Cette vignette a pour but de faire le parallèle entre les macros SAS
de description des AE et les fonctions disponibles dans le package
grstat.
Elle reprend le document Word des macros SAS et n’existe que pour donner la correspondance entre les deux systèmes.
Pour apprendre comment utiliser grstat pour décrire les
AE, utilisez plutôt la vignette dédiée.
Data
On commence par charger la base de données.
Ici j’utilise la fonction grstat_example() pour ne pas
dépendre de données réelles privées, mais en pratique on utiliserait
plutôt EDCimport::read_trialmaster("path/to/file.zip").
On s’intéresse à deux datasets : - ae qui contient les
données d’adverse events - enrolres qui contient tous les
patients et leur bras de traitement.
library(grstat)
library(flextable)
library(dplyr)
# tm = EDCimport::read_trialmaster("path/to/file.zip")
tm = grstat_example()
attach(tm)
head(ae)
#> # A tibble: 6 × 7
#> subjid aesoc aeterm aegr sae aerel crfname
#> <int> <chr> <chr> <dbl> <chr> <chr> <chr>
#> 1 2 Eye disorders Eyeli… 1 No Expe… ae
#> 2 2 Cardiac disorders Heart… 4 Yes Stan… ae
#> 3 2 Surgical and medical procedures Thera… 1 No Other ae
#> 4 3 Respiratory, thoracic and mediastinal… Pulmo… 1 No Stan… ae
#> 5 3 Surgical and medical procedures Diagn… 3 No Canc… ae
#> 6 3 Neoplasms benign, malignant, and unsp… Malig… 1 Yes Radi… ae
head(enrolres)
#> # A tibble: 6 × 4
#> subjid arm arm3 crfname
#> <int> <chr> <chr> <chr>
#> 1 1 Control Treatment B enrolres
#> 2 2 Control Control enrolres
#> 3 3 Treatment Treatment A enrolres
#> 4 4 Control Control enrolres
#> 5 5 Treatment Treatment A enrolres
#> 6 6 Treatment Treatment A enrolresMacro AE_grades
La macro AE_grades est implémentée dans la fonction
ae_table_grade(). Cette fonction retourne des objets de
classe crosstable, lesquels ont une méthode
as_flextable() qui les transforme en table HTML de classe
flextable.
Voir la description du package crosstable pour plus
d’informations: documentation.
Voir la description du package flextable pour la
liste des modificateurs (comme add_footer_lines()) : documentation.
AE_grades1 : Table des grades maximum par patient
ae_table_grade(df_ae=ae, df_enrol=enrolres, arm=NULL, variant="max") %>%
as_flextable(header_show_n=TRUE) %>%
add_footer_lines("Percentages reflect the proportion of patients whose maximum AE grade was as indicated.")label |
variable |
Treatment arm |
|---|---|---|
All patients (N=200) | ||
Patient maximum AE grade |
No declared AE |
3 (2%) |
Grade 1 |
35 (18%) |
|
Grade 2 |
62 (31%) |
|
Grade 3 |
51 (26%) |
|
Grade 4 |
39 (20%) |
|
Grade 5 |
10 (5%) |
|
Percentages reflect the proportion of patients whose maximum AE grade was as indicated. | ||
AE_grades2 : Table des grades maximum par patient
stratifié sur le bras
On pourrait retrouver exactement la sortie SAS en mettant
total=FALSE.
ae_table_grade(df_ae=ae, df_enrol=enrolres, arm="arm", variant="max") %>%
as_flextable(header_show_n=TRUE) %>%
add_footer_lines("Percentages reflect the proportion of patients presenting at most one AE of given grade")label |
variable |
Treatment arm |
Total |
|
|---|---|---|---|---|
Control (N=100) |
Treatment (N=100) |
|||
Patient maximum AE grade |
No declared AE |
3 (3%) |
0 (0%) |
3 (2%) |
Grade 1 |
27 (27%) |
8 (8%) |
35 (18%) |
|
Grade 2 |
32 (32%) |
30 (30%) |
62 (31%) |
|
Grade 3 |
23 (23%) |
28 (28%) |
51 (26%) |
|
Grade 4 |
14 (14%) |
25 (25%) |
39 (20%) |
|
Grade 5 |
1 (1%) |
9 (9%) |
10 (5%) |
|
Percentages reflect the proportion of patients presenting at most one AE of given grade | ||||
AE_grades3 : Table de tous les grades pour chaque
patient
ae_table_grade(df_ae=ae, df_enrol=enrolres, arm=NULL, variant="eq") %>%
as_flextable(header_show_n=TRUE) %>%
add_footer_lines("Percentages reflect the proportion of patients presenting at least one AE of given grade")label |
variable |
Treatment arm |
|---|---|---|
All patients (N=200) | ||
Patient had at least one AE of grade |
No declared AE |
3 (2%) |
Grade 1 |
164 (82%) |
|
Grade 2 |
117 (58%) |
|
Grade 3 |
62 (31%) |
|
Grade 4 |
44 (22%) |
|
Grade 5 |
10 (5%) |
|
Percentages reflect the proportion of patients presenting at least one AE of given grade | ||
AE_grades3bis : Table de tous les grades pour chaque
patient, stratifié sur le bras
On pourrait retrouver exactement la sortie SAS en mettant
total=FALSE.
ae_table_grade(df_ae=ae, df_enrol=enrolres, arm="arm", variant="eq") %>%
as_flextable(header_show_n=TRUE) %>%
add_footer_lines("Percentages reflect the proportion of patients presenting at least one AE of given grade")label |
variable |
Treatment arm |
Total |
|
|---|---|---|---|---|
Control (N=100) |
Treatment (N=100) |
|||
Patient had at least one AE of grade |
No declared AE |
3 (3%) |
0 (0%) |
3 (2%) |
Grade 1 |
83 (83%) |
81 (81%) |
164 (82%) |
|
Grade 2 |
53 (53%) |
64 (64%) |
117 (58%) |
|
Grade 3 |
25 (25%) |
37 (37%) |
62 (31%) |
|
Grade 4 |
15 (15%) |
29 (29%) |
44 (22%) |
|
Grade 5 |
1 (1%) |
9 (9%) |
10 (5%) |
|
Percentages reflect the proportion of patients presenting at least one AE of given grade | ||||
AE_grades4 : Table des grades maximum par patient,
filtrée sur les SAE
Il suffit de filtrer la table ae en amont et d’indiquer
que le label doit être “SAE”.
ae %>%
filter(sae=="Yes") %>%
ae_table_grade(df_enrol=enrolres, arm=NULL, variant="max", ae_label="SAE") %>%
as_flextable(header_show_n=TRUE) %>%
add_footer_lines("Percentages reflect the proportion of patients whose maximum SAE grade was as indicated.")label |
variable |
Treatment arm |
|---|---|---|
All patients (N=200) | ||
Patient maximum SAE grade |
No declared SAE |
150 (75%) |
Grade 1 |
11 (6%) |
|
Grade 2 |
9 (4%) |
|
Grade 3 |
10 (5%) |
|
Grade 4 |
16 (8%) |
|
Grade 5 |
4 (2%) |
|
Percentages reflect the proportion of patients whose maximum SAE grade was as indicated. | ||
Macro AE_SOC
La macro AE_SOC est implémentée dans la fonction
ae_table_soc(). Cette fonction retourne des objets de
classe ae_table_soc. Ils ont également une méthode
as_flextable qui les transforme en table HTML de classe
flextable, mais différente de celle de
crosstable.
Voir ?as_flextable.ae_table_soc pour plus
d’informations: lien.
Voir la description du package flextable pour la
liste des modificateurs (comme add_footer_lines()) : documentation.
Astuce: Pour les sorties sur officer,
comme ces tables sont très larges, pensez bien à basculer en format
paysage en utilisant
officer::body_end_section_continuous(), puis
officer::body_end_section_landscape() pour revenir au
format portrait.
AE_SOC1 : Table des grades par soc
On peut ajouter total=FALSE pour retirer la colonne
“Tot”.
ae_table_soc(df_ae=ae, df_enrol=enrolres, arm=NULL, term=NULL,
sort_by_count=FALSE) %>%
as_flextable() %>%
add_footer_lines("In the header, N represents the number of patients.") %>%
add_footer_lines("Percentages reflect the proportion of patients whose maximum AE grade was as indicated.")All patients (N=200) |
|||||||
|---|---|---|---|---|---|---|---|
CTCAE SOC |
G1 |
G2 |
G3 |
G4 |
G5 |
NA |
Tot |
Blood and lymphatic system disorders |
6 (3%) |
1 (0%) |
1 (0%) |
1 (0%) |
9 (4%) |
||
Cardiac disorders |
11 (6%) |
8 (4%) |
4 (2%) |
5 (2%) |
2 (1%) |
30 (15%) |
|
Congenital, familial and genetic disorders |
27 (14%) |
15 (8%) |
6 (3%) |
3 (2%) |
51 (26%) |
||
Ear and labyrinth disorders |
10 (5%) |
5 (2%) |
1 (0%) |
16 (8%) |
|||
Endocrine disorders |
10 (5%) |
7 (4%) |
4 (2%) |
3 (2%) |
24 (12%) |
||
Eye disorders |
19 (10%) |
7 (4%) |
7 (4%) |
2 (1%) |
35 (18%) |
||
Gastrointestinal disorders |
2 (1%) |
2 (1%) |
4 (2%) |
1 (0%) |
9 (4%) |
||
General disorders and administration site conditions |
8 (4%) |
3 (2%) |
1 (0%) |
12 (6%) |
|||
Hepatobiliary disorders |
13 (6%) |
9 (4%) |
1 (0%) |
1 (0%) |
24 (12%) |
||
Immune system disorders |
15 (8%) |
7 (4%) |
3 (2%) |
2 (1%) |
27 (14%) |
||
Infections and infestations |
6 (3%) |
3 (2%) |
1 (0%) |
10 (5%) |
|||
Injury, poisoning and procedural complications |
11 (6%) |
9 (4%) |
8 (4%) |
1 (0%) |
1 (0%) |
30 (15%) |
|
Investigations |
4 (2%) |
2 (1%) |
1 (0%) |
1 (0%) |
8 (4%) |
||
Metabolism and nutrition disorders |
7 (4%) |
3 (2%) |
4 (2%) |
14 (7%) |
|||
Musculoskeletal and connective tissue disorders |
9 (4%) |
5 (2%) |
2 (1%) |
5 (2%) |
21 (10%) |
||
Neoplasms benign, malignant, and unspecified |
17 (8%) |
11 (6%) |
2 (1%) |
7 (4%) |
2 (1%) |
39 (20%) |
|
Nervous system disorders |
7 (4%) |
4 (2%) |
1 (0%) |
12 (6%) |
|||
Pregnancy, puerperium and perinatal conditions |
18 (9%) |
8 (4%) |
7 (4%) |
33 (16%) |
|||
Psychiatric disorders |
16 (8%) |
3 (2%) |
2 (1%) |
2 (1%) |
1 (0%) |
24 (12%) |
|
Renal and urinary disorders |
1 (0%) |
3 (2%) |
1 (0%) |
1 (0%) |
6 (3%) |
||
Reproductive system and breast disorders |
7 (4%) |
2 (1%) |
9 (4%) |
||||
Respiratory, thoracic and mediastinal disorders |
8 (4%) |
6 (3%) |
2 (1%) |
1 (0%) |
1 (0%) |
18 (9%) |
|
Skin and subcutaneous tissue disorders |
4 (2%) |
5 (2%) |
1 (0%) |
2 (1%) |
12 (6%) |
||
Social circumstances |
19 (10%) |
14 (7%) |
7 (4%) |
5 (2%) |
45 (22%) |
||
Surgical and medical procedures |
26 (13%) |
5 (2%) |
8 (4%) |
3 (2%) |
1 (0%) |
43 (22%) |
|
Vascular disorders |
12 (6%) |
5 (2%) |
2 (1%) |
2 (1%) |
1 (0%) |
22 (11%) |
|
No Declared AE |
3 (2%) |
3 (2%) |
|||||
In the header, N represents the number of patients. | |||||||
Percentages reflect the proportion of patients whose maximum AE grade was as indicated. | |||||||
AE_SOC2 : Table des grades par soc et termes
ae_table_soc(df_ae=ae, df_enrol=enrolres, arm=NULL, term="aeterm",
sort_by_count=FALSE) %>%
as_flextable() %>%
add_footer_lines("In the header, N represents the number of patients.") %>%
add_footer_lines("Percentages reflect the proportion of patients whose maximum AE grade was as indicated.")All patients (N=200) |
||||||||
|---|---|---|---|---|---|---|---|---|
CTCAE SOC |
CTCAE v4.0 Term |
G1 |
G2 |
G3 |
G4 |
G5 |
NA |
Tot |
Blood and lymphatic system disorders |
Bone marrow disorders |
1 (0%) |
1 (0%) |
|||||
Hematologic neoplasms |
4 (2%) |
1 (0%) |
1 (0%) |
6 (3%) |
||||
Red blood cell disorders |
1 (0%) |
1 (0%) |
2 (1%) |
|||||
Cardiac disorders |
Cardiac arrhythmias |
5 (2%) |
2 (1%) |
2 (1%) |
9 (4%) |
|||
Cardiac valve disorders |
2 (1%) |
1 (0%) |
2 (1%) |
1 (0%) |
2 (1%) |
8 (4%) |
||
Coronary artery disorders |
1 (0%) |
4 (2%) |
1 (0%) |
1 (0%) |
7 (4%) |
|||
Heart failures |
5 (2%) |
1 (0%) |
1 (0%) |
1 (0%) |
8 (4%) |
|||
Congenital, familial and genetic disorders |
Chromosomal abnormalities |
11 (6%) |
5 (2%) |
1 (0%) |
1 (0%) |
18 (9%) |
||
Congenital nervous system disorders |
6 (3%) |
3 (2%) |
9 (4%) |
|||||
Familial hematologic disorders |
7 (4%) |
1 (0%) |
3 (2%) |
2 (1%) |
13 (6%) |
|||
Hereditary connective tissue disorders |
9 (4%) |
6 (3%) |
2 (1%) |
17 (8%) |
||||
Ear and labyrinth disorders |
Hearing disorders |
2 (1%) |
1 (0%) |
3 (2%) |
||||
Labyrinth disorders |
1 (0%) |
1 (0%) |
||||||
Tinnitus |
6 (3%) |
1 (0%) |
7 (4%) |
|||||
Vertigo and balance disorders |
3 (2%) |
4 (2%) |
7 (4%) |
|||||
Endocrine disorders |
Adrenal gland disorders |
2 (1%) |
5 (2%) |
7 (4%) |
||||
Parathyroid gland disorders |
1 (0%) |
3 (2%) |
1 (0%) |
5 (2%) |
||||
Pituitary gland disorders |
6 (3%) |
2 (1%) |
1 (0%) |
9 (4%) |
||||
Thyroid gland disorders |
3 (2%) |
1 (0%) |
2 (1%) |
6 (3%) |
||||
Eye disorders |
Corneal disorders |
4 (2%) |
2 (1%) |
2 (1%) |
8 (4%) |
|||
Eyelid disorders |
6 (3%) |
1 (0%) |
1 (0%) |
8 (4%) |
||||
Retinal disorders |
5 (2%) |
2 (1%) |
2 (1%) |
9 (4%) |
||||
Vision disorders |
7 (4%) |
4 (2%) |
2 (1%) |
13 (6%) |
||||
Gastrointestinal disorders |
Esophageal disorders |
1 (0%) |
1 (0%) |
|||||
Gastric disorders |
2 (1%) |
1 (0%) |
2 (1%) |
5 (2%) |
||||
Intestinal disorders |
1 (0%) |
2 (1%) |
3 (2%) |
|||||
General disorders and administration site conditions |
Device issues |
4 (2%) |
1 (0%) |
5 (2%) |
||||
General physical health deterioration |
3 (2%) |
3 (2%) |
||||||
Injection site reactions |
1 (0%) |
1 (0%) |
2 (1%) |
|||||
Pain and discomfort |
2 (1%) |
2 (1%) |
||||||
Hepatobiliary disorders |
Bile duct disorders |
4 (2%) |
3 (2%) |
7 (4%) |
||||
Gallbladder disorders |
3 (2%) |
2 (1%) |
5 (2%) |
|||||
Hepatic failure |
3 (2%) |
2 (1%) |
1 (0%) |
1 (0%) |
7 (4%) |
|||
Liver disorders |
3 (2%) |
2 (1%) |
5 (2%) |
|||||
Immune system disorders |
Autoimmune disorders |
6 (3%) |
1 (0%) |
1 (0%) |
8 (4%) |
|||
Hypersensitivity conditions |
4 (2%) |
1 (0%) |
1 (0%) |
1 (0%) |
7 (4%) |
|||
Immunodeficiency |
3 (2%) |
1 (0%) |
4 (2%) |
|||||
Inflammatory responses |
4 (2%) |
5 (2%) |
2 (1%) |
11 (6%) |
||||
Infections and infestations |
Bacterial infectious disorders |
1 (0%) |
1 (0%) |
|||||
Fungal infectious disorders |
1 (0%) |
1 (0%) |
||||||
Parasitic infectious disorders |
2 (1%) |
1 (0%) |
3 (2%) |
|||||
Viral infectious disorders |
3 (2%) |
2 (1%) |
5 (2%) |
|||||
Injury, poisoning and procedural complications |
Poisonings |
3 (2%) |
3 (2%) |
1 (0%) |
1 (0%) |
1 (0%) |
9 (4%) |
|
Procedural complications |
2 (1%) |
3 (2%) |
2 (1%) |
7 (4%) |
||||
Radiation-related toxicities |
2 (1%) |
3 (2%) |
2 (1%) |
7 (4%) |
||||
Traumatic injuries |
6 (3%) |
1 (0%) |
3 (2%) |
10 (5%) |
||||
Investigations |
Blood analyses |
1 (0%) |
1 (0%) |
2 (1%) |
||||
Cardiovascular assessments |
2 (1%) |
2 (1%) |
||||||
Imaging studies |
1 (0%) |
1 (0%) |
2 (1%) |
|||||
Liver function analyses |
1 (0%) |
1 (0%) |
2 (1%) |
|||||
Metabolism and nutrition disorders |
Fluid and electrolyte disorders |
2 (1%) |
1 (0%) |
1 (0%) |
4 (2%) |
|||
Lipid metabolism disorders |
1 (0%) |
1 (0%) |
2 (1%) |
|||||
Nutritional disorders |
4 (2%) |
4 (2%) |
||||||
Vitamin deficiencies |
1 (0%) |
1 (0%) |
2 (1%) |
4 (2%) |
||||
Musculoskeletal and connective tissue disorders |
Arthritis and joint disorders |
6 (3%) |
1 (0%) |
1 (0%) |
8 (4%) |
|||
Bone disorders |
2 (1%) |
1 (0%) |
2 (1%) |
5 (2%) |
||||
Connective tissue disorders |
1 (0%) |
2 (1%) |
1 (0%) |
2 (1%) |
6 (3%) |
|||
Muscle disorders |
2 (1%) |
1 (0%) |
3 (2%) |
|||||
Neoplasms benign, malignant, and unspecified |
Benign neoplasms |
5 (2%) |
4 (2%) |
1 (0%) |
3 (2%) |
13 (6%) |
||
Malignant neoplasms |
6 (3%) |
4 (2%) |
1 (0%) |
2 (1%) |
13 (6%) |
|||
Neoplasms unspecified |
5 (2%) |
1 (0%) |
1 (0%) |
7 (4%) |
||||
Tumor progression |
2 (1%) |
3 (2%) |
1 (0%) |
1 (0%) |
7 (4%) |
|||
Nervous system disorders |
Headache disorders |
3 (2%) |
2 (1%) |
5 (2%) |
||||
Neurological disorders of the central nervous system |
3 (2%) |
1 (0%) |
4 (2%) |
|||||
Peripheral neuropathies |
1 (0%) |
1 (0%) |
||||||
Seizure disorders |
2 (1%) |
1 (0%) |
3 (2%) |
|||||
Pregnancy, puerperium and perinatal conditions |
Breastfeeding issues |
4 (2%) |
1 (0%) |
2 (1%) |
7 (4%) |
|||
Fetal complications |
3 (2%) |
2 (1%) |
2 (1%) |
7 (4%) |
||||
Labor and delivery complications |
7 (4%) |
4 (2%) |
1 (0%) |
12 (6%) |
||||
Pregnancy complications |
5 (2%) |
1 (0%) |
2 (1%) |
8 (4%) |
||||
Psychiatric disorders |
Anxiety disorders |
5 (2%) |
5 (2%) |
|||||
Mood disorders |
2 (1%) |
1 (0%) |
3 (2%) |
|||||
Sleep disorders |
8 (4%) |
1 (0%) |
9 (4%) |
|||||
Substance-related disorders |
2 (1%) |
2 (1%) |
2 (1%) |
1 (0%) |
1 (0%) |
8 (4%) |
||
Renal and urinary disorders |
Bladder disorders |
1 (0%) |
1 (0%) |
2 (1%) |
||||
Kidney disorders |
1 (0%) |
1 (0%) |
1 (0%) |
3 (2%) |
||||
Urinary tract disorders |
1 (0%) |
1 (0%) |
||||||
Reproductive system and breast disorders |
Breast disorders |
2 (1%) |
2 (1%) |
|||||
Female reproductive disorders |
2 (1%) |
2 (1%) |
||||||
Male reproductive disorders |
2 (1%) |
2 (1%) |
4 (2%) |
|||||
Menstrual disorders |
1 (0%) |
1 (0%) |
||||||
Respiratory, thoracic and mediastinal disorders |
Lung function disorders |
3 (2%) |
3 (2%) |
6 (3%) |
||||
Pleural disorders |
1 (0%) |
1 (0%) |
1 (0%) |
1 (0%) |
4 (2%) |
|||
Pulmonary vascular disorders |
3 (2%) |
2 (1%) |
1 (0%) |
6 (3%) |
||||
Respiratory infections |
1 (0%) |
1 (0%) |
2 (1%) |
|||||
Skin and subcutaneous tissue disorders |
Dermatitis |
1 (0%) |
1 (0%) |
1 (0%) |
3 (2%) |
|||
Skin and subcutaneous tissue injuries |
1 (0%) |
2 (1%) |
3 (2%) |
|||||
Skin infections |
2 (1%) |
2 (1%) |
1 (0%) |
5 (2%) |
||||
Skin pigmentation disorders |
1 (0%) |
1 (0%) |
||||||
Social circumstances |
Cultural issues |
5 (2%) |
2 (1%) |
2 (1%) |
1 (0%) |
10 (5%) |
||
Economic conditions affecting care |
3 (2%) |
4 (2%) |
1 (0%) |
1 (0%) |
9 (4%) |
|||
Family support issues |
6 (3%) |
3 (2%) |
3 (2%) |
2 (1%) |
14 (7%) |
|||
Social and environmental issues |
7 (4%) |
5 (2%) |
1 (0%) |
1 (0%) |
14 (7%) |
|||
Surgical and medical procedures |
Device implantation procedures |
13 (6%) |
1 (0%) |
2 (1%) |
1 (0%) |
17 (8%) |
||
Diagnostic procedures |
10 (5%) |
1 (0%) |
5 (2%) |
16 (8%) |
||||
Surgical complications |
3 (2%) |
4 (2%) |
1 (0%) |
1 (0%) |
9 (4%) |
|||
Therapeutic procedures |
2 (1%) |
1 (0%) |
3 (2%) |
|||||
Vascular disorders |
Hypertension-related conditions |
4 (2%) |
2 (1%) |
1 (0%) |
7 (4%) |
|||
Hypotension-related conditions |
4 (2%) |
1 (0%) |
1 (0%) |
6 (3%) |
||||
Vascular hemorrhagic disorders |
1 (0%) |
2 (1%) |
1 (0%) |
1 (0%) |
5 (2%) |
|||
Venous thromboembolic events |
3 (2%) |
1 (0%) |
1 (0%) |
5 (2%) |
||||
No Declared AE |
3 (2%) |
3 (2%) |
||||||
In the header, N represents the number of patients. | ||||||||
Percentages reflect the proportion of patients whose maximum AE grade was as indicated. | ||||||||
AE_SOC3 : Table des grades par termes uniquement,
filtrée sur les SAE
Il suffit de filtrer la table AE en amont.
ae %>%
filter(sae=="Yes") %>%
ae_table_soc(df_enrol=enrolres, term=NULL, arm=NULL, sort_by_count=FALSE) %>%
as_flextable() %>%
add_footer_lines(c("In the header, N represents the number of patients.",
"Percentages reflect the proportion of patients whose maximum SAE grade was as indicated."))All patients (N=200) |
|||||||
|---|---|---|---|---|---|---|---|
CTCAE SOC |
G1 |
G2 |
G3 |
G4 |
G5 |
NA |
Tot |
Blood and lymphatic system disorders |
1 (0%) |
1 (0%) |
2 (1%) |
||||
Cardiac disorders |
1 (0%) |
2 (1%) |
2 (1%) |
5 (2%) |
|||
Congenital, familial and genetic disorders |
2 (1%) |
3 (2%) |
2 (1%) |
7 (4%) |
|||
Endocrine disorders |
1 (0%) |
1 (0%) |
2 (1%) |
||||
Eye disorders |
1 (0%) |
1 (0%) |
2 (1%) |
||||
General disorders and administration site conditions |
1 (0%) |
1 (0%) |
|||||
Hepatobiliary disorders |
1 (0%) |
1 (0%) |
1 (0%) |
3 (2%) |
|||
Immune system disorders |
1 (0%) |
1 (0%) |
1 (0%) |
1 (0%) |
4 (2%) |
||
Injury, poisoning and procedural complications |
2 (1%) |
1 (0%) |
3 (2%) |
||||
Investigations |
1 (0%) |
1 (0%) |
|||||
Metabolism and nutrition disorders |
2 (1%) |
1 (0%) |
3 (2%) |
||||
Musculoskeletal and connective tissue disorders |
3 (2%) |
3 (2%) |
|||||
Neoplasms benign, malignant, and unspecified |
1 (0%) |
1 (0%) |
2 (1%) |
4 (2%) |
|||
Nervous system disorders |
1 (0%) |
1 (0%) |
|||||
Psychiatric disorders |
1 (0%) |
1 (0%) |
|||||
Social circumstances |
4 (2%) |
2 (1%) |
3 (2%) |
9 (4%) |
|||
Surgical and medical procedures |
1 (0%) |
4 (2%) |
2 (1%) |
7 (4%) |
|||
Vascular disorders |
1 (0%) |
1 (0%) |
|||||
No Declared AE |
150 (75%) |
150 (75%) |
|||||
In the header, N represents the number of patients. | |||||||
Percentages reflect the proportion of patients whose maximum SAE grade was as indicated. | |||||||
AE_SOC4/5 : Table des grades stratifiée sur le bras
(sans colonne total)
On peut ajouter total=FALSE pour retirer la colonne
“Tot” et obtenir la sortie AE_SOC5.
ae_table_soc(df_ae=ae, df_enrol=enrolres, term=NULL, arm="arm", sort_by_count=FALSE) %>%
as_flextable() %>%
add_footer_lines("In the header, N represents the number of patients.") %>%
add_footer_lines("Percentages reflect the proportion of patients whose maximum AE grade was as indicated.")Control (N=100) |
Treatment (N=100) |
|||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTCAE SOC |
G1 |
G2 |
G3 |
G4 |
G5 |
NA |
Tot |
G1 |
G2 |
G3 |
G4 |
G5 |
NA |
Tot |
Blood and lymphatic system disorders |
3 (3%) |
1 (1%) |
4 (4%) |
3 (3%) |
1 (1%) |
1 (1%) |
5 (5%) |
|||||||
Cardiac disorders |
7 (7%) |
5 (5%) |
3 (3%) |
2 (2%) |
17 (17%) |
4 (4%) |
3 (3%) |
1 (1%) |
3 (3%) |
2 (2%) |
13 (13%) |
|||
Congenital, familial and genetic disorders |
18 (18%) |
7 (7%) |
2 (2%) |
2 (2%) |
29 (29%) |
9 (9%) |
8 (8%) |
4 (4%) |
1 (1%) |
22 (22%) |
||||
Ear and labyrinth disorders |
5 (5%) |
3 (3%) |
8 (8%) |
5 (5%) |
2 (2%) |
1 (1%) |
8 (8%) |
|||||||
Endocrine disorders |
4 (4%) |
4 (4%) |
2 (2%) |
1 (1%) |
11 (11%) |
6 (6%) |
3 (3%) |
2 (2%) |
2 (2%) |
13 (13%) |
||||
Eye disorders |
7 (7%) |
2 (2%) |
3 (3%) |
2 (2%) |
14 (14%) |
12 (12%) |
5 (5%) |
4 (4%) |
21 (21%) |
|||||
Gastrointestinal disorders |
2 (2%) |
2 (2%) |
4 (4%) |
1 (1%) |
9 (9%) |
|||||||||
General disorders and administration site conditions |
4 (4%) |
1 (1%) |
1 (1%) |
6 (6%) |
4 (4%) |
2 (2%) |
6 (6%) |
|||||||
Hepatobiliary disorders |
2 (2%) |
6 (6%) |
1 (1%) |
9 (9%) |
11 (11%) |
3 (3%) |
1 (1%) |
15 (15%) |
||||||
Immune system disorders |
10 (10%) |
3 (3%) |
2 (2%) |
15 (15%) |
5 (5%) |
4 (4%) |
1 (1%) |
2 (2%) |
12 (12%) |
|||||
Infections and infestations |
5 (5%) |
2 (2%) |
7 (7%) |
1 (1%) |
1 (1%) |
1 (1%) |
3 (3%) |
|||||||
Injury, poisoning and procedural complications |
6 (6%) |
7 (7%) |
4 (4%) |
17 (17%) |
5 (5%) |
2 (2%) |
4 (4%) |
1 (1%) |
1 (1%) |
13 (13%) |
||||
Investigations |
1 (1%) |
1 (1%) |
1 (1%) |
3 (3%) |
3 (3%) |
1 (1%) |
1 (1%) |
5 (5%) |
||||||
Metabolism and nutrition disorders |
4 (4%) |
1 (1%) |
1 (1%) |
6 (6%) |
3 (3%) |
2 (2%) |
3 (3%) |
8 (8%) |
||||||
Musculoskeletal and connective tissue disorders |
6 (6%) |
1 (1%) |
1 (1%) |
1 (1%) |
9 (9%) |
3 (3%) |
4 (4%) |
1 (1%) |
4 (4%) |
12 (12%) |
||||
Neoplasms benign, malignant, and unspecified |
9 (9%) |
5 (5%) |
3 (3%) |
1 (1%) |
18 (18%) |
8 (8%) |
6 (6%) |
2 (2%) |
4 (4%) |
1 (1%) |
21 (21%) |
|||
Nervous system disorders |
3 (3%) |
1 (1%) |
4 (4%) |
4 (4%) |
4 (4%) |
8 (8%) |
||||||||
Pregnancy, puerperium and perinatal conditions |
10 (10%) |
2 (2%) |
3 (3%) |
15 (15%) |
8 (8%) |
6 (6%) |
4 (4%) |
18 (18%) |
||||||
Psychiatric disorders |
9 (9%) |
2 (2%) |
1 (1%) |
12 (12%) |
7 (7%) |
1 (1%) |
1 (1%) |
2 (2%) |
1 (1%) |
12 (12%) |
||||
Renal and urinary disorders |
3 (3%) |
3 (3%) |
1 (1%) |
1 (1%) |
1 (1%) |
3 (3%) |
||||||||
Reproductive system and breast disorders |
3 (3%) |
1 (1%) |
4 (4%) |
4 (4%) |
1 (1%) |
5 (5%) |
||||||||
Respiratory, thoracic and mediastinal disorders |
2 (2%) |
4 (4%) |
2 (2%) |
8 (8%) |
6 (6%) |
2 (2%) |
1 (1%) |
1 (1%) |
10 (10%) |
|||||
Skin and subcutaneous tissue disorders |
3 (3%) |
2 (2%) |
5 (5%) |
1 (1%) |
3 (3%) |
1 (1%) |
2 (2%) |
7 (7%) |
||||||
Social circumstances |
13 (13%) |
5 (5%) |
3 (3%) |
21 (21%) |
6 (6%) |
9 (9%) |
4 (4%) |
5 (5%) |
24 (24%) |
|||||
Surgical and medical procedures |
18 (18%) |
2 (2%) |
2 (2%) |
22 (22%) |
8 (8%) |
3 (3%) |
6 (6%) |
3 (3%) |
1 (1%) |
21 (21%) |
||||
Vascular disorders |
10 (10%) |
2 (2%) |
1 (1%) |
1 (1%) |
14 (14%) |
2 (2%) |
3 (3%) |
1 (1%) |
1 (1%) |
1 (1%) |
8 (8%) |
|||
No Declared AE |
3 (3%) |
3 (3%) |
||||||||||||
In the header, N represents the number of patients. | ||||||||||||||
Percentages reflect the proportion of patients whose maximum AE grade was as indicated. | ||||||||||||||
AE_SOC6 : Table des soc et termes tous grades confondus
stratifiée sur le bras
ae_table_soc(df_ae=ae, df_enrol=enrolres, arm="arm", term="aeterm",
sort_by_count=FALSE) %>%
as_flextable() %>%
add_footer_lines("In the header, N represents the number of patients.") %>%
add_footer_lines("Percentages reflect the proportion of patients whose maximum AE grade was as indicated.")Control (N=100) |
Treatment (N=100) |
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTCAE SOC |
CTCAE v4.0 Term |
G1 |
G2 |
G3 |
G4 |
G5 |
NA |
Tot |
G1 |
G2 |
G3 |
G4 |
G5 |
NA |
Tot |
Blood and lymphatic system disorders |
Bone marrow disorders |
1 (1%) |
1 (1%) |
||||||||||||
Hematologic neoplasms |
2 (2%) |
1 (1%) |
3 (3%) |
2 (2%) |
1 (1%) |
3 (3%) |
|||||||||
Red blood cell disorders |
1 (1%) |
1 (1%) |
2 (2%) |
||||||||||||
Cardiac disorders |
Cardiac arrhythmias |
3 (3%) |
2 (2%) |
5 (5%) |
2 (2%) |
2 (2%) |
4 (4%) |
||||||||
Cardiac valve disorders |
1 (1%) |
1 (1%) |
2 (2%) |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
2 (2%) |
6 (6%) |
||||||
Coronary artery disorders |
1 (1%) |
2 (2%) |
1 (1%) |
1 (1%) |
5 (5%) |
2 (2%) |
2 (2%) |
||||||||
Heart failures |
4 (4%) |
1 (1%) |
1 (1%) |
1 (1%) |
7 (7%) |
1 (1%) |
1 (1%) |
||||||||
Congenital, familial and genetic disorders |
Chromosomal abnormalities |
9 (9%) |
2 (2%) |
1 (1%) |
12 (12%) |
2 (2%) |
3 (3%) |
1 (1%) |
6 (6%) |
||||||
Congenital nervous system disorders |
3 (3%) |
3 (3%) |
6 (6%) |
3 (3%) |
3 (3%) |
||||||||||
Familial hematologic disorders |
6 (6%) |
1 (1%) |
7 (7%) |
1 (1%) |
1 (1%) |
3 (3%) |
1 (1%) |
6 (6%) |
|||||||
Hereditary connective tissue disorders |
4 (4%) |
2 (2%) |
2 (2%) |
8 (8%) |
5 (5%) |
4 (4%) |
9 (9%) |
||||||||
Ear and labyrinth disorders |
Hearing disorders |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
2 (2%) |
|||||||||
Labyrinth disorders |
1 (1%) |
1 (1%) |
|||||||||||||
Tinnitus |
4 (4%) |
1 (1%) |
5 (5%) |
2 (2%) |
2 (2%) |
||||||||||
Vertigo and balance disorders |
2 (2%) |
2 (2%) |
3 (3%) |
2 (2%) |
5 (5%) |
||||||||||
Endocrine disorders |
Adrenal gland disorders |
1 (1%) |
3 (3%) |
4 (4%) |
1 (1%) |
2 (2%) |
3 (3%) |
||||||||
Parathyroid gland disorders |
1 (1%) |
1 (1%) |
2 (2%) |
2 (2%) |
1 (1%) |
3 (3%) |
|||||||||
Pituitary gland disorders |
3 (3%) |
1 (1%) |
1 (1%) |
5 (5%) |
3 (3%) |
1 (1%) |
4 (4%) |
||||||||
Thyroid gland disorders |
1 (1%) |
1 (1%) |
2 (2%) |
2 (2%) |
1 (1%) |
1 (1%) |
4 (4%) |
||||||||
Eye disorders |
Corneal disorders |
3 (3%) |
2 (2%) |
5 (5%) |
1 (1%) |
2 (2%) |
3 (3%) |
||||||||
Eyelid disorders |
2 (2%) |
1 (1%) |
3 (3%) |
4 (4%) |
1 (1%) |
5 (5%) |
|||||||||
Retinal disorders |
1 (1%) |
1 (1%) |
2 (2%) |
4 (4%) |
2 (2%) |
1 (1%) |
7 (7%) |
||||||||
Vision disorders |
2 (2%) |
1 (1%) |
2 (2%) |
5 (5%) |
5 (5%) |
3 (3%) |
8 (8%) |
||||||||
Gastrointestinal disorders |
Esophageal disorders |
1 (1%) |
1 (1%) |
||||||||||||
Gastric disorders |
2 (2%) |
1 (1%) |
2 (2%) |
5 (5%) |
|||||||||||
Intestinal disorders |
1 (1%) |
2 (2%) |
3 (3%) |
||||||||||||
General disorders and administration site conditions |
Device issues |
2 (2%) |
1 (1%) |
3 (3%) |
2 (2%) |
2 (2%) |
|||||||||
General physical health deterioration |
1 (1%) |
1 (1%) |
2 (2%) |
2 (2%) |
|||||||||||
Injection site reactions |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
|||||||||||
Pain and discomfort |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
|||||||||||
Hepatobiliary disorders |
Bile duct disorders |
2 (2%) |
2 (2%) |
4 (4%) |
2 (2%) |
1 (1%) |
3 (3%) |
||||||||
Gallbladder disorders |
1 (1%) |
1 (1%) |
3 (3%) |
1 (1%) |
4 (4%) |
||||||||||
Hepatic failure |
1 (1%) |
1 (1%) |
2 (2%) |
3 (3%) |
1 (1%) |
1 (1%) |
5 (5%) |
||||||||
Liver disorders |
2 (2%) |
2 (2%) |
3 (3%) |
3 (3%) |
|||||||||||
Immune system disorders |
Autoimmune disorders |
5 (5%) |
5 (5%) |
1 (1%) |
1 (1%) |
1 (1%) |
3 (3%) |
||||||||
Hypersensitivity conditions |
2 (2%) |
2 (2%) |
2 (2%) |
1 (1%) |
1 (1%) |
1 (1%) |
5 (5%) |
||||||||
Immunodeficiency |
3 (3%) |
1 (1%) |
4 (4%) |
||||||||||||
Inflammatory responses |
2 (2%) |
2 (2%) |
2 (2%) |
6 (6%) |
2 (2%) |
3 (3%) |
5 (5%) |
||||||||
Infections and infestations |
Bacterial infectious disorders |
1 (1%) |
1 (1%) |
||||||||||||
Fungal infectious disorders |
1 (1%) |
1 (1%) |
|||||||||||||
Parasitic infectious disorders |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
2 (2%) |
||||||||||
Viral infectious disorders |
3 (3%) |
1 (1%) |
4 (4%) |
1 (1%) |
1 (1%) |
||||||||||
Injury, poisoning and procedural complications |
Poisonings |
1 (1%) |
3 (3%) |
1 (1%) |
5 (5%) |
2 (2%) |
1 (1%) |
1 (1%) |
4 (4%) |
||||||
Procedural complications |
2 (2%) |
3 (3%) |
1 (1%) |
6 (6%) |
1 (1%) |
1 (1%) |
|||||||||
Radiation-related toxicities |
1 (1%) |
1 (1%) |
2 (2%) |
1 (1%) |
2 (2%) |
2 (2%) |
5 (5%) |
||||||||
Traumatic injuries |
2 (2%) |
1 (1%) |
2 (2%) |
5 (5%) |
4 (4%) |
1 (1%) |
5 (5%) |
||||||||
Investigations |
Blood analyses |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
||||||||||
Cardiovascular assessments |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
|||||||||||
Imaging studies |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
|||||||||||
Liver function analyses |
1 (1%) |
1 (1%) |
2 (2%) |
||||||||||||
Metabolism and nutrition disorders |
Fluid and electrolyte disorders |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
3 (3%) |
||||||||
Lipid metabolism disorders |
1 (1%) |
1 (1%) |
2 (2%) |
||||||||||||
Nutritional disorders |
3 (3%) |
3 (3%) |
1 (1%) |
1 (1%) |
|||||||||||
Vitamin deficiencies |
1 (1%) |
1 (1%) |
2 (2%) |
4 (4%) |
|||||||||||
Musculoskeletal and connective tissue disorders |
Arthritis and joint disorders |
4 (4%) |
4 (4%) |
2 (2%) |
1 (1%) |
1 (1%) |
4 (4%) |
||||||||
Bone disorders |
1 (1%) |
1 (1%) |
2 (2%) |
1 (1%) |
1 (1%) |
1 (1%) |
3 (3%) |
||||||||
Connective tissue disorders |
1 (1%) |
1 (1%) |
1 (1%) |
3 (3%) |
1 (1%) |
2 (2%) |
3 (3%) |
||||||||
Muscle disorders |
2 (2%) |
1 (1%) |
3 (3%) |
||||||||||||
Neoplasms benign, malignant, and unspecified |
Benign neoplasms |
3 (3%) |
1 (1%) |
1 (1%) |
5 (5%) |
2 (2%) |
3 (3%) |
1 (1%) |
2 (2%) |
8 (8%) |
|||||
Malignant neoplasms |
3 (3%) |
2 (2%) |
5 (5%) |
3 (3%) |
2 (2%) |
1 (1%) |
2 (2%) |
8 (8%) |
|||||||
Neoplasms unspecified |
3 (3%) |
1 (1%) |
1 (1%) |
5 (5%) |
2 (2%) |
2 (2%) |
|||||||||
Tumor progression |
2 (2%) |
1 (1%) |
3 (3%) |
2 (2%) |
1 (1%) |
1 (1%) |
4 (4%) |
||||||||
Nervous system disorders |
Headache disorders |
1 (1%) |
1 (1%) |
2 (2%) |
2 (2%) |
4 (4%) |
|||||||||
Neurological disorders of the central nervous system |
1 (1%) |
1 (1%) |
2 (2%) |
1 (1%) |
3 (3%) |
||||||||||
Peripheral neuropathies |
1 (1%) |
1 (1%) |
|||||||||||||
Seizure disorders |
2 (2%) |
2 (2%) |
1 (1%) |
1 (1%) |
|||||||||||
Pregnancy, puerperium and perinatal conditions |
Breastfeeding issues |
4 (4%) |
1 (1%) |
1 (1%) |
6 (6%) |
1 (1%) |
1 (1%) |
||||||||
Fetal complications |
3 (3%) |
3 (3%) |
2 (2%) |
2 (2%) |
4 (4%) |
||||||||||
Labor and delivery complications |
2 (2%) |
1 (1%) |
1 (1%) |
4 (4%) |
5 (5%) |
3 (3%) |
8 (8%) |
||||||||
Pregnancy complications |
2 (2%) |
1 (1%) |
3 (3%) |
3 (3%) |
1 (1%) |
1 (1%) |
5 (5%) |
||||||||
Psychiatric disorders |
Anxiety disorders |
3 (3%) |
3 (3%) |
2 (2%) |
2 (2%) |
||||||||||
Mood disorders |
2 (2%) |
2 (2%) |
1 (1%) |
1 (1%) |
|||||||||||
Sleep disorders |
4 (4%) |
1 (1%) |
5 (5%) |
4 (4%) |
4 (4%) |
||||||||||
Substance-related disorders |
1 (1%) |
1 (1%) |
2 (2%) |
2 (2%) |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
6 (6%) |
||||||
Renal and urinary disorders |
Bladder disorders |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
||||||||||
Kidney disorders |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
2 (2%) |
||||||||||
Urinary tract disorders |
1 (1%) |
1 (1%) |
|||||||||||||
Reproductive system and breast disorders |
Breast disorders |
2 (2%) |
2 (2%) |
||||||||||||
Female reproductive disorders |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
|||||||||||
Male reproductive disorders |
1 (1%) |
1 (1%) |
2 (2%) |
1 (1%) |
1 (1%) |
2 (2%) |
|||||||||
Menstrual disorders |
1 (1%) |
1 (1%) |
|||||||||||||
Respiratory, thoracic and mediastinal disorders |
Lung function disorders |
1 (1%) |
2 (2%) |
3 (3%) |
2 (2%) |
1 (1%) |
3 (3%) |
||||||||
Pleural disorders |
1 (1%) |
1 (1%) |
1 (1%) |
3 (3%) |
1 (1%) |
1 (1%) |
|||||||||
Pulmonary vascular disorders |
1 (1%) |
1 (1%) |
3 (3%) |
1 (1%) |
1 (1%) |
5 (5%) |
|||||||||
Respiratory infections |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
|||||||||||
Skin and subcutaneous tissue disorders |
Dermatitis |
1 (1%) |
1 (1%) |
1 (1%) |
1 (1%) |
2 (2%) |
|||||||||
Skin and subcutaneous tissue injuries |
1 (1%) |
1 (1%) |
2 (2%) |
2 (2%) |
|||||||||||
Skin infections |
1 (1%) |
1 (1%) |
2 (2%) |
1 (1%) |
1 (1%) |
1 (1%) |
3 (3%) |
||||||||
Skin pigmentation disorders |
1 (1%) |
1 (1%) |
|||||||||||||
Social circumstances |
Cultural issues |
3 (3%) |
1 (1%) |
4 (4%) |
2 (2%) |
1 (1%) |
2 (2%) |
1 (1%) |
6 (6%) |
||||||
Economic conditions affecting care |
2 (2%) |
2 (2%) |
1 (1%) |
5 (5%) |
1 (1%) |
2 (2%) |
1 (1%) |
4 (4%) |
|||||||
Family support issues |
3 (3%) |
1 (1%) |
4 (4%) |
3 (3%) |
3 (3%) |
2 (2%) |
2 (2%) |
10 (10%) |
|||||||
Social and environmental issues |
5 (5%) |
2 (2%) |
1 (1%) |
8 (8%) |
2 (2%) |
3 (3%) |
1 (1%) |
6 (6%) |
|||||||
Surgical and medical procedures |
Device implantation procedures |
10 (10%) |
10 (10%) |
3 (3%) |
1 (1%) |
2 (2%) |
1 (1%) |
7 (7%) |
|||||||
Diagnostic procedures |
5 (5%) |
1 (1%) |
1 (1%) |
7 (7%) |
5 (5%) |
4 (4%) |
9 (9%) |
||||||||
Surgical complications |
2 (2%) |
1 (1%) |
3 (3%) |
1 (1%) |
3 (3%) |
1 (1%) |
1 (1%) |
6 (6%) |
|||||||
Therapeutic procedures |
1 (1%) |
1 (1%) |
2 (2%) |
1 (1%) |
1 (1%) |
||||||||||
Vascular disorders |
Hypertension-related conditions |
3 (3%) |
1 (1%) |
4 (4%) |
1 (1%) |
1 (1%) |
1 (1%) |
3 (3%) |
|||||||
Hypotension-related conditions |
3 (3%) |
3 (3%) |
1 (1%) |
1 (1%) |
1 (1%) |
3 (3%) |
|||||||||
Vascular hemorrhagic disorders |
1 (1%) |
1 (1%) |
1 (1%) |
3 (3%) |
2 (2%) |
2 (2%) |
|||||||||
Venous thromboembolic events |
3 (3%) |
1 (1%) |
4 (4%) |
1 (1%) |
1 (1%) |
||||||||||
No Declared AE |
3 (3%) |
3 (3%) |
|||||||||||||
In the header, N represents the number of patients. | |||||||||||||||
Percentages reflect the proportion of patients whose maximum AE grade was as indicated. | |||||||||||||||