Lung cancer cohort

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 agecat    stage   PS CCI CCI_cat
## 1                        0       0  74-79    early Good   3 CCI 3-4
## 2                        0       0   >=80 advanced Poor   4 CCI 3-4
## 3                        0       0  15-65 advanced Poor   2 CCI 1-2
## 4                        0       0  66-73 advanced Good   3 CCI 3-4
## 5                        0       0  66-73 advanced Poor   3 CCI 3-4
## 6                        0       0   >=80 advanced Poor  10  CCI >5
hist(lung12boost$CCI, main = "Distribution of the Charston Comorbidity Index", xlab = "CCI")

table(lung12boost$CCI_cat)
## 
##  CCI >5 CCI 1-2 CCI 3-4 
##    9325    9045   15143
library(survival)
library(survminer)

ggsurvplot(survfit(Surv(survtday,dead)~  CCI_cat,data = na.omit(lung12boost)), risk.table=TRUE)

Random survival forest analysis

library(randomForestSRC)

start_time <- Sys.time()
RF_lung <- rfsrc(Surv(survtday,dead)~ factor(agecat) + factor(stage) + factor(PS) + factor(dep)  + factor(CCI_cat), data = na.omit(lung12boost), nodesize = 500, ntree =100, importance =TRUE, membership = TRUE)
end_time <- Sys.time()
end_time - start_time
## Time difference of 3.604972 mins
barplot(RF_lung$importance[order(RF_lung$importance)], main = "Variable Importance", horiz=T, xlab ="Importance")

Life table