Application - Descriptive analysis

National cancer registry and HES data (England)

Question: What are the comorbidities that affect the survival of patients with lung cancer, taking into account the stage of the disease?

Retrospective longitudinal assessment of comorbidities for cancer patients diagnosed in England during 2013.

Cancer infomation: patients with a malignant invasive primary tumour (cancer registrations from Public Health England).
Comorbidities: extracted from Hospital Episode Statistics (HES) data.

Data set

Preparation

Original R.data file:

head(lung12boost, n=3)

##   sex IsexWomen agediag dep gor tnm_group_restr performance_status typeKC dead
## 1   1         0      76   1   H               1                  0  NSCLC    0
## 2   1         0      81   3   H               3                  2  NSCLC    1
## 3   1         0      64   3   H               3                  2  NSCLC    1
##   survtday  diagdate2   findate2 CM_HES_6_108_cm1 CM_HES_6_108_cm2
## 1     1252 2012-08-01 2016-01-05                0                0
## 2      220 2012-12-22 2013-07-30                0                0
## 3      146 2012-04-16 2012-09-09                0                0
##   CM_HES_6_108_cm3 CM_HES_6_108_cm4 CM_HES_6_108_cm5 CM_HES_6_108_cm6
## 1                0                0                0                0
## 2                0                0                0                0
## 3                0                0                0                0
##   CM_HES_6_108_cm7 CM_HES_6_108_cm8 CM_HES_6_108_cm9 CM_HES_6_108_cm10
## 1                0                0                0                 0
## 2                0                0                0                 0
## 3                0                0                0                 0
##   CM_HES_6_108_cm11 CM_HES_6_108_cm12 CM_HES_6_108_cm13 CM_HES_6_108_cm14
## 1                 0                 0                 0                 0
## 2                 0                 0                 0                 0
## 3                 0                 0                 0                 0
##   CM_HES_6_108_cm15 CM_HES_6_108_cm16 CM_HES_6_108_cm17 CM_HES_6_108_cm18
## 1                 0                 0                 0                 0
## 2                 0                 0                 0                 0
## 3                 0                 0                 0                 0

Categorizing stage (I-II and III-IV) and performance status (good and poor):

library(dplyr)

lung12boost <- lung12boost %>%
  mutate(
      sex = factor(sex),
      dep = factor(dep),
      typeKC = factor(typeKC),
      
   # categorized age 
   # Based on quartiles of age : 
   # Min = 15, Q1 = 65 , Q2 = 73, Q3 = 80, Max = 100     
     age_cat = case_when(
       agediag >= 15 & agediag < 65 ~ "[15, 65)",
       agediag >= 65 & agediag < 73 ~ "[65, 73)",
       agediag >= 73 & agediag < 80 ~ "[73, 80)",
       agediag >= 80 & agediag < 100 ~ "[80, 100)",
       ),
          
   # stage
      stage =  case_when(
        tnm_group_restr  == 1|
        tnm_group_restr  == 2 ~"I-II",
        tnm_group_restr  == 3|
        tnm_group_restr  == 4 ~"III-IV"
      ),
   # performance status 
      PS =  case_when(
        performance_status   == 0|
        performance_status   == 1 ~"Good",

        performance_status   == 2|
        performance_status   == 3|
        performance_status   == 4 ~"Poor"
      ),
   # government office region 
      gor    = factor(gor),
      typeKC = factor(typeKC),
   # comorbidities + obesity
      CM_HES_6_108_cm1  = factor(CM_HES_6_108_cm1),
      CM_HES_6_108_cm2  = factor(CM_HES_6_108_cm2),
      CM_HES_6_108_cm3  = factor(CM_HES_6_108_cm3),
      CM_HES_6_108_cm4  = factor(CM_HES_6_108_cm4),
      CM_HES_6_108_cm5  = factor(CM_HES_6_108_cm5),
      CM_HES_6_108_cm6  = factor(CM_HES_6_108_cm6),
      CM_HES_6_108_cm7  = factor(CM_HES_6_108_cm7),
      CM_HES_6_108_cm8  = factor(CM_HES_6_108_cm8),
      CM_HES_6_108_cm9  = factor(CM_HES_6_108_cm9),
      CM_HES_6_108_cm10 = factor(CM_HES_6_108_cm10),
      CM_HES_6_108_cm11 = factor(CM_HES_6_108_cm11),
      CM_HES_6_108_cm12 = factor(CM_HES_6_108_cm12),
      CM_HES_6_108_cm13 = factor(CM_HES_6_108_cm13),
      CM_HES_6_108_cm14 = factor(CM_HES_6_108_cm14),
      CM_HES_6_108_cm15 = factor(CM_HES_6_108_cm15),
      CM_HES_6_108_cm16 = factor(CM_HES_6_108_cm16),
      CM_HES_6_108_cm17 = factor(CM_HES_6_108_cm17),
      CM_HES_6_108_cm18 = factor(CM_HES_6_108_cm18)
    )

lung12boost <-lung12boost[,-c(2,6,7,11,12)]
lung12boost$stage <- factor(lung12boost$stage)
lung12boost$PS <- factor(lung12boost$PS)

Decoding comorbidities:

lung12boost <- lung12boost  %>%
  rename(
         # Comorbidities
           "myocardial_infection"          = "CM_HES_6_108_cm1",
           "congestive_heart_failure"      = "CM_HES_6_108_cm2",
           "peripheral_vascular_disease"   = "CM_HES_6_108_cm3",
           "cerebrovascular_disease"       = "CM_HES_6_108_cm4",
           "dementia"                      = "CM_HES_6_108_cm5",
           "COPD"                          = "CM_HES_6_108_cm6",
           "rheumatic_disease"             = "CM_HES_6_108_cm7", # Chronic obstrutive pulmonary disease
           "peptic_ulcer_disease"          = "CM_HES_6_108_cm8",
           "mild_liver_disease"            = "CM_HES_6_108_cm9",
           "diabetes_without_comp"         = "CM_HES_6_108_cm10",
           "diabetes_with_comp"            = "CM_HES_6_108_cm11",
           "hemiplegia_paraplegia"         = "CM_HES_6_108_cm12",
           "renal_disease"                 = "CM_HES_6_108_cm13",
           "moderate_severe_liver_disease" = "CM_HES_6_108_cm14",
           "AIDS_HIV"                      = "CM_HES_6_108_cm15",
           "any_malignancy"                = "CM_HES_6_108_cm16",
           "metastatic_solid_tumours"      = "CM_HES_6_108_cm17",
           "obesity"                       = "CM_HES_6_108_cm18",
    )

Removing category

lung12boost <-  lung12boost[lung12boost$typeKC =="NSCLC",]

Final data set

head(lung12boost)

##   sex agediag dep gor typeKC dead survtday myocardial_infection
## 1   1      76   1   H  NSCLC    0     1252                    0
## 2   1      81   3   H  NSCLC    1      220                    0
## 3   1      64   3   H  NSCLC    1      146                    0
## 4   2      73   3   H  NSCLC    1      377                    0
## 5   2      73   5   H  NSCLC    1       47                    0
## 6   2      81   2   H  NSCLC    1       21                    0
##   congestive_heart_failure peripheral_vascular_disease cerebrovascular_disease
## 1                        0                           0                       0
## 2                        0                           0                       0
## 3                        0                           0                       0
## 4                        0                           0                       0
## 5                        0                           0                       0
## 6                        0                           0                       0
##   dementia COPD rheumatic_disease peptic_ulcer_disease mild_liver_disease
## 1        0    0                 0                    0                  0
## 2        0    0                 0                    0                  0
## 3        0    0                 0                    0                  0
## 4        0    0                 0                    0                  0
## 5        0    0                 0                    0                  0
## 6        0    1                 0                    0                  0
##   diabetes_without_comp diabetes_with_comp hemiplegia_paraplegia renal_disease
## 1                     0                  0                     0             0
## 2                     0                  0                     0             0
## 3                     0                  0                     0             0
## 4                     0                  0                     0             0
## 5                     0                  0                     0             0
## 6                     0                  0                     0             0
##   moderate_severe_liver_disease AIDS_HIV any_malignancy
## 1                             0        0              0
## 2                             0        0              0
## 3                             0        0              0
## 4                             0        0              0
## 5                             0        0              0
## 6                             0        0              0
##   metastatic_solid_tumours obesity   age_cat  stage   PS
## 1                        0       0  [73, 80)   I-II Good
## 2                        0       0 [80, 100) III-IV Poor
## 3                        0       0  [15, 65) III-IV Poor
## 4                        0       0  [73, 80) III-IV Good
## 5                        0       0  [73, 80) III-IV Poor
## 6                        0       0 [80, 100) III-IV Poor

Descriptive analysis

Tumor and patient factors:

summary(tableby(~sex + agediag + age_cat + dep + gor + stage + PS , 
                data = lung12boost))

	Overall (N=30535)
sex
1	16716 (54.7%)
2	13819 (45.3%)
agediag
Mean (SD)	72.717 (10.901)
Range	15.000 - 100.000
age_cat
N-Miss	7
[15, 65)	6596 (21.6%)
[65, 73)	7643 (25.0%)
[73, 80)	7436 (24.4%)
[80, 100)	8853 (29.0%)
dep
1	4337 (14.2%)
2	5328 (17.4%)
3	6093 (20.0%)
4	7215 (23.6%)
5	7562 (24.8%)
gor
A	2291 (7.5%)
B	5187 (17.0%)
D	3701 (12.1%)
E	2526 (8.3%)
F	3090 (10.1%)
G	3296 (10.8%)
H	3199 (10.5%)
J	4292 (14.1%)
K	2953 (9.7%)
stage
N-Miss	2474
I-II	7139 (25.4%)
III-IV	20922 (74.6%)
PS
N-Miss	7060
Good	13034 (55.5%)
Poor	10441 (44.5%)

Comorbidities:

summary(tableby(~ myocardial_infection + congestive_heart_failure + 
                  peripheral_vascular_disease + cerebrovascular_disease +  
                  dementia + COPD + rheumatic_disease + 
                  peptic_ulcer_disease + mild_liver_disease + 
                  diabetes_without_comp + diabetes_with_comp +
                  hemiplegia_paraplegia + renal_disease +
                  moderate_severe_liver_disease + AIDS_HIV + 
                  any_malignancy + metastatic_solid_tumours + 
                  obesity,data = lung12boost) )

	Overall (N=30535)
myocardial_infection
0	28887 (94.6%)
1	1648 (5.4%)
congestive_heart_failure
0	28947 (94.8%)
1	1588 (5.2%)
peripheral_vascular_disease
0	28585 (93.6%)
1	1950 (6.4%)
cerebrovascular_disease
0	28678 (93.9%)
1	1857 (6.1%)
dementia
0	30056 (98.4%)
1	479 (1.6%)
COPD
0	23990 (78.6%)
1	6545 (21.4%)
rheumatic_disease
0	29770 (97.5%)
1	765 (2.5%)
peptic_ulcer_disease
0	29750 (97.4%)
1	785 (2.6%)
mild_liver_disease
0	30159 (98.8%)
1	376 (1.2%)
diabetes_without_comp
0	27975 (91.6%)
1	2560 (8.4%)
diabetes_with_comp
0	30320 (99.3%)
1	215 (0.7%)
hemiplegia_paraplegia
0	30183 (98.8%)
1	352 (1.2%)
renal_disease
0	29304 (96.0%)
1	1231 (4.0%)
moderate_severe_liver_disease
0	30460 (99.8%)
1	75 (0.2%)
AIDS_HIV
0	30531 (100.0%)
1	4 (0.0%)
any_malignancy
0	30361 (99.4%)
1	174 (0.6%)
metastatic_solid_tumours
0	30535 (100.0%)
obesity
0	29966 (98.1%)
1	569 (1.9%)

Crossed tables

Age * comord

summary(tableby(myocardial_infection~age_cat,data = lung12boost) )

	0 (N=28887)	1 (N=1648)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	7	0	7
[15, 65)	6414 (22.2%)	182 (11.0%)	6596 (21.6%)
[65, 73)	7288 (25.2%)	355 (21.5%)	7643 (25.0%)
[73, 80)	6984 (24.2%)	452 (27.4%)	7436 (24.4%)
[80, 100)	8194 (28.4%)	659 (40.0%)	8853 (29.0%)

summary(tableby(congestive_heart_failure~age_cat,data = lung12boost) )

	0 (N=28947)	1 (N=1588)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	6	1	7
[15, 65)	6508 (22.5%)	88 (5.5%)	6596 (21.6%)
[65, 73)	7365 (25.4%)	278 (17.5%)	7643 (25.0%)
[73, 80)	7039 (24.3%)	397 (25.0%)	7436 (24.4%)
[80, 100)	8029 (27.7%)	824 (51.9%)	8853 (29.0%)

summary(tableby(peripheral_vascular_disease~age_cat,data = lung12boost) )

	0 (N=28585)	1 (N=1950)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	7	0	7
[15, 65)	6437 (22.5%)	159 (8.2%)	6596 (21.6%)
[65, 73)	7215 (25.2%)	428 (21.9%)	7643 (25.0%)
[73, 80)	6825 (23.9%)	611 (31.3%)	7436 (24.4%)
[80, 100)	8101 (28.3%)	752 (38.6%)	8853 (29.0%)

summary(tableby(cerebrovascular_disease ~age_cat,data = lung12boost) )

	0 (N=28678)	1 (N=1857)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	7	0	7
[15, 65)	6429 (22.4%)	167 (9.0%)	6596 (21.6%)
[65, 73)	7255 (25.3%)	388 (20.9%)	7643 (25.0%)
[73, 80)	6961 (24.3%)	475 (25.6%)	7436 (24.4%)
[80, 100)	8026 (28.0%)	827 (44.5%)	8853 (29.0%)

summary(tableby(dementia~age_cat,data = lung12boost) )

	0 (N=30056)	1 (N=479)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	7	0	7
[15, 65)	6584 (21.9%)	12 (2.5%)	6596 (21.6%)
[65, 73)	7613 (25.3%)	30 (6.3%)	7643 (25.0%)
[73, 80)	7345 (24.4%)	91 (19.0%)	7436 (24.4%)
[80, 100)	8507 (28.3%)	346 (72.2%)	8853 (29.0%)

summary(tableby(COPD~age_cat,data = lung12boost) )

	0 (N=23990)	1 (N=6545)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	7	0	7
[15, 65)	5655 (23.6%)	941 (14.4%)	6596 (21.6%)
[65, 73)	6126 (25.5%)	1517 (23.2%)	7643 (25.0%)
[73, 80)	5573 (23.2%)	1863 (28.5%)	7436 (24.4%)
[80, 100)	6629 (27.6%)	2224 (34.0%)	8853 (29.0%)

summary(tableby(rheumatic_disease~age_cat,data = lung12boost) )

	0 (N=29770)	1 (N=765)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	7	0	7
[15, 65)	6500 (21.8%)	96 (12.5%)	6596 (21.6%)
[65, 73)	7444 (25.0%)	199 (26.0%)	7643 (25.0%)
[73, 80)	7210 (24.2%)	226 (29.5%)	7436 (24.4%)
[80, 100)	8609 (28.9%)	244 (31.9%)	8853 (29.0%)

summary(tableby(peptic_ulcer_disease~age_cat,data = lung12boost) )

	0 (N=29750)	1 (N=785)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	7	0	7
[15, 65)	6492 (21.8%)	104 (13.2%)	6596 (21.6%)
[65, 73)	7466 (25.1%)	177 (22.5%)	7643 (25.0%)
[73, 80)	7236 (24.3%)	200 (25.5%)	7436 (24.4%)
[80, 100)	8549 (28.7%)	304 (38.7%)	8853 (29.0%)

summary(tableby(mild_liver_disease~age_cat,data = lung12boost) )

	0 (N=30159)	1 (N=376)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	7	0	7
[15, 65)	6468 (21.5%)	128 (34.0%)	6596 (21.6%)
[65, 73)	7546 (25.0%)	97 (25.8%)	7643 (25.0%)
[73, 80)	7358 (24.4%)	78 (20.7%)	7436 (24.4%)
[80, 100)	8780 (29.1%)	73 (19.4%)	8853 (29.0%)

summary(tableby(diabetes_without_comp~age_cat,data = lung12boost) )

	0 (N=27975)	1 (N=2560)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	7	0	7
[15, 65)	6361 (22.7%)	235 (9.2%)	6596 (21.6%)
[65, 73)	7049 (25.2%)	594 (23.2%)	7643 (25.0%)
[73, 80)	6634 (23.7%)	802 (31.3%)	7436 (24.4%)
[80, 100)	7924 (28.3%)	929 (36.3%)	8853 (29.0%)

summary(tableby(diabetes_with_comp~age_cat,data = lung12boost) )

	0 (N=30320)	1 (N=215)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	7	0	7
[15, 65)	6570 (21.7%)	26 (12.1%)	6596 (21.6%)
[65, 73)	7601 (25.1%)	42 (19.5%)	7643 (25.0%)
[73, 80)	7375 (24.3%)	61 (28.4%)	7436 (24.4%)
[80, 100)	8767 (28.9%)	86 (40.0%)	8853 (29.0%)

summary(tableby(hemiplegia_paraplegia~age_cat,data = lung12boost) )

	0 (N=30183)	1 (N=352)	Total (N=30535)	p value
age_cat				0.022
N-Miss	7	0	7
[15, 65)	6541 (21.7%)	55 (15.6%)	6596 (21.6%)
[65, 73)	7558 (25.0%)	85 (24.1%)	7643 (25.0%)
[73, 80)	7344 (24.3%)	92 (26.1%)	7436 (24.4%)
[80, 100)	8733 (28.9%)	120 (34.1%)	8853 (29.0%)

summary(tableby(renal_disease~age_cat,data = lung12boost) )

	0 (N=29304)	1 (N=1231)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	6	1	7
[15, 65)	6530 (22.3%)	66 (5.4%)	6596 (21.6%)
[65, 73)	7455 (25.4%)	188 (15.3%)	7643 (25.0%)
[73, 80)	7136 (24.4%)	300 (24.4%)	7436 (24.4%)
[80, 100)	8177 (27.9%)	676 (55.0%)	8853 (29.0%)

summary(tableby(moderate_severe_liver_disease~age_cat,data = lung12boost) )

	0 (N=30460)	1 (N=75)	Total (N=30535)	p value
age_cat				0.008
N-Miss	7	0	7
[15, 65)	6568 (21.6%)	28 (37.3%)	6596 (21.6%)
[65, 73)	7627 (25.0%)	16 (21.3%)	7643 (25.0%)
[73, 80)	7419 (24.4%)	17 (22.7%)	7436 (24.4%)
[80, 100)	8839 (29.0%)	14 (18.7%)	8853 (29.0%)

summary(tableby(any_malignancy~age_cat,data = lung12boost) )

	0 (N=30361)	1 (N=174)	Total (N=30535)	p value
age_cat				0.570
N-Miss	7	0	7
[15, 65)	6553 (21.6%)	43 (24.7%)	6596 (21.6%)
[65, 73)	7603 (25.0%)	40 (23.0%)	7643 (25.0%)
[73, 80)	7399 (24.4%)	37 (21.3%)	7436 (24.4%)
[80, 100)	8799 (29.0%)	54 (31.0%)	8853 (29.0%)

summary(tableby(obesity~age_cat,data = lung12boost) )

	0 (N=29966)	1 (N=569)	Total (N=30535)	p value
age_cat				< 0.001
N-Miss	7	0	7
[15, 65)	6466 (21.6%)	130 (22.8%)	6596 (21.6%)
[65, 73)	7464 (24.9%)	179 (31.5%)	7643 (25.0%)
[73, 80)	7274 (24.3%)	162 (28.5%)	7436 (24.4%)
[80, 100)	8755 (29.2%)	98 (17.2%)	8853 (29.0%)

summary(tableby(metastatic_solid_tumours~age_cat,data = lung12boost) )

	0 (N=30535)	Total (N=30535)
age_cat
N-Miss	7	7
[15, 65)	6596 (21.6%)	6596 (21.6%)
[65, 73)	7643 (25.0%)	7643 (25.0%)
[73, 80)	7436 (24.4%)	7436 (24.4%)
[80, 100)	8853 (29.0%)	8853 (29.0%)

Stage * comord

summary(tableby(myocardial_infection~stage,data = lung12boost) )

	0 (N=28887)	1 (N=1648)	Total (N=30535)	p value
stage				< 0.001
N-Miss	2302	172	2474
I-II	6682 (25.1%)	457 (31.0%)	7139 (25.4%)
III-IV	19903 (74.9%)	1019 (69.0%)	20922 (74.6%)

summary(tableby(congestive_heart_failure~stage,data = lung12boost) )

	0 (N=28947)	1 (N=1588)	Total (N=30535)	p value
stage				0.023
N-Miss	2255	219	2474
I-II	6755 (25.3%)	384 (28.0%)	7139 (25.4%)
III-IV	19937 (74.7%)	985 (72.0%)	20922 (74.6%)

summary(tableby(peripheral_vascular_disease~stage,data = lung12boost) )

	0 (N=28585)	1 (N=1950)	Total (N=30535)	p value
stage				< 0.001
N-Miss	2301	173	2474
I-II	6568 (25.0%)	571 (32.1%)	7139 (25.4%)
III-IV	19716 (75.0%)	1206 (67.9%)	20922 (74.6%)

summary(tableby(cerebrovascular_disease ~stage,data = lung12boost) )

	0 (N=28678)	1 (N=1857)	Total (N=30535)	p value
stage				0.085
N-Miss	2262	212	2474
I-II	6691 (25.3%)	448 (27.2%)	7139 (25.4%)
III-IV	19725 (74.7%)	1197 (72.8%)	20922 (74.6%)

summary(tableby(dementia~stage,data = lung12boost) )

	0 (N=30056)	1 (N=479)	Total (N=30535)	p value
stage				0.937
N-Miss	2358	116	2474
I-II	7046 (25.4%)	93 (25.6%)	7139 (25.4%)
III-IV	20652 (74.6%)	270 (74.4%)	20922 (74.6%)

summary(tableby(COPD~stage,data = lung12boost) )

	0 (N=23990)	1 (N=6545)	Total (N=30535)	p value
stage				< 0.001
N-Miss	1865	609	2474
I-II	5158 (23.3%)	1981 (33.4%)	7139 (25.4%)
III-IV	16967 (76.7%)	3955 (66.6%)	20922 (74.6%)

summary(tableby(rheumatic_disease~stage,data = lung12boost) )

	0 (N=29770)	1 (N=765)	Total (N=30535)	p value
stage				< 0.001
N-Miss	2419	55	2474
I-II	6900 (25.2%)	239 (33.7%)	7139 (25.4%)
III-IV	20451 (74.8%)	471 (66.3%)	20922 (74.6%)

summary(tableby(peptic_ulcer_disease~stage,data = lung12boost) )

	0 (N=29750)	1 (N=785)	Total (N=30535)	p value
stage				0.033
N-Miss	2399	75	2474
I-II	6934 (25.4%)	205 (28.9%)	7139 (25.4%)
III-IV	20417 (74.6%)	505 (71.1%)	20922 (74.6%)

summary(tableby(mild_liver_disease~stage,data = lung12boost) )

	0 (N=30159)	1 (N=376)	Total (N=30535)	p value
stage				0.327
N-Miss	2433	41	2474
I-II	7046 (25.4%)	93 (27.8%)	7139 (25.4%)
III-IV	20680 (74.6%)	242 (72.2%)	20922 (74.6%)

summary(tableby(diabetes_without_comp~stage,data = lung12boost) )

	0 (N=27975)	1 (N=2560)	Total (N=30535)	p value
stage				0.105
N-Miss	2227	247	2474
I-II	6518 (25.3%)	621 (26.8%)	7139 (25.4%)
III-IV	19230 (74.7%)	1692 (73.2%)	20922 (74.6%)

summary(tableby(diabetes_with_comp~stage,data = lung12boost) )

	0 (N=30320)	1 (N=215)	Total (N=30535)	p value
stage				0.112
N-Miss	2446	28	2474
I-II	7082 (25.4%)	57 (30.5%)	7139 (25.4%)
III-IV	20792 (74.6%)	130 (69.5%)	20922 (74.6%)

summary(tableby(hemiplegia_paraplegia~stage,data = lung12boost) )

	0 (N=30183)	1 (N=352)	Total (N=30535)	p value
stage				0.201
N-Miss	2426	48	2474
I-II	7052 (25.4%)	87 (28.6%)	7139 (25.4%)
III-IV	20705 (74.6%)	217 (71.4%)	20922 (74.6%)

summary(tableby(renal_disease~stage,data = lung12boost) )

	0 (N=29304)	1 (N=1231)	Total (N=30535)	p value
stage				0.017
N-Miss	2311	163	2474
I-II	6834 (25.3%)	305 (28.6%)	7139 (25.4%)
III-IV	20159 (74.7%)	763 (71.4%)	20922 (74.6%)

summary(tableby(moderate_severe_liver_disease~stage,data = lung12boost) )

	0 (N=30460)	1 (N=75)	Total (N=30535)	p value
stage				0.769
N-Miss	2466	8	2474
I-II	7123 (25.4%)	16 (23.9%)	7139 (25.4%)
III-IV	20871 (74.6%)	51 (76.1%)	20922 (74.6%)

summary(tableby(any_malignancy~stage,data = lung12boost) )

	0 (N=30361)	1 (N=174)	Total (N=30535)	p value
stage				0.814
N-Miss	2460	14	2474
I-II	7097 (25.4%)	42 (26.2%)	7139 (25.4%)
III-IV	20804 (74.6%)	118 (73.8%)	20922 (74.6%)

summary(tableby(obesity~stage,data = lung12boost) )

	0 (N=29966)	1 (N=569)	Total (N=30535)	p value
stage				< 0.001
N-Miss	2411	63	2474
I-II	6978 (25.3%)	161 (31.8%)	7139 (25.4%)
III-IV	20577 (74.7%)	345 (68.2%)	20922 (74.6%)

summary(tableby(metastatic_solid_tumours~stage,data = lung12boost) )

	0 (N=30535)	Total (N=30535)
stage
N-Miss	2474	2474
I-II	7139 (25.4%)	7139 (25.4%)
III-IV	20922 (74.6%)	20922 (74.6%)

Stage * demographic vars

summary(tableby(sex~stage,data = lung12boost) )

	1 (N=16716)	2 (N=13819)	Total (N=30535)	p value
stage				< 0.001
N-Miss	1298	1176	2474
I-II	3699 (24.0%)	3440 (27.2%)	7139 (25.4%)
III-IV	11719 (76.0%)	9203 (72.8%)	20922 (74.6%)

summary(tableby(dep~stage,data = lung12boost) )

	1 (N=4337)	2 (N=5328)	3 (N=6093)	4 (N=7215)	5 (N=7562)	Total (N=30535)	p value
stage							0.096
N-Miss	349	479	474	601	571	2474
I-II	985 (24.7%)	1247 (25.7%)	1380 (24.6%)	1674 (25.3%)	1853 (26.5%)	7139 (25.4%)
III-IV	3003 (75.3%)	3602 (74.3%)	4239 (75.4%)	4940 (74.7%)	5138 (73.5%)	20922 (74.6%)

summary(tableby(age_cat~stage,data = lung12boost) )

	[15, 65) (N=6596)	[65, 73) (N=7643)	[73, 80) (N=7436)	[80, 100) (N=8853)	Total (N=30528)	p value
stage						< 0.001
N-Miss	379	407	520	1165	2471
I-II	1437 (23.1%)	1921 (26.5%)	1858 (26.9%)	1922 (25.0%)	7138 (25.4%)
III-IV	4780 (76.9%)	5315 (73.5%)	5058 (73.1%)	5766 (75.0%)	20919 (74.6%)

summary(tableby(PS~stage,data = lung12boost) )

	Good (N=13034)	Poor (N=10441)	Total (N=23475)	p value
stage				< 0.001
N-Miss	158	263	421
I-II	4244 (33.0%)	1754 (17.2%)	5998 (26.0%)
III-IV	8632 (67.0%)	8424 (82.8%)	17056 (74.0%)

Survival times

library(survival)
library(ggplot2)
library(survminer)

summary(tableby(~Surv(survtday,dead),data = lung12boost) )

	Overall (N=30535)
Surv(survtday, dead)
Events	25890
Median Survival	196.000

86% events
14% censored obsevations

\(~\)

Cohort survival

survfit <- survfit(Surv(survtday, dead)~ 1, data = lung12boost)

ggsurvplot(survfit, 
           legend.title= "",
           tables.height = 0.3,
           risk.table=TRUE, 
           risk.table.title=" ",
           pval =TRUE )

Stratified cohort survival

Sex

# Sex: 
  ggsurvplot(survfit.sex, 
             legend.title= " ",
             tables.height = 0.3,
             risk.table=TRUE, 
             risk.table.title="",
             pval =TRUE)

Categorized age

# Categorized age: 
  ggsurvplot(survfit.age_cat, 
             legend.title= " ",
             tables.height = 0.4,
             risk.table=TRUE, 
             risk.table.title="",
             pval =TRUE)

Stage

# Stage: 
  ggsurvplot(survfit.stage, 
             legend.title= " ",
             tables.height = 0.4,
             risk.table=TRUE, 
             risk.table.title="",
             pval =TRUE)

PS

# Performance status: 
  ggsurvplot(survfit.PS, 
             legend.title= " ",
             tables.height = 0.4,
             risk.table=TRUE, 
             risk.table.title="",
             pval =TRUE)

Deprivation level

# Deprivation level 
  ggsurvplot(survfit.dep, 
             legend.title= " ",
             tables.height = 0.4,
             risk.table=TRUE, 
             risk.table.title="",
             pval =TRUE)

Government office region

# Government office region: 
  ggsurvplot(survfit.gor, 
             legend.title= " ",
             tables.height = 0.3,
             risk.table=TRUE, 
             risk.table.title="",
             pval =TRUE)

COPD

# Chronic obstrutive pulmonary disease: 
  ggsurvplot(survfit.COPD, 
             legend.title= " ",
             legend.labs = c("0", "1"),
             tables.height = 0.3,
             risk.table=TRUE, 
             risk.table.title="",
             pval =TRUE)

Peptic

# Peptic ulcer disease 
  ggsurvplot(survfit.peptic_ulcer_disease, 
             legend.title= "",
             legend.labs = c("0", "1"),
             tables.height = 0.3,
             risk.table=TRUE, 
             risk.table.title=" ",
             pval =TRUE)

Mild liver disease

# Mild liver disease  
  ggsurvplot(survfit.mild_liver_disease, 
             legend.title= " ",
             legend.labs = c("0", "1"),
             tables.height = 0.3,
             risk.table=TRUE, 
             risk.table.title=" ",
             pval =TRUE)

Diabetes w. comp

# Diabetes with complications 
  ggsurvplot(survfit.diabetes_with_comp, 
             legend.title= " ",
             legend.labs = c("0", "1"),
             tables.height = 0.3,
             risk.table=TRUE, 
             risk.table.title=" ",
             pval =TRUE)

Diabetes w/o comp

# Diabetes without complications
  ggsurvplot(survfit.diabetes_without_comp, 
             legend.title= " ",
             legend.labs = c("0", "1"),
             tables.height = 0.3,
             risk.table=TRUE, 
             risk.table.title=" ",
             pval =TRUE)

Hemiplegia

Survival curves:

# Hemiplegia/paraplegia
  ggsurvplot(survfit.hemiplegia_paraplegia, 
             legend.title= " ",
             legend.labs = c("0", "1"),
             tables.height = 0.3,
             risk.table=TRUE, 
             risk.table.title=" ",
             pval =TRUE)

Renal disease