-06-11 01:05:17	COMPLETED	2023-06-11	731		2023-06-11	2023-06-29	63,113,904	4	4	trm A.1.1.1.2	llt A.1.1.1.2	dcd A.1.1.1.2	hlt A.1.1.1	hlgt A.1.1	cl A.1	cl A	MODERATE	Y	N	2023-02-08 00:00:00	2023-04-15 00:00:00	608	674	2
AB12345	AB12345-BRA-1-id-141	id-141	BRA-1	35	F	WHITE	BRA	BRA-1	C: Combination	ARM C	C: Combination	ARM C	B	S1	7.5	HIGH	Y	Y	Y	Y	2021-02-25	2021-02-28 23:47:16	2023-03-01 11:25:40	COMPLETED	2023-03-01	731		2023-03-01	2023-03-30	63,113,904	1	1	trm B.2.1.2.1	llt B.2.1.2.1	dcd B.2.1.2.1	hlt B.2.1.2	hlgt B.2.1	cl B.2	cl B	MODERATE	N	N	2021-11-14 00:00:00	2021-11-21 00:00:00	259	266	3
AB12345	AB12345-BRA-1-id-141	id-141	BRA-1	35	F	WHITE	BRA	BRA-1	C: Combination	ARM C	C: Combination	ARM C	B	S1	7.5	HIGH	Y	Y	Y	Y	2021-02-25	2021-02-28 23:47:16	2023-03-01 11:25:40	COMPLETED	2023-03-01	731		2023-03-01	2023-03-30	63,113,904	2	2	trm D.2.1.5.3	llt D.2.1.5.3	dcd D.2.1.5.3	hlt D.2.1.5	hlgt D.2.1	cl D.2	cl D	MILD	N	Y	2021-12-28 00:00:00	2023-02-21 00:00:00	303	723	1
AB12345	AB12345-BRA-1-id-141	id-141	BRA-1	35	F	WHITE	BRA	BRA-1	C: Combination	ARM C	C: Combination	ARM C	B	S1	7.5	HIGH	Y	Y	Y	Y	2021-02-25	2021-02-28 23:47:16	2023-03-01 11:25:40	COMPLETED	2023-03-01	731		2023-03-01	2023-03-30	63,113,904	3	3	trm A.1.1.1.1	llt A.1.1.1.1	dcd A.1.1.1.1	hlt A.1.1.1	hlgt A.1.1	cl A.1	cl A	MILD	N	N	2022-07-06 00:00:00	2022-07-29 00:00:00	493	516	1
AB12345	AB12345-BRA-1-id-141	id-141	BRA-1	35	F	WHITE	BRA	BRA-1	C: Combination	ARM C	C: Combination	ARM C	B	S1	7.5	HIGH	Y	Y	Y	Y	2021-02-25	2021-02-28 23:47:16	2023-03-01 11:25:40	COMPLETED	2023-03-01	731		2023-03-01	2023-03-30	63,113,904	4	4	trm A.1.1.1.2	llt A.1.1.1.2	dcd A.1.1.1.2	hlt A.1.1.1	hlgt A.1.1	cl A.1	cl A	MODERATE	Y	N	2022-10-21 00:00:00	2023-01-22 00:00:00	600	693	2
AB12345	AB12345-BRA-1-id-141	id-141	BRA-1	35	F	WHITE	BRA	BRA-1	C: Combination	ARM C	C: Combination	ARM C	B	S1	7.5	HIGH	Y	Y	Y	Y	2021-02-25	2021-02-28 23:47:16	2023-03-01 11:25:40	COMPLETED	2023-03-01	731		2023-03-01	2023-03-30	63,113,904	5	5	trm A.1.1.1.1	llt A.1.1.1.1	dcd A.1.1.1.1	hlt A.1.1.1	hlgt A.1.1	cl A.1	cl A	MILD	N	N	2022-11-25 00:00:00	2023-01-07 00:00:00	635	678	1
AB12345	AB12345-BRA-1-id-141	id-141	BRA-1	35	F	WHITE	BRA	BRA-1	C: Combination	ARM C	C: Combination	ARM C	B	S1	7.5	HIGH	Y	Y	Y	Y	2021-02-25	2021-02-28 23:47:16	2023-03-01 11:25:40	COMPLETED	2023-03-01	731		2023-03-01	2023-03-30	63,113,904	6	6	trm D.1.1.1.1	llt D.1.1.1.1	dcd D.1.1.1.1	hlt D.1.1.1	hlgt D.1.1	cl D.1	cl D	SEVERE	Y	N	2023-02-28 00:00:00	2023-03-01 00:00:00	730	731	5
n: 1934

Code

ex_adsl <- formatters::ex_adsl
ex_adsl

STUDYID	USUBJID	SUBJID	SITEID	AGE	SEX	RACE	COUNTRY	INVID	ARM	ARMCD	ACTARM	ACTARMCD	STRATA1	STRATA2	BMRKR1	BMRKR2	ITTFL	SAFFL	BMEASIFL	BEP01FL	RANDDT	TRTSDTM	TRTEDTM	EOSSTT	EOSDT	EOSDY	DCSREAS	DTHDT	LSTALVDT	study_duration_secs
character	character	character	character	integer	factor	factor	factor	character	factor	factor	factor	factor	factor	factor	numeric	factor	factor	factor	factor	factor	Date	POSIXct	POSIXct	factor	Date	integer	factor	Date	Date	numeric
AB12345	AB12345-CHN-3-id-128	id-128	CHN-3	32	M	ASIAN	CHN	CHN-3	A: Drug X	ARM A	A: Drug X	ARM A	C	S2	14.4	MEDIUM	Y	Y	Y	Y	2019-09-28	2019-09-30 20:45:38	2021-09-30 08:24:02	COMPLETED	2021-09-30	731		2021-09-30	2021-10-22	63,113,904
AB12345	AB12345-CHN-15-id-262	id-262	CHN-15	35	M	BLACK OR AFRICAN AMERICAN	CHN	CHN-15	C: Combination	ARM C	C: Combination	ARM C	C	S1	4.1	LOW	Y	Y	N	N	2019-10-02	2019-10-02 18:41:20	2021-10-02 06:19:44	COMPLETED	2021-10-02	731		2021-10-02	2021-10-24	63,113,904
AB12345	AB12345-RUS-3-id-378	id-378	RUS-3	30	F	ASIAN	RUS	RUS-3	C: Combination	ARM C	C: Combination	ARM C	A	S1	2.8	HIGH	Y	Y	Y	N	2019-09-30	2019-10-04 12:55:28	2021-10-04 00:33:52	COMPLETED	2021-10-04	731		2021-10-04	2021-10-15	63,113,904
AB12345	AB12345-CHN-11-id-220	id-220	CHN-11	26	F	ASIAN	CHN	CHN-11	B: Placebo	ARM B	B: Placebo	ARM B	B	S2	10.3	MEDIUM	Y	Y	Y	Y	2019-10-03	2019-10-05 23:09:23	2021-10-05 10:47:47	COMPLETED	2021-10-05	731		2021-10-05	2021-10-24	63,113,904
AB12345	AB12345-CHN-7-id-267	id-267	CHN-7	40	M	ASIAN	CHN	CHN-7	B: Placebo	ARM B	B: Placebo	ARM B	C	S1	6.2	LOW	Y	Y	N	N	2019-10-05	2019-10-06 09:45:36	2021-10-05 21:24:00	COMPLETED	2021-10-05	731		2021-10-05	2021-11-03	63,113,904
AB12345	AB12345-CHN-15-id-201	id-201	CHN-15	49	M	ASIAN	CHN	CHN-15	C: Combination	ARM C	C: Combination	ARM C	C	S2	6.9	MEDIUM	Y	Y	Y	N	2019-10-10	2019-10-10 01:00:04	2021-09-24 06:00:13	DISCONTINUED	2021-09-24	716	WITHDRAWAL BY PARENT/GUARDIAN	2021-09-24	2021-10-22	63,113,904
AB12345	AB12345-USA-1-id-45	id-45	USA-1	34	F	ASIAN	USA	USA-1	A: Drug X	ARM A	A: Drug X	ARM A	C	S1	0.5	LOW	Y	Y	N	N	2019-10-08	2019-10-10 16:08:24	2021-10-10 03:46:48	COMPLETED	2021-10-10	731		2021-10-10	2021-10-24	63,113,904
AB12345	AB12345-USA-1-id-261	id-261	USA-1	32	F	ASIAN	USA	USA-1	B: Placebo	ARM B	B: Placebo	ARM B	C	S1	2.9	HIGH	Y	Y	Y	N	2019-10-07	2019-10-11 02:57:15	2021-10-10 14:35:39	COMPLETED	2021-10-10	731		2021-10-10	2021-10-26	63,113,904
AB12345	AB12345-NGA-11-id-173	id-173	NGA-11	24	F	BLACK OR AFRICAN AMERICAN	NGA	NGA-11	C: Combination	ARM C	C: Combination	ARM C	C	S2	5.0	LOW	Y	Y	Y	Y	2019-10-12	2019-10-14 19:11:18	2021-10-14 06:49:42	COMPLETED	2021-10-14	731		2021-10-14	2021-10-25	63,113,904
AB12345	AB12345-CHN-1-id-307	id-307	CHN-1	24	M	ASIAN	CHN	CHN-1	B: Placebo	ARM B	B: Placebo	ARM B	C	S1	4.6	LOW	Y	Y	Y	N	2019-10-12	2019-10-15 17:37:13	2021-10-15 05:15:37	COMPLETED	2021-10-15	731		2021-10-15	2021-11-03	63,113,904
n: 400

On va préparer quelques pré-calculs et deux fonctions de résumé.

Code

subject_counts <- table(ex_adsl$ARM)

countpercentid <- function(num, ARM) {
  n <- length(unique(num))
  if (n == 0) {
    pct <- 0
  } else {
    pct <- 100*n/subject_counts[ARM[1]]
  }
  sprintf("%d (%.2f%%)", length(unique(num)), pct)
}

count <- function(x) sprintf("(N=%d)", length(x))

On peut enfin exprimer le tableau de suivi des évènements indésirables avec ‘tables’.

Code

library(tables)
body <- tabular( 
  Heading("Patients with at least one event")*1*
    Heading("")*countpercentid*Arguments(ARM = ARM)*
    Heading()*USUBJID +
    Heading("Total number of events")*1*Heading("")*1 +
    Heading()*AEBODSYS*
    (Heading("Patients with at least one event")*
       Percent(denom = ARM, fn = countpercentid)*
       Heading()*USUBJID +
       Heading("Total number of events")*1 +
       Heading()*AEDECOD*DropEmpty(which = "row")*
       Heading()*Percent(denom = ARM, fn = countpercentid)*
       Heading()*USUBJID) ~ 
    Heading()*ARM, 
data = ex_adae )

Code

body

		A: Drug X	B: Placebo	C: Combination
Patients with at least one event		122 (91.04%)	123 (91.79%)	120 (90.91%)
Total number of events		609	622	703
cl A.1	Patients with at least one event	78 (58.21%)	75 (55.97%)	89 (66.42%)
	Total number of events	132	130	160
	dcd A.1.1.1.1	50 (37.31%)	45 (33.58%)	63 (47.01%)
	dcd A.1.1.1.2	48 (35.82%)	48 (35.82%)	50 (37.31%)
cl B.1	Patients with at least one event	47 (35.07%)	49 (36.57%)	43 (32.09%)
	Total number of events	56	60	62
	dcd B.1.1.1.1	47 (35.07%)	49 (36.57%)	43 (32.09%)
cl B.2	Patients with at least one event	79 (58.96%)	74 (55.22%)	85 (63.43%)
	Total number of events	129	138	143
	dcd B.2.1.2.1	49 (36.57%)	44 (32.84%)	52 (38.81%)
	dcd B.2.2.3.1	48 (35.82%)	54 (40.30%)	51 (38.06%)
cl C.1	Patients with at least one event	43 (32.09%)	46 (34.33%)	43 (32.09%)
	Total number of events	55	63	64
	dcd C.1.1.1.3	43 (32.09%)	46 (34.33%)	43 (32.09%)
cl C.2	Patients with at least one event	35 (26.12%)	48 (35.82%)	55 (41.04%)
	Total number of events	48	53	65
	dcd C.2.1.2.1	35 (26.12%)	48 (35.82%)	55 (41.04%)
cl D.1	Patients with at least one event	79 (58.96%)	67 (50.00%)	80 (59.70%)
	Total number of events	127	106	135
	dcd D.1.1.1.1	50 (37.31%)	42 (31.34%)	51 (38.06%)
	dcd D.1.1.4.2	48 (35.82%)	42 (31.34%)	50 (37.31%)
cl D.2	Patients with at least one event	47 (35.07%)	58 (43.28%)	57 (42.54%)
	Total number of events	62	72	74
	dcd D.2.1.5.3	47 (35.07%)	58 (43.28%)	57 (42.54%)

5.3 La fonction as_flextable

Code

library(flextable)
as_flextable(body, spread_first_col = TRUE, add_tab = TRUE) |>
  align(j = 1, part = "all", align = "left") |> 
  padding(padding = 4, part = "all") |> 
  add_header_row(
    values = c("", fmt_header_n(subject_counts, newline = FALSE)),
    top = FALSE) |> 
  hline(i = 1, part = "header", border = fp_border_default(width = 0))

	A: Drug X	B: Placebo	C: Combination
	(N=134)	(N=134)	(N=132)
Patients with at least one event	122 (91.04%)	123 (91.79%)	120 (90.91%)
Total number of events	609	622	703
cl A.1
Patients with at least one event	78 (58.21%)	75 (55.97%)	89 (66.42%)
Total number of events	132	130	160
dcd A.1.1.1.1	50 (37.31%)	45 (33.58%)	63 (47.01%)
dcd A.1.1.1.2	48 (35.82%)	48 (35.82%)	50 (37.31%)
cl B.1
Patients with at least one event	47 (35.07%)	49 (36.57%)	43 (32.09%)
Total number of events	56	60	62
dcd B.1.1.1.1	47 (35.07%)	49 (36.57%)	43 (32.09%)
cl B.2
Patients with at least one event	79 (58.96%)	74 (55.22%)	85 (63.43%)
Total number of events	129	138	143
dcd B.2.1.2.1	49 (36.57%)	44 (32.84%)	52 (38.81%)
dcd B.2.2.3.1	48 (35.82%)	54 (40.30%)	51 (38.06%)
cl C.1
Patients with at least one event	43 (32.09%)	46 (34.33%)	43 (32.09%)
Total number of events	55	63	64
dcd C.1.1.1.3	43 (32.09%)	46 (34.33%)	43 (32.09%)
cl C.2
Patients with at least one event	35 (26.12%)	48 (35.82%)	55 (41.04%)
Total number of events	48	53	65
dcd C.2.1.2.1	35 (26.12%)	48 (35.82%)	55 (41.04%)
cl D.1
Patients with at least one event	79 (58.96%)	67 (50.00%)	80 (59.70%)
Total number of events	127	106	135
dcd D.1.1.1.1	50 (37.31%)	42 (31.34%)	51 (38.06%)
dcd D.1.1.4.2	48 (35.82%)	42 (31.34%)	50 (37.31%)
cl D.2
Patients with at least one event	47 (35.07%)	58 (43.28%)	57 (42.54%)
Total number of events	62	72	74
dcd D.2.1.5.3	47 (35.07%)	58 (43.28%)	57 (42.54%)